基于RNA-Seq技术的葡萄不同花型新转录本预测和基因结构优化
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摘要
由于葡萄(Vitis spp.)基因组注释的不完善,本文以3个生长时期3种性状葡萄花器官(雌能花、雄花和两性花)为材料提取总RNA进行高通量测序,开展了葡萄新转录本发掘和已注释基因结构优化工作。获得173.41Gb高质量的过滤后的数据(clean data),发掘出839个新转录本,其中697个新转录本得到了注释信息,同时对10 163个已注释基因的结构进行了优化。本研究旨在为后续葡萄基因组学、表型研究和其他生物基因组注释信息的完善提供参考。
Because of the imperfect explanation of grapes' genome annotation. In this paper, the grape transcript excavation and annotated gene structure optimization were discussed depends on the RNA high-throughput sequencing technology. All the RNA are extracted from three traits of grape floral organs which are female flower, male flower and bisexual flower in three growing periods. After that, 173.41 Gb high accuracy clean data were collected. Depending on those data, 839 new transcripts were excavated. In addition, 697 of the 839 new transcripts got the annotated information, and 10 163 annotated gene structures were optimized. The result of this research could provide useful references for the future genomics and phenotypic studies in grape and the improvement of other biological genome annotation.
Because of the imperfect explanation of grapes' genome annotation. In this paper, the grape transcript excavation and annotated gene structure optimization were discussed depends on the RNA high-throughput sequencing technology. All the RNA are extracted from three traits of grape floral organs which are female flower, male flower and bisexual flower in three growing periods. After that, 173.41 Gb high accuracy clean data were collected. Depending on those data, 839 new transcripts were excavated. In addition, 697 of the 839 new transcripts got the annotated information, and 10 163 annotated gene structures were optimized. The result of this research could provide useful references for the future genomics and phenotypic studies in grape and the improvement of other biological genome annotation.
引文
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Ashburner M,Ball CA,Blake JA,et al(2000).Gene ontology:tool for the unification of biology.Nat Genet,25:25-29
Cheng X(2015).Biological characteristics and transcriptome analysis of selenium enriched Chlamydomonas reinhardtii in Rhine(dissertation).Shenzhen,Guangdong:Shenzhen University(in Chinese with English abstract)[程雪薇(2015).莱茵衣藻富硒生物学特性及其转录组学研究(学位论文).广州深圳:深圳大学]
Darwish O,Shahan R,Liu Z,et al(2015).Re-annotation of the woodland strawberry(Fragaria vesca)genome.BMCGenomics,16:29
Dassanayake M,Haas JS,Bohnert HJ,et al(2010).Shedding light on an extremophile lifestyle through transcriptomics.New Phytol,183(3):764-775
Deng Y,Li J,Wu S,et al(2006).Integrated nr database in protein annotation system and its localization.Comput Eng,32(5):71-73,76(in Chinese with English abstract)[邓泱泱,荔建琦,吴松锋等(2006).nr数据库分析及其本地化.计算机工程,32(5):71-73,76]
Eveland AL,Satoh-Nagasawa N,Goldshmidt A,et al(2010).Digital gene expression signatures for maize development.Plant Physiol,154(3):1024-1039
Fan J(2018).Transcriptomic analysis of the protocorms in Dendrobium officinale Kimura et Migo(dissertation).Chengdu:Southwest Jiaotong University(in Chinese with English abstract)[范静(2018).铁皮石斛原球茎转录组测序分析(学位论文).成都:西南交通大学]
Jiang N,Zhang L,Li C,et al(2014).Progress in the study of Myb transcription factors which influence the color of grape skin.Chin Agr Sci Bull,30(13):80-86(in Chinese with English abstract)[江楠,张雷,李春霞等(2014).影响葡萄果皮颜色的MYB类转录因子的研究进展.中国农学通报,30(13):80-86]
Jiao X,Luo Y,Zhao W,et al(2018).Analysis of grape MYBgene family and its regulation on sex differentiation of flower organs.J Shanxi Agr Univ-Nat Sci,38(5):23-32,39(in Chinese with English abstract)[焦晓博,罗尧幸,赵伟等(2018).葡萄MYB基因家族及其对花器官性别分化调控的分析.山西农业大学学报(自然科学版),38(5):23-32,39]
Kanehisa M,Goto S,Kawashima S,et al(2004).The KEGGresource for deciphering the genome.Nucleic Acids Res,32:D277-D280
Kozarewa I,Ning Z,Quail MA,et al(2009).Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of(G+C)-biased genomes.Nat Methods,6(4):291-295
Lan DL,Xiong XR,Wei YL,et al(2014).RNA-Seq analysis of yak ovary:improving yak gene structure information and mining reproduction-related genes.Sci China Life Sci,44(3):307-317(in Chinese with English abstract)[兰道亮,熊显荣,位艳丽等(2014).基于RNA-Seq高通量测序技术的牦牛卵巢转录组研究:进一步完善牦牛基因结构及挖掘与繁殖相关新转录本.中国科学:生命科学,44(3):307-317]
Li C,Wang Y,Huang X,et al(2013).De novo assembly and characterization of fruit transcriptome in Litchi chinensis Sonn and analysis of differentially regulated genes in fruit in response to shading.BMC Genomics,14:552
Li X,Wang SL(2017).Research advances of transcriptomics in horticulture plants pigments metabolism.Biotechnol Bull,33(7):7-14(in Chinese with English abstract)[李霞,王顺利(2017).高通量转录组在园艺植物色素代谢中的研究进展.生物技术通报,33(7):7-14]
Lodhi MA,Reisch BI(1995).Nuclear DNA content of Vitis species,cultivars,and other genera of the Vitaceae.Theor Appl Genet,90(1):11-16
Lu T,Lu G,Fan D,et al(2010).Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq.Genome Res,20:1238-1249
Mu CQ,Zhang RJ,Qu CL,et al(2016).Identification of novel genes and optimization of annotated genes in foxtail millet by RNA-Seq technology.Plant Physiol J,52(7):1066-1072(in Chinese with English abstract)[穆彩琴,张瑞娟,屈聪玲等(2016).基于RNA-Seq技术的谷子新转录本发掘及基因结构优化.植物生理学报,52(7):1066-1072]
Ni W,Gao FF,Yang HF,et al(2017).Identification of novel transcripts and optimization of annotated genes in apple(Malus domestica)by RNA-Seq.Plant Physiol J,53(8):1532-1538(in Chinese with English abstract)[倪伟,高付凤,杨恒峰等(2017).基于RNA-Seq技术苹果基因结构优化与新转录本预测.植物生理学报,53(8):1532-1538]
Pareek CS,Smoczynski R,Tretyn A(2011).Sequencing technologies and genome sequencing.J Appl Genet,52(4):413-435
Qi YX,Liu YB,Rong WH(2011).RNA-Seq and its applications:a new technology for transcriptomics.Hereditas Beijing,33(11):1191-1202(in Chinese with English abstract)[祁云霞,刘永斌,荣威恒(2011).转录组研究新技术:RNA-Seq及其应用.遗传,33(11):1191-1202]
Sangwan RS,Tripathi S,Singh J,et al(2013).De novo sequencing and assembly of Centella asiatica leaf transcriptome for mapping of structural,functional and regulatory genes with special reference to secondary metabolism.Gene,525:58-76
Shi W(2012).Research on the transcriptome of Prunus mume through RNA-Seq(dissertation).Beijing:Beijing Forestry University(in Chinese with English abstract)[石文芳(2012).基于RNA-seq测序的梅花转录组分析(学位论文).北京:北京林业大学]
Tang HG,Huang YH,Lu HB,et al(2016).The application persspective of transcriptome sequencing on discovering the genes and variety breeding of bioenergy grass.Acta Agrestia Sin,24(4):731-737(in Chinese with English abstract)[汤海港,黄艳华,路海博等(2016).转录组测序技术及其在能源草基因挖掘和品种选育中的应用前景分析.草地学报,24(4):731-737]
Tariq MA,Kim HJ,Jejelowo O,et al(2011).Whole-transcriptome RNAseq analysis from minute amount of total RNA.Nucleic Acids Res,39(18):e120
Tatusov RL,Galperin MY,Natale DA,et al(2000).The COGdatabase:a tool for genome-scale analysis of protein functions and evolution.Nucleic Acids Res,28(1):33-36
The French-Italian Public Consortium for Grapevine Genome Characterization(2007).The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.Nature,449(7161):463-467
Tian X,Luo L,Zhong Y,et al(2017).Nutrients characteristics of wine-growing region at east piedmont of Helan Mountains in Xixia District,Yinchuan.North Hortic,(3):173-178(in Chinese with English abstract)[田欣,罗玲玲,钟艳霞等(2017).银川市西夏区贺兰山东麓葡萄种植区土壤养分特征.北方园艺,(3):173-178]
Trapnell C,Williams BA,Pertea G,et al(2010).Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.Nat Biotechnol,28(5):511-515
Wang Y,Nie F,Lin S(2015).The latest research progress in high-throughput sequencing of fruit tree.Genom Appl Biol,34(9):2034-2043(in Chinese with English abstract)[王云生,聂飞,林顺权(2015).果树高通量测序的最新研究进展.基因组学与应用生物学,34(9):2034-2043]
Wang Z,Gerstein M,Snyder M(2009).RNA-Seq:a revolutionary tool for transcriptomics.Nature Rev Genet,10:57-63
Yang K(2015).Analysis of genes differentially expressed in watermelon rind color based on RNA-seq(dissertation).Nanchang:Jiangxi Agricultural University(in Chinese with English abstract)[杨侃侃(2015).基于RNA-seq技术对西瓜果皮色泽差异表达基因的分析(学位论文).南昌:江西农业大学]
Zhao W,Luo Y,Jiao X,et al(2018).Expression and bioinformatics analysis of four MADS-box genes related to flower development in grape.Mol Plant Breed,16(20):6572-6582(in Chinese with English abstract)[赵伟,罗尧幸,焦晓博等(2018).葡萄中4个花发育相关MADS-box基因的表达与生物信息分析.分子植物育种,16(20):6572-6582]
Zhou X,Zheng J,Han K,et al(2018).Effect of fertilization on the growth of Hutai 8 grape.J Shanxi Agr Sci,46(6):942-948(in Chinese with English abstract)[周璇,郑精杰,韩凯等(2018).施肥对户太8号葡萄生长的影响.山西农业科学,46(6):942-948]
Ashburner M,Ball CA,Blake JA,et al(2000).Gene ontology:tool for the unification of biology.Nat Genet,25:25-29
Cheng X(2015).Biological characteristics and transcriptome analysis of selenium enriched Chlamydomonas reinhardtii in Rhine(dissertation).Shenzhen,Guangdong:Shenzhen University(in Chinese with English abstract)[程雪薇(2015).莱茵衣藻富硒生物学特性及其转录组学研究(学位论文).广州深圳:深圳大学]
Darwish O,Shahan R,Liu Z,et al(2015).Re-annotation of the woodland strawberry(Fragaria vesca)genome.BMCGenomics,16:29
Dassanayake M,Haas JS,Bohnert HJ,et al(2010).Shedding light on an extremophile lifestyle through transcriptomics.New Phytol,183(3):764-775
Deng Y,Li J,Wu S,et al(2006).Integrated nr database in protein annotation system and its localization.Comput Eng,32(5):71-73,76(in Chinese with English abstract)[邓泱泱,荔建琦,吴松锋等(2006).nr数据库分析及其本地化.计算机工程,32(5):71-73,76]
Eveland AL,Satoh-Nagasawa N,Goldshmidt A,et al(2010).Digital gene expression signatures for maize development.Plant Physiol,154(3):1024-1039
Fan J(2018).Transcriptomic analysis of the protocorms in Dendrobium officinale Kimura et Migo(dissertation).Chengdu:Southwest Jiaotong University(in Chinese with English abstract)[范静(2018).铁皮石斛原球茎转录组测序分析(学位论文).成都:西南交通大学]
Jiang N,Zhang L,Li C,et al(2014).Progress in the study of Myb transcription factors which influence the color of grape skin.Chin Agr Sci Bull,30(13):80-86(in Chinese with English abstract)[江楠,张雷,李春霞等(2014).影响葡萄果皮颜色的MYB类转录因子的研究进展.中国农学通报,30(13):80-86]
Jiao X,Luo Y,Zhao W,et al(2018).Analysis of grape MYBgene family and its regulation on sex differentiation of flower organs.J Shanxi Agr Univ-Nat Sci,38(5):23-32,39(in Chinese with English abstract)[焦晓博,罗尧幸,赵伟等(2018).葡萄MYB基因家族及其对花器官性别分化调控的分析.山西农业大学学报(自然科学版),38(5):23-32,39]
Kanehisa M,Goto S,Kawashima S,et al(2004).The KEGGresource for deciphering the genome.Nucleic Acids Res,32:D277-D280
Kozarewa I,Ning Z,Quail MA,et al(2009).Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of(G+C)-biased genomes.Nat Methods,6(4):291-295
Lan DL,Xiong XR,Wei YL,et al(2014).RNA-Seq analysis of yak ovary:improving yak gene structure information and mining reproduction-related genes.Sci China Life Sci,44(3):307-317(in Chinese with English abstract)[兰道亮,熊显荣,位艳丽等(2014).基于RNA-Seq高通量测序技术的牦牛卵巢转录组研究:进一步完善牦牛基因结构及挖掘与繁殖相关新转录本.中国科学:生命科学,44(3):307-317]
Li C,Wang Y,Huang X,et al(2013).De novo assembly and characterization of fruit transcriptome in Litchi chinensis Sonn and analysis of differentially regulated genes in fruit in response to shading.BMC Genomics,14:552
Li X,Wang SL(2017).Research advances of transcriptomics in horticulture plants pigments metabolism.Biotechnol Bull,33(7):7-14(in Chinese with English abstract)[李霞,王顺利(2017).高通量转录组在园艺植物色素代谢中的研究进展.生物技术通报,33(7):7-14]
Lodhi MA,Reisch BI(1995).Nuclear DNA content of Vitis species,cultivars,and other genera of the Vitaceae.Theor Appl Genet,90(1):11-16
Lu T,Lu G,Fan D,et al(2010).Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq.Genome Res,20:1238-1249
Mu CQ,Zhang RJ,Qu CL,et al(2016).Identification of novel genes and optimization of annotated genes in foxtail millet by RNA-Seq technology.Plant Physiol J,52(7):1066-1072(in Chinese with English abstract)[穆彩琴,张瑞娟,屈聪玲等(2016).基于RNA-Seq技术的谷子新转录本发掘及基因结构优化.植物生理学报,52(7):1066-1072]
Ni W,Gao FF,Yang HF,et al(2017).Identification of novel transcripts and optimization of annotated genes in apple(Malus domestica)by RNA-Seq.Plant Physiol J,53(8):1532-1538(in Chinese with English abstract)[倪伟,高付凤,杨恒峰等(2017).基于RNA-Seq技术苹果基因结构优化与新转录本预测.植物生理学报,53(8):1532-1538]
Pareek CS,Smoczynski R,Tretyn A(2011).Sequencing technologies and genome sequencing.J Appl Genet,52(4):413-435
Qi YX,Liu YB,Rong WH(2011).RNA-Seq and its applications:a new technology for transcriptomics.Hereditas Beijing,33(11):1191-1202(in Chinese with English abstract)[祁云霞,刘永斌,荣威恒(2011).转录组研究新技术:RNA-Seq及其应用.遗传,33(11):1191-1202]
Sangwan RS,Tripathi S,Singh J,et al(2013).De novo sequencing and assembly of Centella asiatica leaf transcriptome for mapping of structural,functional and regulatory genes with special reference to secondary metabolism.Gene,525:58-76
Shi W(2012).Research on the transcriptome of Prunus mume through RNA-Seq(dissertation).Beijing:Beijing Forestry University(in Chinese with English abstract)[石文芳(2012).基于RNA-seq测序的梅花转录组分析(学位论文).北京:北京林业大学]
Tang HG,Huang YH,Lu HB,et al(2016).The application persspective of transcriptome sequencing on discovering the genes and variety breeding of bioenergy grass.Acta Agrestia Sin,24(4):731-737(in Chinese with English abstract)[汤海港,黄艳华,路海博等(2016).转录组测序技术及其在能源草基因挖掘和品种选育中的应用前景分析.草地学报,24(4):731-737]
Tariq MA,Kim HJ,Jejelowo O,et al(2011).Whole-transcriptome RNAseq analysis from minute amount of total RNA.Nucleic Acids Res,39(18):e120
Tatusov RL,Galperin MY,Natale DA,et al(2000).The COGdatabase:a tool for genome-scale analysis of protein functions and evolution.Nucleic Acids Res,28(1):33-36
The French-Italian Public Consortium for Grapevine Genome Characterization(2007).The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.Nature,449(7161):463-467
Tian X,Luo L,Zhong Y,et al(2017).Nutrients characteristics of wine-growing region at east piedmont of Helan Mountains in Xixia District,Yinchuan.North Hortic,(3):173-178(in Chinese with English abstract)[田欣,罗玲玲,钟艳霞等(2017).银川市西夏区贺兰山东麓葡萄种植区土壤养分特征.北方园艺,(3):173-178]
Trapnell C,Williams BA,Pertea G,et al(2010).Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.Nat Biotechnol,28(5):511-515
Wang Y,Nie F,Lin S(2015).The latest research progress in high-throughput sequencing of fruit tree.Genom Appl Biol,34(9):2034-2043(in Chinese with English abstract)[王云生,聂飞,林顺权(2015).果树高通量测序的最新研究进展.基因组学与应用生物学,34(9):2034-2043]
Wang Z,Gerstein M,Snyder M(2009).RNA-Seq:a revolutionary tool for transcriptomics.Nature Rev Genet,10:57-63
Yang K(2015).Analysis of genes differentially expressed in watermelon rind color based on RNA-seq(dissertation).Nanchang:Jiangxi Agricultural University(in Chinese with English abstract)[杨侃侃(2015).基于RNA-seq技术对西瓜果皮色泽差异表达基因的分析(学位论文).南昌:江西农业大学]
Zhao W,Luo Y,Jiao X,et al(2018).Expression and bioinformatics analysis of four MADS-box genes related to flower development in grape.Mol Plant Breed,16(20):6572-6582(in Chinese with English abstract)[赵伟,罗尧幸,焦晓博等(2018).葡萄中4个花发育相关MADS-box基因的表达与生物信息分析.分子植物育种,16(20):6572-6582]
Zhou X,Zheng J,Han K,et al(2018).Effect of fertilization on the growth of Hutai 8 grape.J Shanxi Agr Sci,46(6):942-948(in Chinese with English abstract)[周璇,郑精杰,韩凯等(2018).施肥对户太8号葡萄生长的影响.山西农业科学,46(6):942-948]