菊花‘神马’花芽分化期的数字基因表达谱及关键基因的克隆和表达分析
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摘要
菊花（Chrysanthemum morifolium Ramat.）是菊科（Asteraceae）菊属（Chrysanthemum）植物，是世界四大鲜切花之一。栽培品种3000多个，用于切花菊的品种多为典型的短日照植物，光周期途径调控开花主要由光受体基因接受光信号，传递给节律钟基因，通过节律钟调控输出基因激活下游转录因子的表达，在叶中上调促进开花基因的表达，输送到茎尖与成花整合因子作用完成花芽分化。
本研究以白色切花菊‘神马’为试材，因其典型的短日照特点，能较准确人工调控花芽分化进程，是研究菊花花芽分化分子机理的模式材料。通过大规模高通量测序，获得数据与NCBI核酸蛋白数据库进行比对，经生物信息分析，确定功能分类及涉及的代谢途径，获得菊花花芽分化期相关的基因表达信息，探索在菊花不同花芽分化阶段相关基因的差异表达富集模式及表达谱；对光周期途径的关键基因进行全长的克隆与表达分析，在分子水平上对菊花开花时间的网络途径有初步的了解，为后期进一步进行基因的功能验证及通过分子育种方法（反义抑制或转基因）培育目标花期新品种提供基础理论依据。
本研究主要成果如下：
1.本试验获得菊花花芽分化期转录组ESTs，对所有unigenes进行功能分类，收集到54,488条分属于分子功能、细胞组分和生物学过程的unigenes。其中参与分子功能的共12种，参与细胞组分的共11种，参与生物学过程的共18种。得到编码蛋白框（CDS）的核酸序列和氨基酸序列为54,644条。用ESTscan比对所有unigenes，得到其CDS的核酸序列和氨基酸序列均为8,506条。将所有unigenes与COG数据库BLAST比对显示，共获得22,871条与已知其他植物同源，属于23类直系同源簇群，未知功能的有780条；得到25,001条参与代谢通路的unigenes，从中收集到与植物节律代谢通路相关unigenes共269条，从中比对到参与光周期途径的光受体基因、生物节律钟基因和生物节律钟输入和输出基因等相似功能基因共20个。
2.初步得出菊花花芽分化期涉及植物节律途径的数字基因表达谱：
菊花光受体PHYB在花芽分化启动期表达量达最高值，是暗处理前的近五倍，随后稍有下降，到总苞鳞片分化中期仍维持暗处理前的近三倍，到分化完成一直还维持近两倍的表达量；
节律钟组件APRS、 TOC1表达高峰值均出现在总苞鳞片分化中期；PIF3高峰值出现在花芽分化启动期，到总苞鳞片分化中期仍维持暗处理前的近三倍；FKF1在花芽分化启动期上调到高峰值，总苞鳞片分化中期下调表达，随后在小花原基分化中期和分化完成期又上调到高峰。
节律钟输出基因GI在花芽分化启动期表达量达最高值，在总苞鳞片分化中期稍有下降，分化完成期又有回升。
CO暗处理一天后反而表达量降低，在总苞鳞片分化中期表达量达最高值。
CHS（查尔酮合成酶）在暗处理一天后表达量上调，启动期达近五倍的最高值，总苞鳞片分化中期表达量稍下降，随后在小花原基分化中期下调表达。
3.初步得出菊花花芽分化期差异表达基因显著富集的最主要生化代谢途径和信号转导途径：集中在光合作用及核蛋白体途径中。
4.初步得出菊花不同花芽分化阶段差异表达基因富集参与的生物功能：
花芽未分化期，植物中蛋白质精氨酸甲基转移酶家族基因和蛋白参与基因转录调控、氧化还原酶活性基因转录加强；花芽分化启动期，脂肪酸合成酶、糖氢共转运蛋白活性基因差异表达富集，蛋白质精氨酸甲基转移酶的差异表达显著；总苞鳞片分化中期，信息显示富集在各种蛋白质、核苷酸糖的合成；小花原基分化中期，蛋白质精氨酸甲基转移酶活性加强，氧化还原酶活性基因转录加强；花冠分化末期即花芽分化完成期，基因差异表达富集仍在结构分子活动、砷酸盐还原酶活性和作为花和花粉发育的能量来源的脯氨酸的累积等方面。
5.从菊花‘神马’中克隆得到节律钟输出基因GIGANTEA的cDNA全长序列，命名为CmGI基因，登录号为JQ043439。对其做序列信息分析；菊花CmGI的表达呈昼夜节律表达模式，高峰值出现在16:00；不同花芽分化阶段叶片中CmGI基因mRNA水平差异大，两个高峰值分别出现在花芽分化启动期和小花原基分化中期；盛花期表达量较高。
6.从菊花‘神马’中克隆得到开花相关基因CmCOL的cDNA全长序列，登录号为KC589293，对其做序列信息分析；菊花CmCOL mRNA在叶中高表达，呈昼夜节律表达模式，表达高峰值出现在04:00；短日照处理能上调叶中CmCOL，对芽中的影响不明显；不同花芽分化阶段叶片中高峰值出现在小花原基分化中期；盛花期叶片中高表达。
7.菊花CmFTL mRNA只在短日照条件下的叶片中呈现节律表达，00:00时为高峰值；芽中及长日照叶、芽中均检测不到昼夜起伏；不同花芽分化阶段叶片中CmFTLmRNA水平差异大，小花原基分化中期达最高峰值；花蕾期叶中高表达。
8.研究显示菊花叶片感应光周期，短日照条件下CmGI首先于暗处理1d后启动上调，花芽分化启动期出现第一个峰值，而CmCOL则滞后CmGI，于花芽分化启动期轻微上调，暗示CmGI位于CmCOL上游，小花原基分化中期CmGI上调至高峰值时CmCOL上调到高峰。CmFTL在CmCOL微调时则无明显变化，在小花原基分化中期CmCOL上调至高峰值时CmFTL也上调到高峰值，暗示CmFTL滞后CmCOL，位于其下游。
实验揭示菊花CmGI、CmCOL、CmFTL在SD条件下与拟南芥LD下及水稻SD下的GI-CO-FT调控模式相似。
Chrysanthemum morifolium Ramat. is a chrysanthemum plant species in the Asteraceaefamily. This plant is one of four major cut flowers worldwide, and it has more than3000cultivated varieties. Cut flowers are typically obtained from short-day (SD) plant species, thephotoperiod regulation technique primarily controls flowering through light receptor geneproducts which receive a light signal and transmit the signal to circadian gene products. Thecircadian rhythm clock output gene activates the expression of the transcription factor andthen enhances the expression of the flowering-promoting gene in the leaves. Then transportedto the shoot-tip and functions together with flowering-integrating factors, regulation ofdownstream flowering-promoting factors in the photoperiod pathway.
This study with white cut-flower chrysanthemum‘Jinba’as test materials, because of itstypical characteristics of short day, can be accurately controlled flower bud differentiationprocess, is the study of molecular mechanism of chrysanthemum flower bud differentiationmodel material. By high-throughput EST sequencing technique, the data compare with theNCBI nucleic acid protein database, through bioinformatics analysis, determine the functionclassification and metabolic pathways involved, into chrysanthemum flowering related geneexpression information, explore different in chrysanthemum flower bud differentiation phasedifferentially expressed enrichment pattern and expression of related genes，the photoperiodpathway related the key gene cloning and expression analysis, at the molecular level ofchrysanthemum flowering time of network way to have a preliminary understanding,
So the information might be the base of system research the chrysanthemum into themolecular regulation mechanism and its biological function and sellecting flowering relatedgenes and using for transgenes.
The main research results are as follows:
1. Studies on transcriptomic express sequence tags (ESTs) of chrysanthemum duringfloral differentiation. sellected54,488unigenes which of moleculor functions, cell conpenentsand bioprocesses. All of the above unigenes involved12of molecular functions and11of cellcomponents, and18of bioprocesses. Sequences of nucleic acids and amino acids of54,644 encoding protein boxes (CDS) were sellected from all of the unigenes of chrysanthemumduring floral differentiation by BLAST software. Also8,506unigene sequences of nucleicacids and amino acids of CDS by ESTscan software. Comparison to the GenBanknon-redundant (nr) database in COG database revealed that22,871unigenes sequences weresimilar to other known plant homologous genes which classfied to23homologys and780unigenes sequences maybe new genes in chrysanthemum. Also25,001unigenes weresellected which of participating in metabolism pathway using KEGG database. From there269unigenes also sellected that related to participating circation rhythm metablism pathways,and also sellected20homologous genes which related to photoperiod pathways includingphotoreceptor genes, circadian rhthm clock genes, circadian rhythm import and export genes.
2. Digital gene expression of chrysanthemum bud differentiation period involving plantrhythm pathways：
Chrysanthemum light receptors PHYB orthologous genes expressed peaked at buddifferentiation initiation stage, is nearly five times more the pre-treatment level, then a slightdecline, until the involucre scales middle differentiation stage, nearly three times more thepre-treatment level，at bud differentiation completion stage，nearly two times the amount ofexpression.
Circadian clock component APRS, TOC1expressed peaked at involucre scaledifferentiation mid-term stage.
PIF3expressed peaked at bud differentiation initiation stage.
FKF1express the change of the peak, dark treatment decreased expression a day after，the expression peaked at bud differentiation initiation stage and the floret primordiumdifferentiation and bud differentiation completion stages.
Circadian clock output gene expression GI dark treatment after a day's slight decline,expressed in bud differentiation initiation periods reaches peak, in the involucre scales middledifferentiation are down a bit, at bud differentiation completion stages have rebounded.
Expression of CO dark treatment after a day's slight decline, expressed in involucrescales differentiation medium quantity reaches peak, is nearly two times more thepre-treatment level; CHS on dark expression quantity rise, a day after start-up of the highest innearly five times more, involucre scales differentiation medium expression quantity slightlydecreased, then in the middle of the floret primordium differentiation decline.
3. Preliminary concluded that chrysanthemum flower bud differentiation periodsignificant enrichment of differentially expressed genes of the main biochemical metabolic pathways and signal transduction pathways, concentrated in photosynthesis and ribosomepathways.
4. Preliminary concluded that different chrysanthemum flower bud differentiation stageenrichment of differentially expressed genes involved in biological function：
At the bud un-differentiated：single stranded RNA binding，poly-pyrimidine tractbinding，protein-arginine N-methyltransferase，oxidoreductase activity，acting on paireddonors，with incorporation or reduction of molecular oxygen. At the bud differentiationinitiation：protein-arginine N-methyl transferase activity，fatty acid synthase activity，sugar-hydrogen symporter activity. At the involucre scale differentiation mid-term stages：protein transmembrane transporter activity，pyrimidine nucleotide sugar transmembranetransporter activity. At the floret primordia differentiated mid-term stage：oxidoreductaseactivity，oxidizing metal ions，NAD-NADP as acceptor，protein-arginine N-methyltransferaseactivity. At the corolla differentiation mid-term and bud differentiation completion stages：structural molecule activity，guanyl ribonucleotide binding，arsenate reductase activity.
5. The cDNA sequence of GIGANTEA was cloned from chrysanthemum‘Jniba’，The sequence was submitted to GenBank, and the registration number is JQ043439. Sequenceinformation is done in the analysis. Fluorescent relative quantitative analysis shows that theexpression patterns of chrysanthemum CmGI are circadian rhythms expression, with its peakexpression occurring at16:00. At different flower bud differentiation stage, the CmGI gene inthe leaf blade mRNA level is different, two peak values were appeared in the flower buddifferentiation start-up and floret primordia middle differentiation periods. CmGI mRNA ishighly expressed in the leaves at the full-blossom stage.
6. We cloned the flowering gene CmCOL (GenBank accession:KC589293) fromChrysanthemum morifolium‘Jinba’. Sequence information is done in the analysis. Relativefluorescence quantitative analysis showed that CmCOL mRNA is most highly expressed inthe leaves and demonstrates a circadian expression pattern, with its peak expression occurringat04:00. A short-day treatment elevated CmCOL mRNA expression in the leaves but did notsignificantly affect expression in the buds. The CmCOL mRNA level in the leaves changedsignificantly at various flower bud differentiation stages, and it peaked at the floret primordiadifferentiation mid-term stage. CmCOL mRNA is highly expressed in the leaves at thefull-blossom stage.
7. Relative fluorescence quantitative analysis showed that CmFTL mRNA is most highly expressed in the leaves and demonstrates a circadian expression pattern, with its peakexpression occurring at00:00. A short-day treatment elevated CmFTL mRNA expression inthe leaves but did not significantly affect expression in the buds. The CmFTL mRNA level inthe leaves changed significantly at various flower bud differentiation stages, and it peaked atthe floret primordia differentiation mid-term stage. CmFTL mRNA is highly expressed in theleaves at the bud stage.
8. The present study showed that Chrysanthemum morifolium leaves could sense thephotoperiod. Under SD conditions, CmGI mRNA expression began to increase one day afterthe SD treatment and reached the first peak at the bud differentiation initiation stage. CmCOLmRNA expression lagged behind that of CmGI; it increaseds lightly at the bud differentiationinitiation stage, suggesting that CmGI operates upstream of CmCOL. CmCOL expressionreached its peak at the floret primordia differentiated mid-term stage, which occurred afterCmGI expression peaked. The expression of CmFTL and CmCOL did not change significantlyunder micro-regulation. CmFTL mRNA expression peaked at the floret primordiadifferentiated mid-term stage, which occurred after CmCOL mRNA expression peaked,suggesting that CmFTL operates downstream of CmCOL. These results suggest that theGI-CO-FT regulation pattern is similar in Chrysanthemum morifolium under SD conditions,arabidopsis thaliana under LD conditions and Oryza sativa under SD conditions.
本研究以白色切花菊‘神马’为试材，因其典型的短日照特点，能较准确人工调控花芽分化进程，是研究菊花花芽分化分子机理的模式材料。通过大规模高通量测序，获得数据与NCBI核酸蛋白数据库进行比对，经生物信息分析，确定功能分类及涉及的代谢途径，获得菊花花芽分化期相关的基因表达信息，探索在菊花不同花芽分化阶段相关基因的差异表达富集模式及表达谱；对光周期途径的关键基因进行全长的克隆与表达分析，在分子水平上对菊花开花时间的网络途径有初步的了解，为后期进一步进行基因的功能验证及通过分子育种方法（反义抑制或转基因）培育目标花期新品种提供基础理论依据。
本研究主要成果如下：
1.本试验获得菊花花芽分化期转录组ESTs，对所有unigenes进行功能分类，收集到54,488条分属于分子功能、细胞组分和生物学过程的unigenes。其中参与分子功能的共12种，参与细胞组分的共11种，参与生物学过程的共18种。得到编码蛋白框（CDS）的核酸序列和氨基酸序列为54,644条。用ESTscan比对所有unigenes，得到其CDS的核酸序列和氨基酸序列均为8,506条。将所有unigenes与COG数据库BLAST比对显示，共获得22,871条与已知其他植物同源，属于23类直系同源簇群，未知功能的有780条；得到25,001条参与代谢通路的unigenes，从中收集到与植物节律代谢通路相关unigenes共269条，从中比对到参与光周期途径的光受体基因、生物节律钟基因和生物节律钟输入和输出基因等相似功能基因共20个。
2.初步得出菊花花芽分化期涉及植物节律途径的数字基因表达谱：
菊花光受体PHYB在花芽分化启动期表达量达最高值，是暗处理前的近五倍，随后稍有下降，到总苞鳞片分化中期仍维持暗处理前的近三倍，到分化完成一直还维持近两倍的表达量；
节律钟组件APRS、 TOC1表达高峰值均出现在总苞鳞片分化中期；PIF3高峰值出现在花芽分化启动期，到总苞鳞片分化中期仍维持暗处理前的近三倍；FKF1在花芽分化启动期上调到高峰值，总苞鳞片分化中期下调表达，随后在小花原基分化中期和分化完成期又上调到高峰。
节律钟输出基因GI在花芽分化启动期表达量达最高值，在总苞鳞片分化中期稍有下降，分化完成期又有回升。
CO暗处理一天后反而表达量降低，在总苞鳞片分化中期表达量达最高值。
CHS（查尔酮合成酶）在暗处理一天后表达量上调，启动期达近五倍的最高值，总苞鳞片分化中期表达量稍下降，随后在小花原基分化中期下调表达。
3.初步得出菊花花芽分化期差异表达基因显著富集的最主要生化代谢途径和信号转导途径：集中在光合作用及核蛋白体途径中。
4.初步得出菊花不同花芽分化阶段差异表达基因富集参与的生物功能：
花芽未分化期，植物中蛋白质精氨酸甲基转移酶家族基因和蛋白参与基因转录调控、氧化还原酶活性基因转录加强；花芽分化启动期，脂肪酸合成酶、糖氢共转运蛋白活性基因差异表达富集，蛋白质精氨酸甲基转移酶的差异表达显著；总苞鳞片分化中期，信息显示富集在各种蛋白质、核苷酸糖的合成；小花原基分化中期，蛋白质精氨酸甲基转移酶活性加强，氧化还原酶活性基因转录加强；花冠分化末期即花芽分化完成期，基因差异表达富集仍在结构分子活动、砷酸盐还原酶活性和作为花和花粉发育的能量来源的脯氨酸的累积等方面。
5.从菊花‘神马’中克隆得到节律钟输出基因GIGANTEA的cDNA全长序列，命名为CmGI基因，登录号为JQ043439。对其做序列信息分析；菊花CmGI的表达呈昼夜节律表达模式，高峰值出现在16:00；不同花芽分化阶段叶片中CmGI基因mRNA水平差异大，两个高峰值分别出现在花芽分化启动期和小花原基分化中期；盛花期表达量较高。
6.从菊花‘神马’中克隆得到开花相关基因CmCOL的cDNA全长序列，登录号为KC589293，对其做序列信息分析；菊花CmCOL mRNA在叶中高表达，呈昼夜节律表达模式，表达高峰值出现在04:00；短日照处理能上调叶中CmCOL，对芽中的影响不明显；不同花芽分化阶段叶片中高峰值出现在小花原基分化中期；盛花期叶片中高表达。
7.菊花CmFTL mRNA只在短日照条件下的叶片中呈现节律表达，00:00时为高峰值；芽中及长日照叶、芽中均检测不到昼夜起伏；不同花芽分化阶段叶片中CmFTLmRNA水平差异大，小花原基分化中期达最高峰值；花蕾期叶中高表达。
8.研究显示菊花叶片感应光周期，短日照条件下CmGI首先于暗处理1d后启动上调，花芽分化启动期出现第一个峰值，而CmCOL则滞后CmGI，于花芽分化启动期轻微上调，暗示CmGI位于CmCOL上游，小花原基分化中期CmGI上调至高峰值时CmCOL上调到高峰。CmFTL在CmCOL微调时则无明显变化，在小花原基分化中期CmCOL上调至高峰值时CmFTL也上调到高峰值，暗示CmFTL滞后CmCOL，位于其下游。
实验揭示菊花CmGI、CmCOL、CmFTL在SD条件下与拟南芥LD下及水稻SD下的GI-CO-FT调控模式相似。
Chrysanthemum morifolium Ramat. is a chrysanthemum plant species in the Asteraceaefamily. This plant is one of four major cut flowers worldwide, and it has more than3000cultivated varieties. Cut flowers are typically obtained from short-day (SD) plant species, thephotoperiod regulation technique primarily controls flowering through light receptor geneproducts which receive a light signal and transmit the signal to circadian gene products. Thecircadian rhythm clock output gene activates the expression of the transcription factor andthen enhances the expression of the flowering-promoting gene in the leaves. Then transportedto the shoot-tip and functions together with flowering-integrating factors, regulation ofdownstream flowering-promoting factors in the photoperiod pathway.
This study with white cut-flower chrysanthemum‘Jinba’as test materials, because of itstypical characteristics of short day, can be accurately controlled flower bud differentiationprocess, is the study of molecular mechanism of chrysanthemum flower bud differentiationmodel material. By high-throughput EST sequencing technique, the data compare with theNCBI nucleic acid protein database, through bioinformatics analysis, determine the functionclassification and metabolic pathways involved, into chrysanthemum flowering related geneexpression information, explore different in chrysanthemum flower bud differentiation phasedifferentially expressed enrichment pattern and expression of related genes，the photoperiodpathway related the key gene cloning and expression analysis, at the molecular level ofchrysanthemum flowering time of network way to have a preliminary understanding,
So the information might be the base of system research the chrysanthemum into themolecular regulation mechanism and its biological function and sellecting flowering relatedgenes and using for transgenes.
The main research results are as follows:
1. Studies on transcriptomic express sequence tags (ESTs) of chrysanthemum duringfloral differentiation. sellected54,488unigenes which of moleculor functions, cell conpenentsand bioprocesses. All of the above unigenes involved12of molecular functions and11of cellcomponents, and18of bioprocesses. Sequences of nucleic acids and amino acids of54,644 encoding protein boxes (CDS) were sellected from all of the unigenes of chrysanthemumduring floral differentiation by BLAST software. Also8,506unigene sequences of nucleicacids and amino acids of CDS by ESTscan software. Comparison to the GenBanknon-redundant (nr) database in COG database revealed that22,871unigenes sequences weresimilar to other known plant homologous genes which classfied to23homologys and780unigenes sequences maybe new genes in chrysanthemum. Also25,001unigenes weresellected which of participating in metabolism pathway using KEGG database. From there269unigenes also sellected that related to participating circation rhythm metablism pathways,and also sellected20homologous genes which related to photoperiod pathways includingphotoreceptor genes, circadian rhthm clock genes, circadian rhythm import and export genes.
2. Digital gene expression of chrysanthemum bud differentiation period involving plantrhythm pathways：
Chrysanthemum light receptors PHYB orthologous genes expressed peaked at buddifferentiation initiation stage, is nearly five times more the pre-treatment level, then a slightdecline, until the involucre scales middle differentiation stage, nearly three times more thepre-treatment level，at bud differentiation completion stage，nearly two times the amount ofexpression.
Circadian clock component APRS, TOC1expressed peaked at involucre scaledifferentiation mid-term stage.
PIF3expressed peaked at bud differentiation initiation stage.
FKF1express the change of the peak, dark treatment decreased expression a day after，the expression peaked at bud differentiation initiation stage and the floret primordiumdifferentiation and bud differentiation completion stages.
Circadian clock output gene expression GI dark treatment after a day's slight decline,expressed in bud differentiation initiation periods reaches peak, in the involucre scales middledifferentiation are down a bit, at bud differentiation completion stages have rebounded.
Expression of CO dark treatment after a day's slight decline, expressed in involucrescales differentiation medium quantity reaches peak, is nearly two times more thepre-treatment level; CHS on dark expression quantity rise, a day after start-up of the highest innearly five times more, involucre scales differentiation medium expression quantity slightlydecreased, then in the middle of the floret primordium differentiation decline.
3. Preliminary concluded that chrysanthemum flower bud differentiation periodsignificant enrichment of differentially expressed genes of the main biochemical metabolic pathways and signal transduction pathways, concentrated in photosynthesis and ribosomepathways.
4. Preliminary concluded that different chrysanthemum flower bud differentiation stageenrichment of differentially expressed genes involved in biological function：
At the bud un-differentiated：single stranded RNA binding，poly-pyrimidine tractbinding，protein-arginine N-methyltransferase，oxidoreductase activity，acting on paireddonors，with incorporation or reduction of molecular oxygen. At the bud differentiationinitiation：protein-arginine N-methyl transferase activity，fatty acid synthase activity，sugar-hydrogen symporter activity. At the involucre scale differentiation mid-term stages：protein transmembrane transporter activity，pyrimidine nucleotide sugar transmembranetransporter activity. At the floret primordia differentiated mid-term stage：oxidoreductaseactivity，oxidizing metal ions，NAD-NADP as acceptor，protein-arginine N-methyltransferaseactivity. At the corolla differentiation mid-term and bud differentiation completion stages：structural molecule activity，guanyl ribonucleotide binding，arsenate reductase activity.
5. The cDNA sequence of GIGANTEA was cloned from chrysanthemum‘Jniba’，The sequence was submitted to GenBank, and the registration number is JQ043439. Sequenceinformation is done in the analysis. Fluorescent relative quantitative analysis shows that theexpression patterns of chrysanthemum CmGI are circadian rhythms expression, with its peakexpression occurring at16:00. At different flower bud differentiation stage, the CmGI gene inthe leaf blade mRNA level is different, two peak values were appeared in the flower buddifferentiation start-up and floret primordia middle differentiation periods. CmGI mRNA ishighly expressed in the leaves at the full-blossom stage.
6. We cloned the flowering gene CmCOL (GenBank accession:KC589293) fromChrysanthemum morifolium‘Jinba’. Sequence information is done in the analysis. Relativefluorescence quantitative analysis showed that CmCOL mRNA is most highly expressed inthe leaves and demonstrates a circadian expression pattern, with its peak expression occurringat04:00. A short-day treatment elevated CmCOL mRNA expression in the leaves but did notsignificantly affect expression in the buds. The CmCOL mRNA level in the leaves changedsignificantly at various flower bud differentiation stages, and it peaked at the floret primordiadifferentiation mid-term stage. CmCOL mRNA is highly expressed in the leaves at thefull-blossom stage.
7. Relative fluorescence quantitative analysis showed that CmFTL mRNA is most highly expressed in the leaves and demonstrates a circadian expression pattern, with its peakexpression occurring at00:00. A short-day treatment elevated CmFTL mRNA expression inthe leaves but did not significantly affect expression in the buds. The CmFTL mRNA level inthe leaves changed significantly at various flower bud differentiation stages, and it peaked atthe floret primordia differentiation mid-term stage. CmFTL mRNA is highly expressed in theleaves at the bud stage.
8. The present study showed that Chrysanthemum morifolium leaves could sense thephotoperiod. Under SD conditions, CmGI mRNA expression began to increase one day afterthe SD treatment and reached the first peak at the bud differentiation initiation stage. CmCOLmRNA expression lagged behind that of CmGI; it increaseds lightly at the bud differentiationinitiation stage, suggesting that CmGI operates upstream of CmCOL. CmCOL expressionreached its peak at the floret primordia differentiated mid-term stage, which occurred afterCmGI expression peaked. The expression of CmFTL and CmCOL did not change significantlyunder micro-regulation. CmFTL mRNA expression peaked at the floret primordiadifferentiated mid-term stage, which occurred after CmCOL mRNA expression peaked,suggesting that CmFTL operates downstream of CmCOL. These results suggest that theGI-CO-FT regulation pattern is similar in Chrysanthemum morifolium under SD conditions,arabidopsis thaliana under LD conditions and Oryza sativa under SD conditions.
引文
安利忻,陈章良,刘荣维,李毅(2001).花分生组织决定基因AP1转化矮牵牛的研究.植物学报,43:63-66.
陈佩度,李鸿渐.几种中国野生菊的染色体组分析及亲源关系初步研究.园艺学报,1996,23(1):67-72.
陈旭,齐凤坤,康立功,李景富.实时荧光定量PCR技术研究进展及其应用.东北农业大学学报,41(8):148-155.
常立,文国琴.植物蓝光受体研究进展.生物技术通讯,2004(02):169-171.
陈思,焦新之.植物细胞的肌醇磷脂信息传递系统.植物生理学通讯,1994(06):405-413.
戴思兰,中国栽培菊花起源的综合研究.北京林业大学博士学位论文,1994.
戴思兰,陈俊愉.中国菊属一些种的分支分类学研究.武汉植物学研究,1997,15(1):27-34.
戴晓静.拟南芥砷酸还原酶基因AtACR2的表达调控及其功能分析.中科院植物所硕士学位论文,2009.
戴思兰,王文奎,黄家平.菊属系统学与菊花起源研究进展.北京林业大学学报,2002,24(5/6):230-234.
付建新,王翊,戴思兰.高等植物CO基因研究进展.分子植物育种,2010,8(5):1008-1016.
郭春晓,田素波,郑成淑,王文莉，孙宪芝.光周期途径植物开花时间决定关键基因FT.基因组学与应用生态学,2009,28(3):613-618.
郭忠义.菊谱.北京.中国社会出版社，2010.9.
郜爱玲,李建安,刘儒,何志祥,孙颖.高等植物花芽分化机理研究进展.经济林研究,2010,28(2):131-136.
高凤华,张洪亮,王海光.应用cDNA-AFLP比较干旱胁迫条件下水稻和旱稻转录本表达谱.科学通报,2009,54(16):2305-2319.
郭志刚,张伟.菊花.北京:中国林业出版社,2001,9-44.
胡永林.核糖体的结构与功能研究.生物化学与生物物理进展,2009,36(10):1239-1243.
姜丹,梁建丽,陈晓丽,洪波,贾文锁,赵梁军.拟南芥花期基因FT转化切花菊‘神马’.园艺学报,2010,37(3):441-448.
李鸿渐，邵建文.中国菊花品种资源的调查收集和分类.南京农业大学学报，1990，13(1):30-36.
李恐学,张方,陈俊愉.我国某些野生和栽培菊花的细胞学研究.园艺学报,1983,10(3):199-205.
李真,徐惠梅.菊花品种分类初步研究.安徽农学院学报,1989(4):282-284.
李宪利,袁志友,高东升.高等植物成花分子机理研究现状及展望.西北植物学报,2002,22(1):173-183.
刘姗，汪澈，樊金娟，阮燕晔，张立军.质子对植物蔗糖转运蛋白和己糖转运蛋白活性的调节.黑龙江农业科学,2012(7):14-18.
刘金元,陶文静,刘大钧.与小麦自粉病抗性基因Pmt紧密连锁的RAPD分析.遗传学报,2000,27(2):139-145.
刘志勇,杜永臣,王孝宣,国艳梅,高建昌.高温胁迫下番茄叶片差异表达基因的cDNA-AFLP分析.园艺学报,2008,35(7):1011-1016.
刘安娜.锌脂蛋白基因参与砷酸还原酶基因对拟南芥砷抗性的调控研究.内蒙古农业大学硕士学位论文,2011.
李滢,孙超,罗红梅,李西文,牛云云,陈士林.基于高通量测序454GS FLX的丹参转录组学研究.药学学报,2010,45(4):524-529.
林桂玉,黄在范,张翠华,郑成淑.菊花花芽分化期超微弱发光及生理代谢的变化.园艺学报,2008,35(12):1819-1824.
李辛雷,陈发棣.菊花种质资源与遗传改良研究进展.植物学通报,2004,21(4):392-401.
林镕,石铸.中国植物志:76卷第1分册.北京:科学出版社,1983:1-39.
吕晋慧,吴月亮,孙磊,张启翔. AP1基因转化地被菊品种玉人面的研究.林业科学,2007,43(9):128-135.
马力,唐凤敏,曾天舒等.菊花多糖和绿原酸免疫调节作用的研究.医药导报,2008,27(10):1168-1170.
毛静.中国传统菊花文化研究.华中农业大学硕士学位论文.2006.
马月萍,戴思兰.高等植物成花分子机理的研究进展.分子植物育种,2007,5(6s):21-28.
皮伟,李名扬.根癌农杆菌介导FPF1基因转化菊花的研究.西南大学学报(自然科学版),2007,29(4):70-73.
潘才博,张启翔,潘会堂,孙明.菊花FT类似基因的克隆与表达分析.园艺学报,2010,379(5):769-776.
潘才博,张启翔.日中性菊花及其分子育种前景.分子植物育种,2010,8(2):350-358.
彭凌涛.控制拟南芥和水稻开花时间光周期途径的分子机制.植物生理学通讯,2006,42(6):1021-1031.
庞朝友,喻树迅.拟南芥核苷糖转换相关基因研究进展.生物技术通报,2009,9:23-27.
祁云霞,刘永斌,荣威恒.转录组研究新技术: RNA-Seq及其应用.遗传,2011,33(11):1191-1202.
曲波,张微,陈旭辉,李楠,崔娜,李天来.植物花芽分化研究进展.中国农学通报,2010,26(24):109-114.
钱野,王君晖.四吡咯代谢中间产物在植物质体向细胞核信号转导中的作用.细胞生物学杂志,2004,26(2):98-101.
秦云飞.日本三角涡虫转录组、再生表达谱及小RNA谱的鉴定与分析.郑州大学硕士学位论文,2012.
全先庆,张渝洁,单雷,毕玉平.高等植物脯氨酸代谢研究进展.生物技术通报.2007,1:14-18.
任洪艳.光周期途径菊花成花相关基因的筛选及其表达分析.山东农业大学硕士学位论文,2012.
时丽冉.真核细胞内蛋白质的定向转运.衡水师专学报,2004,6(2):31-33.
孙昌辉,邓晓建,方军等.高等植物开花诱导研究进展.遗传,2007,29(10):1182-1190.
邵寒霜,李继红,郑学勤,陈守才.拟南芥LFY cDNA的克隆及转化菊花的研究.植物学报,1999,41(3):268-271.
田素波,郭春晓,郑成淑.光周期诱导植物成花的分子调控机制.园艺学报,2010,37(2):325-330.
田素波.菊花开花时间基因CmCO和CmFT的克隆与表达分析和遗传转化.山东农业大学硕士学位论文,2011.
王正荣.时间生物学.北京:科学出版社,2006, p63-196.
王丽丽,朱祯,李霞.精氨酸甲基转移酶及其生物学功能研究进展.中国农学通报,2008,7:39-44.
王翊,马月萍,戴思兰.观赏植物花期调控途径及其分子机制.植物学报,2010,45(6):641-653.
王台,钱前,袁明,王小菁,杨维才,瞿礼嘉,孔宏智,许亦农,蒋高明,种康.2009年中国植物科学若干领域重要研究进展.植物学报,2010,45(3):265-306.
王曦,汪小我,王立坤,冯智星,张学工.新一代高通量RNA测序数据的处理与分析.生物化学与生物物理进展,2010,37(8):834-846.
王京兆,王斌,徐琼方.用RAPD方法分析水稻光敏核不育基因.遗传学报,1995,22(1):53-58.
王隆华.植物开花生理.植物生理与分子生物学进展.北京:科学出版社,1992.
王庆贵. DNA指纹图谱在农作物品种鉴定中的应用.中国标准化,2001,7:45-47.
王学臣.拟南芥1，3，4-三磷酸肌醇5/6-激酶在光形态建成中的功能研究.中国农业大学博士学位论文,2005.
王海英.草菇不同发育时期菌柄基因表达谱差异初步分析.福建农林大学硕士学位论文,2011.
吴敏生,戴景瑞.扩增片段长度多态性一一种新的分子标记技术.植物学通报,1998,15(4):68-74.
武耀廷,张天真,郭旺珍.陆地棉品种SSR标记的多态性及用于杂交种纯度检测的研究.棉花学报,2001,13(3):131-133.
武耀廷,张大真,殷剑美.利用分子标记和形态学性状检测的陆地棉栽培品种遗传多样性.遗传学报,2001,28(11):1040-1050.
许莹修.菊花形态性状多样性和品种分类的研究.北京林业大学硕士学位论文,2005.
向道权,曹海河,曹永国.玉米SSR遗传图潜的构建及产举陀状笨闪定位.遗传学报,2001,28(8):778-784.
谢志红,孙毅,吴日恒.棉花分子标记研究现状及展望.中国棉花,2002,29(5):5-8.
徐秋华,张献龙,冯纯大.河北省和中棉所育成品种的遗传多样性分析.棉花学报,2001,13(4):238-242.
徐秋华,张献龙,聂以春.长江、黄河流域两棉区陆地棉品种的遗传多样性比较研究.遗传学报,2001,28(7):683-690.
徐秋华,张献龙,聂以春.我国棉花抗枯萎病品种的遗传多样性分析.中国农业科学,2002,35(3):272-276.
叶子飘.光合作用对光和CO2响应模型的研究进展.植物生态学报,2010,34(6):727-740.
杨娜,郭维明,陈发棣,房伟民.光周期对秋菊品种‘神马’花芽分化和开花的影响.园艺学报,2007,34(4):965-972.
雍伟东,种康,许智宏,谭克辉,朱自清.高等植物开花时间决定的基因调控研究.科学通报,2000,45(5):455-466.
晏才毅.浅谈菊文化与菊花栽培育种.中国菊花研究会论文集(三),1999,9-11.
杨俊品,荣廷昭.玉米数量性状RFLP分子标记研究进展.玉米科学,1999,7(l):18-24.
杨龚.植物成花的分子调控研究进展.热带农业科学,2004,24(5):73-78.
义鸣放,游捷.切花菊新品种栽植密度与切花质量的研究.中国菊花研究会论文集(二),1996,619-621.
叶珍.隐花色素与植物的光形态建成.四川农业大学学报,2003(03):267-274.
余梅,江昌俊,房婉萍等.茶树花蕾14-3-3蛋白基因的分子克隆及差异表达分析.中国农业科学,2008,41(10):2983-2991.
曾群,赵仲华,赵淑清.植物开花时间调控的信号途径.遗传,2006,28(8):1031-1036.
赵大中,雍伟东,种康.高等植物开花研究现状简述.植物学通报,1999,16(2):157-162.
钟晓红,罗先实,陈爱华.花芽分化与体内土要代谢产物含量的关系.湖南农业大学学报,1999,25(1):31-35.
张建勇,江和源,袁新跃.菊花总黄酮、多酚及水浸出物含量分析.中国农学通报,2010,26(9):102-105.
张娅.拟南芥精氨酸甲基转移酶SKB1调控植物开花时间的分子机制研究.西北农林科技大学博士学位论文,2007.
张莉俊,戴思兰.菊花种质资源研究进展.植物学报,2009,44(5):526-535.
章国卫,宋怀东,陈竺. mRNA选择性剪接的分子机制.遗传学报,2004,31(1):102-107.
赵宏波,陈发棣,郭维明,汤访评,房伟民.菊属与春黄菊族部分属间杂交亲和性初步研究.南京农业大学学报,2008,31(2):139-143.
种康,谭克辉,白书农.高等植物开花调控的分子基础.北京:科学出版社,1997,563-578.
赵琳,李文滨,杨春亮.光周期控制拟南芥和水稻开花反应差异性的分子生物学研究进展.东北农业大学学报,2006,37(1):93-101.
赵守城,吴子忠,熊建.真核细胞内膜泡运输的分子机制.生命科学,2002,14(5):261-264.
翟中和,王喜忠,丁明孝.细胞生物学.北京:高等教育出版社,2000.
孙之荣主译.生物信息学与功能基因组学(乔纳森·佩服斯纳).北京:化学工业出版社,2006:12-170.
张荻,申晓辉,卓丽环.百子莲(Agapanthus praecox ssp. orientalis)开花生理特征的研究.上海交通大学学报(农业科学版),2011,3:6-13.
赵晓霞.基于RNA测序技术的马氏珠母贝珍珠囊转录组及数字基因表达谱分析.广东海洋大学硕士学位论文,2011.
张彩霞.家蚕正反交F1代SAGE文库的构建与分析及差异基因的时空表达谱研究.苏州大学硕士学位论文,2012.
张献龙.基于新一代测序的数字基因表达谱生物信息学分析平台的建立及应用.华中农业大学硕士学位论文,2012.
Aubert D, Chen L, Moon YH., Martin D, Castle LA, Yang CH, Sung ZR. EMF1, a novelprotein involved in the control of shoot Architecture and flowering in Arabidopsis. PlantCell,2001,13(8):1865-1875.
Awada T, Radoglou K, Fotelli MN, Constantinidou HIA. Ecophysiology of seedlings of threeMediterraneanpine species in contrasting light regimes. Tree Physiology,2003,23,33-41.
Audic S, Claverie JM."The significance of digital gene expression profiles." Genome Res,1997,7(10):986-95.
Abe M, Fujiwara M, Kurotani K, Yokoi S, Shimamoto K. Identification of dynamin as aninteractor of rice GIGANTEAby tandem affinity purification (TAP). Plant Cell Physiol,2008,49:420–32.
Ashburner M, Ball CA, Blake JA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K,Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC,Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene Ontology: tool for the unificationof biology. Nature Genetics.2000,25:25-29.
Asmann YW, Klee EW, Thompson EA, Perez EA, Middha S, Oberg AL, Therneau TM, SmithDI, Poland GA, Wieben ED, Kocher JP.3' tag digital gene expression profiling of humanbrain and universal reference RNA using Illuraina Genome Analyzer. BMC Genomics,2009,10:531.
Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing underdependency. The Annals of Statistics,2001,29:1165-1188.
Bey M, Stueber K, Fellenberg K, Schwarz-Sommer Z, Sommer H, Saedler H.Characterizationof antirrhinum petal development and identification of target genes of the class B MADSbox gene DEFICIENS. Plant Cell,2004,16(12):3197-3215.
Bove J, Lucas P, Godin B, Ogé L, Jullien M, Grappin P. Gene expression analysis bycDNA-AFLP highlights a set of new signaling networksand translational control duringseed dormancy breaking in Nicotiana plumbaginifolia. Plant Molecular Biology,2005,57:593-612.
Bernacchi CJ, Singsaas EL, Pimentel C, Portis AR, Long SP. Improved temperature responsefunctions for models of Rubisco-limited photosynthesis. Plant Cell&Environment,2001,24,253-259.
Ban N, Nissen P, Hansen J, Moore PB, Steitz TA. The complete atomic structure of the largeribosomal subunit at2.4resolution. Science,2000,289(5481):905-920.
Barchowsky A. Stimulation of reactive oxygen, but not reactive nitrogen species, in vascularendothelial cells exposed to low levels of arsenite. Free Radic Bi Med,1992,27:1405-1412.
Briggs WR, Huala E. Blue-light photoreceptors in higher plants. Annu Rev Cell Dev Biol,1999,15:33-62.
Bashir A, Volik S, Collins C, Bafna V, Raphael BJ. Evaluation of paired-end sequencingstrategies for detection of genome rearrangements in cancer. PLoS Comput Biol,2008,4(4): e1000051.
Bosch M, Serras F, Martin-Blanco E, Baguna J. JNK signaling pathway required for woundhealing in regenerating Drosophila wing imaginal discs. Dev Biol,2005,280(1):73-86.
Bosch M, Baguna J, Serras F. Origin and proliferation of blastema cells during regeneration ofDrosophila wing imaginal discs. Int J Dev Biol.2008,52(8):1043-1050.
Blotta I, Prestinaci F, Mirante S, Cantafora A. Quantitative assay of total dsDNA withPicoGreen reagent and real-time fluorescent detection. Ann1st Super Sanita,2005,41(1):119-123.
Cashmore AR, Jarillo JA. Cryptochromes: blue light receptors for plants and animals. Science,1999,284:760-765.
Chung HW. Reverse transcriptase PCR (RT-PCR) and quantitative competitive PCR (QC-PCR). Exp Mol Med,2001,33(11):85-97.
Cech TR. Structural biology-The ribosome is a ribozyme. Science,2000,289(5481):878-879.
Chen SM, Miao HB, Chen FD, Jiang BB, Lu JG, Fang WM. Analysis of expressed sequencetags (ESTs) collected from the inflorescence of chrysanthemum. Plant MolecularBiology Reporter,2009,27:503-510.
Conesa A, Gotz S. Blast2GO: a universal tool for annotation, visualization and analysis infunctional genomics research. Bioinformatics,2005,21(18):3674-3676.
Cao S, Ye M, Jiang S. Involvement of GIGANTEA gene in the regulation of the cold stressresponse in Arabidopsis. Plant Cell Rep,2005,24(11):683-90.
Cai SQ, Xu DQ. Relationship between the CO2compensation point and photoresp iration insoybean leaves. Acta Phytophysiologica Sinica,2000,26:545-550.
Chou ML, Haung MD, Yang CH. EMF genes interact with late-flowering genes in regulatingfloralinitiation genes during shoot development in Arabidopsis thaliana. Plant CellPhysiol,2001,42(5):499-507.
Damesin C. Respiration and photosynthesis characteristics of current2year stems of Fagussylvatica: from the seasonal pattern to an annual balance. New Phytologist,2003,158:465-475.
Ethier GJ, Livingston NJ. On the need to incorporate sensitivity to CO2transfer conductanceinto the Farquhar-von Caemmerer-Berry leaf photosynthesis model. Plant Cell&Environment,2004,27:137-153.
Eun AJ, Seoh M, Wong S. Simultaneous quantification of two orchid viruses by the TaqManreal-time RT-PCR. J Virol Methods,2000,87:151-160.
Eisen MB, Spellman PT, Brown PO, Botstein D."Cluster analysis and display of genome-wide expression patterns." Proc Natl Acad Sci U S A,1998,95(25):14863-14868.
Feldmann KA, Marks MD. Agrobacterium-mediated transformation of germinating seeds ofArabidopsis thaliana:an non tissue culture approach. Genet,1987,208:1-94.
Günl M, Liew EF, David K, Putterill J. Analysis of a post-translational steroid inductionsystem for GIGANTEA in Arabidopsis. BMC Plant Biology2009,9:141.
Gould PD, Locke JC, Larue C, Southern MM, Davis SJ, Hanano S, Moyle R, Milich R,Putterill J, Millar AJ, Hall A. The molecular basis of temperature compensation in theArabidopsis circadian clock. Plant Cell,2006,18(5):1177-1187.
Gocal GFW, King RW. Evolution of floral meristem identity genes: analysis of Loliumtemulentum genes related to APETALA1and LFY of Arabidopsis. Plant Physiol,2001,125:1788-1801.
Griffiths-Jones S, Grocock RJ, Dongen S.v, Bateman A, Enright AJ. Enright. miRBase:microRNA sequences, targets and gene nomenclature. Nucleic Acids. Res,2006,34:D140-D144.
Hayama R, Yokoi S, Tamaki S, Yano M, Shimamoto K. Adaptation of photoperiodic controlpathways produces shortday flowering in rice. Nature,2003,422:719–722.
Huq E, Tepperman JM, Quail PH. GIGANTEA is a nuclear protein involved in phytochromesignaling in Arabidopsis. Proc Natl Acad Sci U S A.2000,15,97(17):9789-9794.
Hooper SD, Bork P."Medusa: a simple tool for interaction graph analysis." Bioinformatics,2005,21(24):4432-4433.
Henderson CD. Control of Arabidopsis flowering: the chill before the bloom. Development,2004,131(16):3829-3838.
Higuchi R, Fockler C. Kinetic PCR analysis real-time monitoring of DNA amplificationreactions. Biotechnology,1993,11(9):1026-1030.
Iseli C, Jongeneel CV, Bucher P. ESTscan: a program for detecting, evaluating, andreconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst MolBiol,1999:138-148.
Imaizumi T, Schultz TF, Harmon FG. FKF1, F-box protein mediates cyclic degradation of arepressorof CONSTANS in Arabidopsis. Science,2005,309(5732):293-297.
Izawa T, Oikawa T, Sugiyama N, Tanisaka T, Yano M, Shimamoto K. Phytochrome mediatesthe external light signal to repress FT orthologs in photoperiodic flowering of rice. GenesDev,2002,16(15):2006-2020.
Jocelyn C, Dupuis S, Jiang ZH, Wu JY. Caspase22pre2mRNA alternative splicing:Identification of an intronic element containing a decoy3′acceptor site. Proc Natl AcadSci USA,2001,98(3):938-943.
Kim WY, Fujiwara S, Suh SS, Kim J, Kim Y, Han L, David K, Putterill J, Nam HG, SomersDE. ZEITLUPE is a circadian photoreceptor stabilized by GIGANTEA in blue light.Nature.2007,20,449(7160):356-60.
Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S,Okuda S, Tokimatsu T, Yamanishi Y. KEGG for linking genomes to life and theenvironment. Nucleic Acids Research,2008,36:480-484.
Kulikow ska GH, Kopcewicz J. Ethylene in the control of photoperiodic flower induction inPharbit is nil Chois. Acta Societatis Botanicorum Poloniae,1999,68:33-37.
Korkaya H, Liu S, Wicha MS. Breast cancer stem cells, cytokine networks, and the tumormicroenvironment. J Clin Invest.2011,3,121(10):3804-3809.
Liu SX, Atnar M, Lippai I, Waldren C, Hei TK. Induction of oxyradicals by arsenic:Implication for mechanism of genotoxicity. Proc Natl Sci USA.2001,98(4):1643-1648.
Li RQ, Zhu HM, Ruan J, Qian WB, Fang X. De novo assembly of human genomes withmassively parallel short read sequencing. Genome Res,2010,20:265-272.
Lin C. Blue light receptors and signal transduction. Plant Cell,2002,(S):207-225.
Lam BJ, Hertel KJ. A general role for splicing enhancers in exon definition. RNA,2002,8:1233-1241.
Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program.Bioinformatics,2008,24:713-714.
Li B, Wachtel C, Miriami E, Yahalom G, Friedlander G, Sharon G, Sperling R, Sperling J.Stop codons affect5′splice site selection by surveillance of splicing. Proc Natl Acad SciU S A,2002,99(8):5277-5282.
Levin JZ, Berger MF, Adiconis X, Rogov P, Melnikov A, Fennell T, Nusbaum C, GarrawayLA, Gnirke A. Targeted next-geneRation sequencing of a cancer transcriptome enhancesdetection of sequence variants and novel fusion transcripts. Genome Biol.2009,10:115.
Meharg AA, Hartley-Whitaker J."Arsenic uptake and metabolism in arsenic resistant andnonresistant plant species." New Phytologist,2002,154(1):29-43.
Morrissy AS, Morin RD, Delaney A, Zeng T, McDonald H, Jones S, Zhao Y, Hirst M, MarraMA. Next-generation tag sequencing for cancer gene expression profiling. Genome Res,2009,19:1825-1835.
Mockler T, Yang H, Yu X, Parikh D, Cheng Y, Dolan S, Lin C. Regulation of photoperiodicflowering by Arabidopsis photoreceptors. Nature,2003,298:780-785.
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifyingmammalian transcriptomes by RNA-Seq. Nature Methods,2008,5(7):621-628.
Mizoguchi T, Wright L, Fujiwara S, Cremer F, Lee K, Onouchi H, Mouradov A, Fowler S,Kamada H, Putterill J, Coupland G. Distinct roles of GIGANTEA in promoting floweringand regulating circadian rhythms in Arabidopsis. Plant Cell.2005,17(8):2255-70.
Ma Laughlin JM, Greene DW. Fruit and hormones influence flowering of apple effects ofhormones. Journal of the American Society for Horticultural Science,1991,116(3):450-453.
McClung CR. Circadian rhythms in plants. Plant Mol Bio,2001,52:139-162.
Magi A, Benelli M, Gozzini A, Girolami F, Torricelli F,Brandi ML. Bioinformatics for nextgeneration sequencing data. Genes,2010,1(2):294-307.
Metzker ML. Sequencing technologies-the next generation. Nat Rev Genet,2010,11(1):31-46.
Nagao A, Mituyama T, Huang H, Chen D, Siomi MC, Siomi H. Biogenesis pathways ofpiRNAs loaded onto AG03in the Drosophila testis. RNA,2010,16:2503-2515.
Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. TheTranscriptional Landscape of the Yeast GenomeDefined by RNA Sequencing. Science,2008,320:1344-1349.
Nowrousian M. Next-generation sequencing techniques for eukaryotic microorganisms:sequencing-based solutions to biological problems. Eukaryot Cell,2010,9(9):1300-1310.
Oliviera CM, B rowning G. Gibberellin structure-activity effects on flower init iation inmature trees and on shoot growth in mature and juvenile Prunusavium. Plant GrowthRegulation,1993,13(1):55-63.
Okada M. Classification of chrysanthemum varieties in view of their environmental responsesto flowering. J. Japan. Soc. Hort. Sci.,1957,26(1):59-72.(in Japanese).
Okoniewski MJ, Miller CJ. Hybridization interactions between probesets in short oligomicroarrays lead to spurious correlations. BMC Bioinformatics,2006,7(1):276-290.
Paltiel J, Amin R, Gover A, Ori N, Samach A. Novel roles for GIGANTEA revealed underenvironmental conditions that modify its expression in Arabidopsis and Medicagotruncatula. Planta,2006,224(6):1255-1268.
Pe a L, Martín-Trillo M, Juárez J, Pina JA, Navarro L, José M, Martínez Z. Constitutiveexpression of Arabidopsis LEAFY or APETALA1genes in citrus reduces theirgeneration time. Nat Biotechnol,2001,19:263-267.
Pei Y, Niu L, Lu F, Liu C, Zhai J, Kong X, Cao X. Mutations in the Type II protein argininemethyltransferase AtPRMT5result in pleiotropic developmental defects in Arabidopsis.Plant Physiol,2007,144:1913-1923.
Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J,Cheung F, Parvizi B, Tsai J, Quackenbush J."TIGR Gene Indices clustering tools(TGICL): a software system for fast clustering of large EST datasets." Bioinformatics,2003,19(5):651-652.
Robertsa CA, Dietzgena RG, Heelanb LA, Macleanb DJ. Real-time RT-PCR fluorescentdetection of tomato spotted wilt virus. J Virol Methods,2000,88(1):1-8.
Roy A, Kucukural A, Zhang Y. I-TASSER: a unified platform for automated protein structureand function prediction. Nature Protocols,2010,5:725-738.
Royce TE, Rozowsky JS, Gerstein MB. Toward a universal microarray: prediction of geneexpression through nearest-neighbor probe sequence identification. Nucleic Acids Res,2007,35(15):99.
Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol,2008,26(10):1135-1145.
Shao HS, Li JH, Zheng XQ, Chen SC. Cloning of the LFY cDNA from arabidopsis thalianaand its transformation to chrysanthemum morifolium. Acta Botanica Sinica,1999,41(3):268-271.
Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, Janell D, Bashan A, Bartels H,Agmon I, Franceschi F, Yonath A. Structure of functionally activated small ribosomalsubunit at3.3resolution. Cell,2000,102(5):615-623.
Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, CateJHD. Structures of the bacterial ribosome at3.5resolution. Science,2005,310:827-834.
Sung S, Amasino RM. Remembering winter: toward a molecular understanding ofvernalization. Annu Rev Plant Biol,2005,56:491-508.
Sawa M, Nusinow DA, Kay SA, Imaizumi T. FKF1and GIGANTEA complex formation isrequired for day-length measurement in Arabidopsis. Science.2007,12,318(5848):261-265.
Salvetti A, Rossi L, Deri P, Batistoni R. An MCM2-related gene is expressed in proliferatingcells of intact and regenerating planarians. Dev. Dyn.2000,218(4):603-614.
Saldanha AJ."Java Treeview--extensible visualization of microarray data." Bioinformatics,2004,20(17):3246-3248.
Sawa M, Kay SA. GIGANTEA directly activates Flowering Locus T in Arabidopsis thaliana.Proc Natl Acad Sci U S A.2011,108(28):11698-11703.
Stockhammer OW, Zakrzewska A, Heged s Z, Spaink HP, Meijer AH. Transcriptomeprofiling and functional analyses of the zebra fish embryonic innate immune response toSalmonella infection. Immunol,2009,182:5641-5653.
Teixeira da Silva JA. Chrysanthemum: advances in tissue culture cryopreservation,postharvestt technology, genetics and transgenic biotechnology. Biotechnology Advances,2003,21:715–766.
Tang F, Barbaeioru C, Nordman E, Li B, Xu N, Bashkirov VI, Lao K, Surani MA.RNA-Seqanalysis to capture the transcriptome landscape of a single cell. Nat Protoc,2010,5:516-535.
Tatusov RL, Koonin EV, Lipman DJ. A genmic perspective on protein families. Science.1997,278(5338):631-637.
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM,Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV,Vasudevan S, Wolf YI, Yin JJ, Natale DA. The COG database: an updated versionincludes eukaryotes. BMC Bioinformatics.2003,4:41-54.
Trapnell C, Salzberg SL. How to map billions of short reads onto genomes. NatureBiotechnology,2009,27(5):455-457.
Tseng TS, Salomé PA, McClung CR, Olszewski NE. SPINDLY and GIGANTEA interact andact in Arabidopsis thaliana pathways involved in light responses, flowering, and rhythmsin cotyledon movements. Plant Cell.2004,16(6):1550-63.
Tocilj A, Schlünzen F, Janell D, Glühmann M, Hansen HAS, Harms J, Bashan A, Bartels H,Agmon I, Franceschi F, Yonath A. The small ribosomal subunit from Thermusthermophilus at4.5resolution: pattern fittings and the identification of a functional site.Proc Natl Acad Sci USA,1999,96(25):14252-14257.
't Hoen PAC, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RHAM, Menezes RX, BoerJM, Ommen GJB, Dunnen JT."Deep sequencing-based expression analysis shows majoradvances in robustness, resolution and inter-lab portability over five microarrayplatforms. Nucleic Acids Res,2008,36(21):141.
Uehara A, Nakata M, Kitajima J, Iwashina T. Internal and external flavonoids from the leavesof Japanese Chrysanthemum species (Asteraceae). Biochemical Systematics and Ecology,2012,41:142-149.
Velculescu VE, Zhang L, Vogelstein B, Kinzler KW. Serial analysis of gene expression.Science,1995,270(5235):484-487.
Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F.Accurate normalization of real-time quantitative RT-PCR data by geometric averaging ofmultiple internal control genes. Genome Biology,2002,3(7):3401-3411.
Wang XW, Luan JB, Li JM, Bao YY, Zhang CX, Liu SS. De novo characterization of awhitefly transcriptome and analysis of its gene expression during development. BMCGenomics,2010,11:400.
Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. NatureReviews Genetics,2009,10(1):57-63.
Wu JF, Wang Y, Wu SH. Two new clock proteins, LWD1and LWD2, mgnlate arabidopsisphotoperiodie flowering. Plant Physiol,2008,148:948-959.
Wang X, Zhang Y, Ma Q, Zhang Z, Xue Y, Bao S, Chong K. SKB1-mediated symmetricdimethylation of histone H4R3controls flowering time in Arabidopsis. The EMBOJournal,2007,26:1934-1941.
Wimberly BT, Brodersen DE, Clemons WM, Morgan-Warren RJ, Carter AP, Vonrhein C,Hartsch T, Ramakrishnan V. Structure of the30S ribosomal subunit. Nature,2000,407(6802):327-339.
Wang B, Guo G, Wang C, Lin Y, Wang X, Zhao M, Guo Y, He M, Zhang Y, Pan L. Surveyof the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing.Nucleic Acids Res,2010,38(15):5075-5087.
Ye J, Fang L, Zheng Hk, Zhang Y, Chen J, Zhang ZJ, Wang J, Li ST, Li RQ, Bolund L,Wang J. WEGO: a web tool for plotting GO annotations. Nucleic Acids Research,2006,34:293-297.
Yonath AE, Mussig J, Tesche B, et al. Crystallization of the large ribosomal subunits fromBacillus stearothermophilus. Biochemistry International,1980,1(5):428-435.
Yin JL, Shackel NA, Zekry A, McGuinness PH, Richards C, Putten KV, McCaughan GW,Eris JM, Bishop GA. Real-time reverse transcriptase-polymerase chain reaction (RT-PCR)for measurement of cytokine and growth factor mRNA expression with fluorescentprobesor SYBR Green I. Immunol Cell Biol,2001,79(3):213-221.
Yanovsky MJ, Kay SA. Molecular basis of seasonal time measurement in Arabidopsis. Nature,2002,419:308-312.
陈佩度,李鸿渐.几种中国野生菊的染色体组分析及亲源关系初步研究.园艺学报,1996,23(1):67-72.
陈旭,齐凤坤,康立功,李景富.实时荧光定量PCR技术研究进展及其应用.东北农业大学学报,41(8):148-155.
常立,文国琴.植物蓝光受体研究进展.生物技术通讯,2004(02):169-171.
陈思,焦新之.植物细胞的肌醇磷脂信息传递系统.植物生理学通讯,1994(06):405-413.
戴思兰,中国栽培菊花起源的综合研究.北京林业大学博士学位论文,1994.
戴思兰,陈俊愉.中国菊属一些种的分支分类学研究.武汉植物学研究,1997,15(1):27-34.
戴晓静.拟南芥砷酸还原酶基因AtACR2的表达调控及其功能分析.中科院植物所硕士学位论文,2009.
戴思兰,王文奎,黄家平.菊属系统学与菊花起源研究进展.北京林业大学学报,2002,24(5/6):230-234.
付建新,王翊,戴思兰.高等植物CO基因研究进展.分子植物育种,2010,8(5):1008-1016.
郭春晓,田素波,郑成淑,王文莉，孙宪芝.光周期途径植物开花时间决定关键基因FT.基因组学与应用生态学,2009,28(3):613-618.
郭忠义.菊谱.北京.中国社会出版社，2010.9.
郜爱玲,李建安,刘儒,何志祥,孙颖.高等植物花芽分化机理研究进展.经济林研究,2010,28(2):131-136.
高凤华,张洪亮,王海光.应用cDNA-AFLP比较干旱胁迫条件下水稻和旱稻转录本表达谱.科学通报,2009,54(16):2305-2319.
郭志刚,张伟.菊花.北京:中国林业出版社,2001,9-44.
胡永林.核糖体的结构与功能研究.生物化学与生物物理进展,2009,36(10):1239-1243.
姜丹,梁建丽,陈晓丽,洪波,贾文锁,赵梁军.拟南芥花期基因FT转化切花菊‘神马’.园艺学报,2010,37(3):441-448.
李鸿渐，邵建文.中国菊花品种资源的调查收集和分类.南京农业大学学报，1990，13(1):30-36.
李恐学,张方,陈俊愉.我国某些野生和栽培菊花的细胞学研究.园艺学报,1983,10(3):199-205.
李真,徐惠梅.菊花品种分类初步研究.安徽农学院学报,1989(4):282-284.
李宪利,袁志友,高东升.高等植物成花分子机理研究现状及展望.西北植物学报,2002,22(1):173-183.
刘姗，汪澈，樊金娟，阮燕晔，张立军.质子对植物蔗糖转运蛋白和己糖转运蛋白活性的调节.黑龙江农业科学,2012(7):14-18.
刘金元,陶文静,刘大钧.与小麦自粉病抗性基因Pmt紧密连锁的RAPD分析.遗传学报,2000,27(2):139-145.
刘志勇,杜永臣,王孝宣,国艳梅,高建昌.高温胁迫下番茄叶片差异表达基因的cDNA-AFLP分析.园艺学报,2008,35(7):1011-1016.
刘安娜.锌脂蛋白基因参与砷酸还原酶基因对拟南芥砷抗性的调控研究.内蒙古农业大学硕士学位论文,2011.
李滢,孙超,罗红梅,李西文,牛云云,陈士林.基于高通量测序454GS FLX的丹参转录组学研究.药学学报,2010,45(4):524-529.
林桂玉,黄在范,张翠华,郑成淑.菊花花芽分化期超微弱发光及生理代谢的变化.园艺学报,2008,35(12):1819-1824.
李辛雷,陈发棣.菊花种质资源与遗传改良研究进展.植物学通报,2004,21(4):392-401.
林镕,石铸.中国植物志:76卷第1分册.北京:科学出版社,1983:1-39.
吕晋慧,吴月亮,孙磊,张启翔. AP1基因转化地被菊品种玉人面的研究.林业科学,2007,43(9):128-135.
马力,唐凤敏,曾天舒等.菊花多糖和绿原酸免疫调节作用的研究.医药导报,2008,27(10):1168-1170.
毛静.中国传统菊花文化研究.华中农业大学硕士学位论文.2006.
马月萍,戴思兰.高等植物成花分子机理的研究进展.分子植物育种,2007,5(6s):21-28.
皮伟,李名扬.根癌农杆菌介导FPF1基因转化菊花的研究.西南大学学报(自然科学版),2007,29(4):70-73.
潘才博,张启翔,潘会堂,孙明.菊花FT类似基因的克隆与表达分析.园艺学报,2010,379(5):769-776.
潘才博,张启翔.日中性菊花及其分子育种前景.分子植物育种,2010,8(2):350-358.
彭凌涛.控制拟南芥和水稻开花时间光周期途径的分子机制.植物生理学通讯,2006,42(6):1021-1031.
庞朝友,喻树迅.拟南芥核苷糖转换相关基因研究进展.生物技术通报,2009,9:23-27.
祁云霞,刘永斌,荣威恒.转录组研究新技术: RNA-Seq及其应用.遗传,2011,33(11):1191-1202.
曲波,张微,陈旭辉,李楠,崔娜,李天来.植物花芽分化研究进展.中国农学通报,2010,26(24):109-114.
钱野,王君晖.四吡咯代谢中间产物在植物质体向细胞核信号转导中的作用.细胞生物学杂志,2004,26(2):98-101.
秦云飞.日本三角涡虫转录组、再生表达谱及小RNA谱的鉴定与分析.郑州大学硕士学位论文,2012.
全先庆,张渝洁,单雷,毕玉平.高等植物脯氨酸代谢研究进展.生物技术通报.2007,1:14-18.
任洪艳.光周期途径菊花成花相关基因的筛选及其表达分析.山东农业大学硕士学位论文,2012.
时丽冉.真核细胞内蛋白质的定向转运.衡水师专学报,2004,6(2):31-33.
孙昌辉,邓晓建,方军等.高等植物开花诱导研究进展.遗传,2007,29(10):1182-1190.
邵寒霜,李继红,郑学勤,陈守才.拟南芥LFY cDNA的克隆及转化菊花的研究.植物学报,1999,41(3):268-271.
田素波,郭春晓,郑成淑.光周期诱导植物成花的分子调控机制.园艺学报,2010,37(2):325-330.
田素波.菊花开花时间基因CmCO和CmFT的克隆与表达分析和遗传转化.山东农业大学硕士学位论文,2011.
王正荣.时间生物学.北京:科学出版社,2006, p63-196.
王丽丽,朱祯,李霞.精氨酸甲基转移酶及其生物学功能研究进展.中国农学通报,2008,7:39-44.
王翊,马月萍,戴思兰.观赏植物花期调控途径及其分子机制.植物学报,2010,45(6):641-653.
王台,钱前,袁明,王小菁,杨维才,瞿礼嘉,孔宏智,许亦农,蒋高明,种康.2009年中国植物科学若干领域重要研究进展.植物学报,2010,45(3):265-306.
王曦,汪小我,王立坤,冯智星,张学工.新一代高通量RNA测序数据的处理与分析.生物化学与生物物理进展,2010,37(8):834-846.
王京兆,王斌,徐琼方.用RAPD方法分析水稻光敏核不育基因.遗传学报,1995,22(1):53-58.
王隆华.植物开花生理.植物生理与分子生物学进展.北京:科学出版社,1992.
王庆贵. DNA指纹图谱在农作物品种鉴定中的应用.中国标准化,2001,7:45-47.
王学臣.拟南芥1，3，4-三磷酸肌醇5/6-激酶在光形态建成中的功能研究.中国农业大学博士学位论文,2005.
王海英.草菇不同发育时期菌柄基因表达谱差异初步分析.福建农林大学硕士学位论文,2011.
吴敏生,戴景瑞.扩增片段长度多态性一一种新的分子标记技术.植物学通报,1998,15(4):68-74.
武耀廷,张天真,郭旺珍.陆地棉品种SSR标记的多态性及用于杂交种纯度检测的研究.棉花学报,2001,13(3):131-133.
武耀廷,张大真,殷剑美.利用分子标记和形态学性状检测的陆地棉栽培品种遗传多样性.遗传学报,2001,28(11):1040-1050.
许莹修.菊花形态性状多样性和品种分类的研究.北京林业大学硕士学位论文,2005.
向道权,曹海河,曹永国.玉米SSR遗传图潜的构建及产举陀状笨闪定位.遗传学报,2001,28(8):778-784.
谢志红,孙毅,吴日恒.棉花分子标记研究现状及展望.中国棉花,2002,29(5):5-8.
徐秋华,张献龙,冯纯大.河北省和中棉所育成品种的遗传多样性分析.棉花学报,2001,13(4):238-242.
徐秋华,张献龙,聂以春.长江、黄河流域两棉区陆地棉品种的遗传多样性比较研究.遗传学报,2001,28(7):683-690.
徐秋华,张献龙,聂以春.我国棉花抗枯萎病品种的遗传多样性分析.中国农业科学,2002,35(3):272-276.
叶子飘.光合作用对光和CO2响应模型的研究进展.植物生态学报,2010,34(6):727-740.
杨娜,郭维明,陈发棣,房伟民.光周期对秋菊品种‘神马’花芽分化和开花的影响.园艺学报,2007,34(4):965-972.
雍伟东,种康,许智宏,谭克辉,朱自清.高等植物开花时间决定的基因调控研究.科学通报,2000,45(5):455-466.
晏才毅.浅谈菊文化与菊花栽培育种.中国菊花研究会论文集(三),1999,9-11.
杨俊品,荣廷昭.玉米数量性状RFLP分子标记研究进展.玉米科学,1999,7(l):18-24.
杨龚.植物成花的分子调控研究进展.热带农业科学,2004,24(5):73-78.
义鸣放,游捷.切花菊新品种栽植密度与切花质量的研究.中国菊花研究会论文集(二),1996,619-621.
叶珍.隐花色素与植物的光形态建成.四川农业大学学报,2003(03):267-274.
余梅,江昌俊,房婉萍等.茶树花蕾14-3-3蛋白基因的分子克隆及差异表达分析.中国农业科学,2008,41(10):2983-2991.
曾群,赵仲华,赵淑清.植物开花时间调控的信号途径.遗传,2006,28(8):1031-1036.
赵大中,雍伟东,种康.高等植物开花研究现状简述.植物学通报,1999,16(2):157-162.
钟晓红,罗先实,陈爱华.花芽分化与体内土要代谢产物含量的关系.湖南农业大学学报,1999,25(1):31-35.
张建勇,江和源,袁新跃.菊花总黄酮、多酚及水浸出物含量分析.中国农学通报,2010,26(9):102-105.
张娅.拟南芥精氨酸甲基转移酶SKB1调控植物开花时间的分子机制研究.西北农林科技大学博士学位论文,2007.
张莉俊,戴思兰.菊花种质资源研究进展.植物学报,2009,44(5):526-535.
章国卫,宋怀东,陈竺. mRNA选择性剪接的分子机制.遗传学报,2004,31(1):102-107.
赵宏波,陈发棣,郭维明,汤访评,房伟民.菊属与春黄菊族部分属间杂交亲和性初步研究.南京农业大学学报,2008,31(2):139-143.
种康,谭克辉,白书农.高等植物开花调控的分子基础.北京:科学出版社,1997,563-578.
赵琳,李文滨,杨春亮.光周期控制拟南芥和水稻开花反应差异性的分子生物学研究进展.东北农业大学学报,2006,37(1):93-101.
赵守城,吴子忠,熊建.真核细胞内膜泡运输的分子机制.生命科学,2002,14(5):261-264.
翟中和,王喜忠,丁明孝.细胞生物学.北京:高等教育出版社,2000.
孙之荣主译.生物信息学与功能基因组学(乔纳森·佩服斯纳).北京:化学工业出版社,2006:12-170.
张荻,申晓辉,卓丽环.百子莲(Agapanthus praecox ssp. orientalis)开花生理特征的研究.上海交通大学学报(农业科学版),2011,3:6-13.
赵晓霞.基于RNA测序技术的马氏珠母贝珍珠囊转录组及数字基因表达谱分析.广东海洋大学硕士学位论文,2011.
张彩霞.家蚕正反交F1代SAGE文库的构建与分析及差异基因的时空表达谱研究.苏州大学硕士学位论文,2012.
张献龙.基于新一代测序的数字基因表达谱生物信息学分析平台的建立及应用.华中农业大学硕士学位论文,2012.
Aubert D, Chen L, Moon YH., Martin D, Castle LA, Yang CH, Sung ZR. EMF1, a novelprotein involved in the control of shoot Architecture and flowering in Arabidopsis. PlantCell,2001,13(8):1865-1875.
Awada T, Radoglou K, Fotelli MN, Constantinidou HIA. Ecophysiology of seedlings of threeMediterraneanpine species in contrasting light regimes. Tree Physiology,2003,23,33-41.
Audic S, Claverie JM."The significance of digital gene expression profiles." Genome Res,1997,7(10):986-95.
Abe M, Fujiwara M, Kurotani K, Yokoi S, Shimamoto K. Identification of dynamin as aninteractor of rice GIGANTEAby tandem affinity purification (TAP). Plant Cell Physiol,2008,49:420–32.
Ashburner M, Ball CA, Blake JA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K,Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC,Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene Ontology: tool for the unificationof biology. Nature Genetics.2000,25:25-29.
Asmann YW, Klee EW, Thompson EA, Perez EA, Middha S, Oberg AL, Therneau TM, SmithDI, Poland GA, Wieben ED, Kocher JP.3' tag digital gene expression profiling of humanbrain and universal reference RNA using Illuraina Genome Analyzer. BMC Genomics,2009,10:531.
Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing underdependency. The Annals of Statistics,2001,29:1165-1188.
Bey M, Stueber K, Fellenberg K, Schwarz-Sommer Z, Sommer H, Saedler H.Characterizationof antirrhinum petal development and identification of target genes of the class B MADSbox gene DEFICIENS. Plant Cell,2004,16(12):3197-3215.
Bove J, Lucas P, Godin B, Ogé L, Jullien M, Grappin P. Gene expression analysis bycDNA-AFLP highlights a set of new signaling networksand translational control duringseed dormancy breaking in Nicotiana plumbaginifolia. Plant Molecular Biology,2005,57:593-612.
Bernacchi CJ, Singsaas EL, Pimentel C, Portis AR, Long SP. Improved temperature responsefunctions for models of Rubisco-limited photosynthesis. Plant Cell&Environment,2001,24,253-259.
Ban N, Nissen P, Hansen J, Moore PB, Steitz TA. The complete atomic structure of the largeribosomal subunit at2.4resolution. Science,2000,289(5481):905-920.
Barchowsky A. Stimulation of reactive oxygen, but not reactive nitrogen species, in vascularendothelial cells exposed to low levels of arsenite. Free Radic Bi Med,1992,27:1405-1412.
Briggs WR, Huala E. Blue-light photoreceptors in higher plants. Annu Rev Cell Dev Biol,1999,15:33-62.
Bashir A, Volik S, Collins C, Bafna V, Raphael BJ. Evaluation of paired-end sequencingstrategies for detection of genome rearrangements in cancer. PLoS Comput Biol,2008,4(4): e1000051.
Bosch M, Serras F, Martin-Blanco E, Baguna J. JNK signaling pathway required for woundhealing in regenerating Drosophila wing imaginal discs. Dev Biol,2005,280(1):73-86.
Bosch M, Baguna J, Serras F. Origin and proliferation of blastema cells during regeneration ofDrosophila wing imaginal discs. Int J Dev Biol.2008,52(8):1043-1050.
Blotta I, Prestinaci F, Mirante S, Cantafora A. Quantitative assay of total dsDNA withPicoGreen reagent and real-time fluorescent detection. Ann1st Super Sanita,2005,41(1):119-123.
Cashmore AR, Jarillo JA. Cryptochromes: blue light receptors for plants and animals. Science,1999,284:760-765.
Chung HW. Reverse transcriptase PCR (RT-PCR) and quantitative competitive PCR (QC-PCR). Exp Mol Med,2001,33(11):85-97.
Cech TR. Structural biology-The ribosome is a ribozyme. Science,2000,289(5481):878-879.
Chen SM, Miao HB, Chen FD, Jiang BB, Lu JG, Fang WM. Analysis of expressed sequencetags (ESTs) collected from the inflorescence of chrysanthemum. Plant MolecularBiology Reporter,2009,27:503-510.
Conesa A, Gotz S. Blast2GO: a universal tool for annotation, visualization and analysis infunctional genomics research. Bioinformatics,2005,21(18):3674-3676.
Cao S, Ye M, Jiang S. Involvement of GIGANTEA gene in the regulation of the cold stressresponse in Arabidopsis. Plant Cell Rep,2005,24(11):683-90.
Cai SQ, Xu DQ. Relationship between the CO2compensation point and photoresp iration insoybean leaves. Acta Phytophysiologica Sinica,2000,26:545-550.
Chou ML, Haung MD, Yang CH. EMF genes interact with late-flowering genes in regulatingfloralinitiation genes during shoot development in Arabidopsis thaliana. Plant CellPhysiol,2001,42(5):499-507.
Damesin C. Respiration and photosynthesis characteristics of current2year stems of Fagussylvatica: from the seasonal pattern to an annual balance. New Phytologist,2003,158:465-475.
Ethier GJ, Livingston NJ. On the need to incorporate sensitivity to CO2transfer conductanceinto the Farquhar-von Caemmerer-Berry leaf photosynthesis model. Plant Cell&Environment,2004,27:137-153.
Eun AJ, Seoh M, Wong S. Simultaneous quantification of two orchid viruses by the TaqManreal-time RT-PCR. J Virol Methods,2000,87:151-160.
Eisen MB, Spellman PT, Brown PO, Botstein D."Cluster analysis and display of genome-wide expression patterns." Proc Natl Acad Sci U S A,1998,95(25):14863-14868.
Feldmann KA, Marks MD. Agrobacterium-mediated transformation of germinating seeds ofArabidopsis thaliana:an non tissue culture approach. Genet,1987,208:1-94.
Günl M, Liew EF, David K, Putterill J. Analysis of a post-translational steroid inductionsystem for GIGANTEA in Arabidopsis. BMC Plant Biology2009,9:141.
Gould PD, Locke JC, Larue C, Southern MM, Davis SJ, Hanano S, Moyle R, Milich R,Putterill J, Millar AJ, Hall A. The molecular basis of temperature compensation in theArabidopsis circadian clock. Plant Cell,2006,18(5):1177-1187.
Gocal GFW, King RW. Evolution of floral meristem identity genes: analysis of Loliumtemulentum genes related to APETALA1and LFY of Arabidopsis. Plant Physiol,2001,125:1788-1801.
Griffiths-Jones S, Grocock RJ, Dongen S.v, Bateman A, Enright AJ. Enright. miRBase:microRNA sequences, targets and gene nomenclature. Nucleic Acids. Res,2006,34:D140-D144.
Hayama R, Yokoi S, Tamaki S, Yano M, Shimamoto K. Adaptation of photoperiodic controlpathways produces shortday flowering in rice. Nature,2003,422:719–722.
Huq E, Tepperman JM, Quail PH. GIGANTEA is a nuclear protein involved in phytochromesignaling in Arabidopsis. Proc Natl Acad Sci U S A.2000,15,97(17):9789-9794.
Hooper SD, Bork P."Medusa: a simple tool for interaction graph analysis." Bioinformatics,2005,21(24):4432-4433.
Henderson CD. Control of Arabidopsis flowering: the chill before the bloom. Development,2004,131(16):3829-3838.
Higuchi R, Fockler C. Kinetic PCR analysis real-time monitoring of DNA amplificationreactions. Biotechnology,1993,11(9):1026-1030.
Iseli C, Jongeneel CV, Bucher P. ESTscan: a program for detecting, evaluating, andreconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst MolBiol,1999:138-148.
Imaizumi T, Schultz TF, Harmon FG. FKF1, F-box protein mediates cyclic degradation of arepressorof CONSTANS in Arabidopsis. Science,2005,309(5732):293-297.
Izawa T, Oikawa T, Sugiyama N, Tanisaka T, Yano M, Shimamoto K. Phytochrome mediatesthe external light signal to repress FT orthologs in photoperiodic flowering of rice. GenesDev,2002,16(15):2006-2020.
Jocelyn C, Dupuis S, Jiang ZH, Wu JY. Caspase22pre2mRNA alternative splicing:Identification of an intronic element containing a decoy3′acceptor site. Proc Natl AcadSci USA,2001,98(3):938-943.
Kim WY, Fujiwara S, Suh SS, Kim J, Kim Y, Han L, David K, Putterill J, Nam HG, SomersDE. ZEITLUPE is a circadian photoreceptor stabilized by GIGANTEA in blue light.Nature.2007,20,449(7160):356-60.
Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S,Okuda S, Tokimatsu T, Yamanishi Y. KEGG for linking genomes to life and theenvironment. Nucleic Acids Research,2008,36:480-484.
Kulikow ska GH, Kopcewicz J. Ethylene in the control of photoperiodic flower induction inPharbit is nil Chois. Acta Societatis Botanicorum Poloniae,1999,68:33-37.
Korkaya H, Liu S, Wicha MS. Breast cancer stem cells, cytokine networks, and the tumormicroenvironment. J Clin Invest.2011,3,121(10):3804-3809.
Liu SX, Atnar M, Lippai I, Waldren C, Hei TK. Induction of oxyradicals by arsenic:Implication for mechanism of genotoxicity. Proc Natl Sci USA.2001,98(4):1643-1648.
Li RQ, Zhu HM, Ruan J, Qian WB, Fang X. De novo assembly of human genomes withmassively parallel short read sequencing. Genome Res,2010,20:265-272.
Lin C. Blue light receptors and signal transduction. Plant Cell,2002,(S):207-225.
Lam BJ, Hertel KJ. A general role for splicing enhancers in exon definition. RNA,2002,8:1233-1241.
Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program.Bioinformatics,2008,24:713-714.
Li B, Wachtel C, Miriami E, Yahalom G, Friedlander G, Sharon G, Sperling R, Sperling J.Stop codons affect5′splice site selection by surveillance of splicing. Proc Natl Acad SciU S A,2002,99(8):5277-5282.
Levin JZ, Berger MF, Adiconis X, Rogov P, Melnikov A, Fennell T, Nusbaum C, GarrawayLA, Gnirke A. Targeted next-geneRation sequencing of a cancer transcriptome enhancesdetection of sequence variants and novel fusion transcripts. Genome Biol.2009,10:115.
Meharg AA, Hartley-Whitaker J."Arsenic uptake and metabolism in arsenic resistant andnonresistant plant species." New Phytologist,2002,154(1):29-43.
Morrissy AS, Morin RD, Delaney A, Zeng T, McDonald H, Jones S, Zhao Y, Hirst M, MarraMA. Next-generation tag sequencing for cancer gene expression profiling. Genome Res,2009,19:1825-1835.
Mockler T, Yang H, Yu X, Parikh D, Cheng Y, Dolan S, Lin C. Regulation of photoperiodicflowering by Arabidopsis photoreceptors. Nature,2003,298:780-785.
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifyingmammalian transcriptomes by RNA-Seq. Nature Methods,2008,5(7):621-628.
Mizoguchi T, Wright L, Fujiwara S, Cremer F, Lee K, Onouchi H, Mouradov A, Fowler S,Kamada H, Putterill J, Coupland G. Distinct roles of GIGANTEA in promoting floweringand regulating circadian rhythms in Arabidopsis. Plant Cell.2005,17(8):2255-70.
Ma Laughlin JM, Greene DW. Fruit and hormones influence flowering of apple effects ofhormones. Journal of the American Society for Horticultural Science,1991,116(3):450-453.
McClung CR. Circadian rhythms in plants. Plant Mol Bio,2001,52:139-162.
Magi A, Benelli M, Gozzini A, Girolami F, Torricelli F,Brandi ML. Bioinformatics for nextgeneration sequencing data. Genes,2010,1(2):294-307.
Metzker ML. Sequencing technologies-the next generation. Nat Rev Genet,2010,11(1):31-46.
Nagao A, Mituyama T, Huang H, Chen D, Siomi MC, Siomi H. Biogenesis pathways ofpiRNAs loaded onto AG03in the Drosophila testis. RNA,2010,16:2503-2515.
Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. TheTranscriptional Landscape of the Yeast GenomeDefined by RNA Sequencing. Science,2008,320:1344-1349.
Nowrousian M. Next-generation sequencing techniques for eukaryotic microorganisms:sequencing-based solutions to biological problems. Eukaryot Cell,2010,9(9):1300-1310.
Oliviera CM, B rowning G. Gibberellin structure-activity effects on flower init iation inmature trees and on shoot growth in mature and juvenile Prunusavium. Plant GrowthRegulation,1993,13(1):55-63.
Okada M. Classification of chrysanthemum varieties in view of their environmental responsesto flowering. J. Japan. Soc. Hort. Sci.,1957,26(1):59-72.(in Japanese).
Okoniewski MJ, Miller CJ. Hybridization interactions between probesets in short oligomicroarrays lead to spurious correlations. BMC Bioinformatics,2006,7(1):276-290.
Paltiel J, Amin R, Gover A, Ori N, Samach A. Novel roles for GIGANTEA revealed underenvironmental conditions that modify its expression in Arabidopsis and Medicagotruncatula. Planta,2006,224(6):1255-1268.
Pe a L, Martín-Trillo M, Juárez J, Pina JA, Navarro L, José M, Martínez Z. Constitutiveexpression of Arabidopsis LEAFY or APETALA1genes in citrus reduces theirgeneration time. Nat Biotechnol,2001,19:263-267.
Pei Y, Niu L, Lu F, Liu C, Zhai J, Kong X, Cao X. Mutations in the Type II protein argininemethyltransferase AtPRMT5result in pleiotropic developmental defects in Arabidopsis.Plant Physiol,2007,144:1913-1923.
Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J,Cheung F, Parvizi B, Tsai J, Quackenbush J."TIGR Gene Indices clustering tools(TGICL): a software system for fast clustering of large EST datasets." Bioinformatics,2003,19(5):651-652.
Robertsa CA, Dietzgena RG, Heelanb LA, Macleanb DJ. Real-time RT-PCR fluorescentdetection of tomato spotted wilt virus. J Virol Methods,2000,88(1):1-8.
Roy A, Kucukural A, Zhang Y. I-TASSER: a unified platform for automated protein structureand function prediction. Nature Protocols,2010,5:725-738.
Royce TE, Rozowsky JS, Gerstein MB. Toward a universal microarray: prediction of geneexpression through nearest-neighbor probe sequence identification. Nucleic Acids Res,2007,35(15):99.
Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol,2008,26(10):1135-1145.
Shao HS, Li JH, Zheng XQ, Chen SC. Cloning of the LFY cDNA from arabidopsis thalianaand its transformation to chrysanthemum morifolium. Acta Botanica Sinica,1999,41(3):268-271.
Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, Janell D, Bashan A, Bartels H,Agmon I, Franceschi F, Yonath A. Structure of functionally activated small ribosomalsubunit at3.3resolution. Cell,2000,102(5):615-623.
Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, CateJHD. Structures of the bacterial ribosome at3.5resolution. Science,2005,310:827-834.
Sung S, Amasino RM. Remembering winter: toward a molecular understanding ofvernalization. Annu Rev Plant Biol,2005,56:491-508.
Sawa M, Nusinow DA, Kay SA, Imaizumi T. FKF1and GIGANTEA complex formation isrequired for day-length measurement in Arabidopsis. Science.2007,12,318(5848):261-265.
Salvetti A, Rossi L, Deri P, Batistoni R. An MCM2-related gene is expressed in proliferatingcells of intact and regenerating planarians. Dev. Dyn.2000,218(4):603-614.
Saldanha AJ."Java Treeview--extensible visualization of microarray data." Bioinformatics,2004,20(17):3246-3248.
Sawa M, Kay SA. GIGANTEA directly activates Flowering Locus T in Arabidopsis thaliana.Proc Natl Acad Sci U S A.2011,108(28):11698-11703.
Stockhammer OW, Zakrzewska A, Heged s Z, Spaink HP, Meijer AH. Transcriptomeprofiling and functional analyses of the zebra fish embryonic innate immune response toSalmonella infection. Immunol,2009,182:5641-5653.
Teixeira da Silva JA. Chrysanthemum: advances in tissue culture cryopreservation,postharvestt technology, genetics and transgenic biotechnology. Biotechnology Advances,2003,21:715–766.
Tang F, Barbaeioru C, Nordman E, Li B, Xu N, Bashkirov VI, Lao K, Surani MA.RNA-Seqanalysis to capture the transcriptome landscape of a single cell. Nat Protoc,2010,5:516-535.
Tatusov RL, Koonin EV, Lipman DJ. A genmic perspective on protein families. Science.1997,278(5338):631-637.
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM,Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV,Vasudevan S, Wolf YI, Yin JJ, Natale DA. The COG database: an updated versionincludes eukaryotes. BMC Bioinformatics.2003,4:41-54.
Trapnell C, Salzberg SL. How to map billions of short reads onto genomes. NatureBiotechnology,2009,27(5):455-457.
Tseng TS, Salomé PA, McClung CR, Olszewski NE. SPINDLY and GIGANTEA interact andact in Arabidopsis thaliana pathways involved in light responses, flowering, and rhythmsin cotyledon movements. Plant Cell.2004,16(6):1550-63.
Tocilj A, Schlünzen F, Janell D, Glühmann M, Hansen HAS, Harms J, Bashan A, Bartels H,Agmon I, Franceschi F, Yonath A. The small ribosomal subunit from Thermusthermophilus at4.5resolution: pattern fittings and the identification of a functional site.Proc Natl Acad Sci USA,1999,96(25):14252-14257.
't Hoen PAC, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RHAM, Menezes RX, BoerJM, Ommen GJB, Dunnen JT."Deep sequencing-based expression analysis shows majoradvances in robustness, resolution and inter-lab portability over five microarrayplatforms. Nucleic Acids Res,2008,36(21):141.
Uehara A, Nakata M, Kitajima J, Iwashina T. Internal and external flavonoids from the leavesof Japanese Chrysanthemum species (Asteraceae). Biochemical Systematics and Ecology,2012,41:142-149.
Velculescu VE, Zhang L, Vogelstein B, Kinzler KW. Serial analysis of gene expression.Science,1995,270(5235):484-487.
Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F.Accurate normalization of real-time quantitative RT-PCR data by geometric averaging ofmultiple internal control genes. Genome Biology,2002,3(7):3401-3411.
Wang XW, Luan JB, Li JM, Bao YY, Zhang CX, Liu SS. De novo characterization of awhitefly transcriptome and analysis of its gene expression during development. BMCGenomics,2010,11:400.
Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. NatureReviews Genetics,2009,10(1):57-63.
Wu JF, Wang Y, Wu SH. Two new clock proteins, LWD1and LWD2, mgnlate arabidopsisphotoperiodie flowering. Plant Physiol,2008,148:948-959.
Wang X, Zhang Y, Ma Q, Zhang Z, Xue Y, Bao S, Chong K. SKB1-mediated symmetricdimethylation of histone H4R3controls flowering time in Arabidopsis. The EMBOJournal,2007,26:1934-1941.
Wimberly BT, Brodersen DE, Clemons WM, Morgan-Warren RJ, Carter AP, Vonrhein C,Hartsch T, Ramakrishnan V. Structure of the30S ribosomal subunit. Nature,2000,407(6802):327-339.
Wang B, Guo G, Wang C, Lin Y, Wang X, Zhao M, Guo Y, He M, Zhang Y, Pan L. Surveyof the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing.Nucleic Acids Res,2010,38(15):5075-5087.
Ye J, Fang L, Zheng Hk, Zhang Y, Chen J, Zhang ZJ, Wang J, Li ST, Li RQ, Bolund L,Wang J. WEGO: a web tool for plotting GO annotations. Nucleic Acids Research,2006,34:293-297.
Yonath AE, Mussig J, Tesche B, et al. Crystallization of the large ribosomal subunits fromBacillus stearothermophilus. Biochemistry International,1980,1(5):428-435.
Yin JL, Shackel NA, Zekry A, McGuinness PH, Richards C, Putten KV, McCaughan GW,Eris JM, Bishop GA. Real-time reverse transcriptase-polymerase chain reaction (RT-PCR)for measurement of cytokine and growth factor mRNA expression with fluorescentprobesor SYBR Green I. Immunol Cell Biol,2001,79(3):213-221.
Yanovsky MJ, Kay SA. Molecular basis of seasonal time measurement in Arabidopsis. Nature,2002,419:308-312.