青梗花椰菜和白梗花椰菜转录组分析
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摘要
为探讨花椰菜花梗颜色的遗传基础,采用高通量测序技术(Illumina Hi Seq 4000)对青梗和白梗花椰菜进行转录组测序,共获得52 253 822个序列读取片段(reads),对测序的结果从头组装获得66 450个单基因(Unigene),N50为1 285 bp,平均长度为717.40 bp。转录物注释结果显示,45 390个基因有同源比对信息;21 060个基因无匹配序列信息,可能为花椰菜特异的基因序列。对所得差异基因(DEGS)进行不同数据库注释,GO注释到2 540个DEGS,分为细胞组分、分子功能及生物学过程3大类54个功能组;COG注释到的753个Unigene功能系统分为24类;以KEGG数据库为参考,将946个DEGS定位到119个代谢途径分支,注释到6个差异基因与类胡萝卜合成途径有关,9个DEGS与类黄酮生物合成途径有关,1个DEGS与叶绿素代谢相关,且与花椰菜的花梗颜色形成密切相关。16个差异基因通过qRT-PCR验证,结果与RNA-Seq测序结果一致。本研究结果进一步揭示花椰菜花梗颜色的形成机理,为花椰菜品种遗传改良奠定了一定的理论基础。
In order to explore the genetic basis for the colour of cauliflower curd stalk formation,the green stalk and the white stalk were sequenced by Illumina Hi Seq 4000 platform,a total of 52 253 822 readings were generated. And 66 450 unigenes with 1 285 bp length of N50,were obtained by denovo assembly method,the average unigenes length was717. 40 bp. Annotation analysis of unigene indicated that 45 390 unigenes had homologes in public protein database;However,21 060 sequences had no hits and might be specific in Brassica oleracea L. var. botrytis L. specific. All DEGS were annotated by different databases. By GO database,the 2 540 DEGS were divided into 3 categories containing 54 function groups; by COG databases,753 DEGS were grouped into 24 functional categories; By KEGG database,946 DEGS were divided into 119 metabolism pathways,among which 6 DEGS which were involved in Carotenoid biosynthesis pathway,9 DEGS may take part in Flavonoid biosynthesis pathway and 1 DEGS may take part in chlorophyll metabolism pathway and vesponsible for the colour formation. 16 DEGS were verified by qRT-PCR,and showed consistent with the results of RNA-Seq sequencing. These findings provide a scientific basis for further revealing the mechanism of the colour in cauliflower stalk and lay a theoretical foundation for the genetic improvement on cauliflower.
In order to explore the genetic basis for the colour of cauliflower curd stalk formation,the green stalk and the white stalk were sequenced by Illumina Hi Seq 4000 platform,a total of 52 253 822 readings were generated. And 66 450 unigenes with 1 285 bp length of N50,were obtained by denovo assembly method,the average unigenes length was717. 40 bp. Annotation analysis of unigene indicated that 45 390 unigenes had homologes in public protein database;However,21 060 sequences had no hits and might be specific in Brassica oleracea L. var. botrytis L. specific. All DEGS were annotated by different databases. By GO database,the 2 540 DEGS were divided into 3 categories containing 54 function groups; by COG databases,753 DEGS were grouped into 24 functional categories; By KEGG database,946 DEGS were divided into 119 metabolism pathways,among which 6 DEGS which were involved in Carotenoid biosynthesis pathway,9 DEGS may take part in Flavonoid biosynthesis pathway and 1 DEGS may take part in chlorophyll metabolism pathway and vesponsible for the colour formation. 16 DEGS were verified by qRT-PCR,and showed consistent with the results of RNA-Seq sequencing. These findings provide a scientific basis for further revealing the mechanism of the colour in cauliflower stalk and lay a theoretical foundation for the genetic improvement on cauliflower.
引文
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[36]罗平.玫瑰类黄酮合成相关基因的克隆和功能解析[D].武汉:华中农业大学,2016
[37]王世界.茄子花青素生物合成关键MYB转录因子的筛选及克隆[D].泰安:山东农业大学,2016
[38]彭刚.柑橘果实转色的叶绿素和类胡萝卜素代谢基础[D].杨凌:西北农林大学,2013
[39]董立花.金心吊兰的叶绿素生物合成以及光胁迫的耐受性[D].雅安:四川农业大学,2015
[2]林珲,朱海生,陈敏氡,温庆放.花椰菜游离小孢子培养技术研究进展[J].中国农学通报,2014,30(13):71-75
[3]丁云花,何洪巨,赵学志,王文琪,宋曙辉.不同类型花椰菜主要营养品质分析[J].中国蔬菜,2016(4):58-63
[4]顾宏辉,金昌林,赵振卿,盛小光,虞慧芳,王建升.我国松花菜产业现状及前景分析[J].中国蔬菜,2012(23):1-5
[5]徐丽红,陈联和,杨刚,曹淑瑛.高山松花菜营养品质分析与安全性评价[J].浙江农业科学,2014(6):897-902
[6]Li R,Fan W,Tian G,Zhu H,He L,Cai J,Huang Q,Cai Q,Li B,Bai Y.The sequence and de novo assembly of the giant panda genome[J].Nature,2010,463:311-317
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[8]Sebastien M,Antonio O,Haissam J,Thierry C.Current impact and future directions of high throughput sequencing[J].Virus Research,2014,188:90-96
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[10]江香梅,伍艳芳,肖复明,熊振宇,徐海宁.樟树种化学类型叶片转录组分析[J].遗传,2014,36(1):58-68
[11]刘永明,张玲,邱涛,赵卓凡,曹墨菊.高通量转录组测序技术在植物雄性不育研究中的应用[J].遗传,2016,38(8):677-687
[12]李满堂,张仕林,邓鹏,侯喜林,王建军.洋葱转录组SSR信息分析及其多态性研究[J].园艺学报,2015,42(6):1103-1111
[13]潜宗伟,陈海丽,崔彦玲.菠菜转录组SSR位点分析及其分子标记的开发[J].农业生物技术学报,2016,24(11):1688-1697
[14]李荣华,王直亮,陈静芳,夏岩石,郭培国,张华.菜薹转录组中信息与可用性分析[J].园艺学报,2016,43(9):1816-1824
[15]王洋洋,单文琪,徐文龙,崔崇士,屈淑平.印度南瓜转录组SSR信息分析及其多态性研究[J].园艺学报,2016,43(3):578-586
[16]魏明明,陈钰辉,刘富中,张映,连勇.基于转录组测序的茄子SSR标记开发[J].植物遗传资源学报,2016,17(6):1082-1091
[17]庞强强,李植良,罗少波,陈日远,金庆敏,黎振兴,李德明,孙保娟,孙光闻.高温胁迫下茄子qRT-PCR内参基因筛选及稳定性分析[J].园艺学报,2017,44(3):475-486
[18]张蕊,邓文亚,杨柳,王亚萍,肖芳枝,禾健,卢坤.盐胁迫下甘蓝型油菜发芽期下胚轴和根长的全基因组关联分析[J].中国农业科学,2017,50(1):15-27
[19]张少平,邱珊莲,郑云云,张帅,吴松海,何炎森,郑开斌.紫色黄秋葵转录组功能基因测序及分析[J].核农学报,2017,31(4):643-653
[20]Tyvaert L,Franc'a S C,Debode J,H7¨fte M.The endophyte Verticillium Vt305 protects cauliflower against Verticilliumwilt[J].Journal of Applied Microbiology,2014,116(6):1563-1571
[21]Francesco G,Carla C,Angelo M,Cherubino L.Effects of salt stress imposed during twogrowth phases on cauliflower production and quality[J].Journal of the Science of Food and Agriculture,2016,97(5):1552-1560
[22]Annalisa L,Amalia C,Matteo Alessandro D N.Shelf life of readyto-cook cauliflower mixtures as affected bypackaging film mass transport properties[J].International Journal of Food Science and Technology,2012,47:1598-1604
[23]李文萍,林俊城,黄科.全球花椰菜生产与贸易现状分析[J].中国蔬菜,2014(9):5-10
[24]孙勃,许映君,袁高峰,郭容芳,魏佳,李振,刘娜,汪俏梅.花椰菜主要生物活性物质及其抗氧化能力分析[J].核农学报,2010,24(2):330-335
[25]丁云花,宋曙辉,赵学志,王文琪,何洪巨.不同类型花椰菜硫代葡萄糖苷组分与含量分析[J].中国蔬菜,2015(12):38-43
[26]张青丽,金川,秦二军,王玉,武美,李丽红,李慧,陈成彬,宋文芹,王春国.花椰菜中器官早期发育调控相关的miRNA(BramiR07)的克隆及功能研究[J].园艺学报,2016,43(1):141-150
[27]陶兴林,侯栋,朱惠霞,刘明霞,张金文,胡立敏.花椰菜温敏雄性不育系GS-19花药败育的细胞学及转录组分析[J].中国农业科学,2017,50(13):2538-2552
[28]赵风治,马钰婕,韦韬,江汉民,王春国,宋文芹,孙德岭,陈成彬.花椰菜查尔酮合酶基因的克隆及功能分析[J].南开大学学报(自然科学版),2016,49(4):61-66
[29]陈昊,蒋桂雄,龙洪旭,谭晓风.基于油桐种子个不同发育时期转录组的油脂合成代谢途径分析[J].遗传,2013,35(12):1403-1413
[30]王建升,赵振卿,盛小光,虞慧芳,顾宏辉.松花菜花球中主要生物活性成分及抗氧化能力分析[C]//中国园艺学会十字花科分会第十届学术研讨会论文集.天津:中国园艺学会十字花科蔬菜分会,2012:129-134
[31]陈日远.芥蓝菜薹色泽形成生理及其环境调控研究[D].上海:上海交通大学,2015
[32]杨立志.橙色大白菜球叶中类胡萝卜素合成相关基因的表达研究[D].杨凌:西北农林科技大学,2010
[33]宋成秀.黄肉苹果胡萝卜合成相关基因的表达研究[D].北京:中国农业科学院,2016:5-8
[34]李招娣.枸杞类胡萝卜素生物合成途径关键基因的克隆及功能表达[D].天津:天津大学,2015
[35]夏涛,高丽萍.类黄酮及茶儿茶素生物合成途径及其调控研究进展[J].中国农业科学,2009,42(8):2899-2908
[36]罗平.玫瑰类黄酮合成相关基因的克隆和功能解析[D].武汉:华中农业大学,2016
[37]王世界.茄子花青素生物合成关键MYB转录因子的筛选及克隆[D].泰安:山东农业大学,2016
[38]彭刚.柑橘果实转色的叶绿素和类胡萝卜素代谢基础[D].杨凌:西北农林大学,2013
[39]董立花.金心吊兰的叶绿素生物合成以及光胁迫的耐受性[D].雅安:四川农业大学,2015