梁山慈竹高通量转录组测序及差异表达基因分析

doi:10.7668/hbnxb.2016.03.010

华北农学报 ›› 2016, Vol. 31 ›› Issue (3): 65-71. doi: 10.7668/hbnxb.2016.03.010

所属专题： 生物技术；

梁山慈竹高通量转录组测序及差异表达基因分析

王身昌^1,2, 胡尚连^1,2, 曹颖^1,2, 徐刚^1,2

1. 西南科技大学植物细胞工程实验室, 四川绵阳 621010;
2. 四川省生物质资源利用与改性工程技术研究中心, 四川绵阳 621010

收稿日期:2016-03-10 出版日期:2016-06-28
通讯作者: 胡尚连(1966-),女,河北秦皇岛人,教授,博士,主要从事植物生理与生物技术研究。
作者简介:王身昌(1989-),男,山东菏泽人,在读硕士,主要从事植物遗传与品种改良研究。
基金资助:
国家自然科学基金青年基金项目(31400257;31400333);四川省"十三五"育种公关资助项目;四川省生物质资源利用与改性工程技术研究中心基金项目(12zxsk07;13zxsk01);西南科技大学研究生创新基金项目(15ycx092)

High-throughput RNA-seq and Analysis on Differential Expressed Gene from Dendrocalamus farinosus

WANG Shenchang^1,2, HU Shanglian^1,2, CAO Ying^1,2, XU Gang^1,2

1. Lab of Plant Cell Engineering, Southwest University of Science and Technology, Mianyang 621010, China;
2. Engineering Research Center for Biomass Resource Utilization and Modification of Sichuan Province, Mianyang 621010, China

Received:2016-03-10 Published:2016-06-28

摘要/Abstract

摘要： 分析梁山慈竹及其体细胞突变体的转录组,挖掘功能基因并对其差异表达基因进行筛选和分析,为梁山慈竹遗传改良提供理论依据。利用RNA-Seq技术进行转录组测序,对测序结果进行denovo拼接和功能注释;并对差异表达基因进行筛选及COG、GO、KEGG数据库中进行比对注释,此外,基于Swiss-Prot功能注释结果,分析纤维素和木质素相关功能基因的表达量差异。测序结果表明,共获得86575631条reads,denovo组装得到84741条unigenes,共有49829条被Nr、COG、GO、KEGG、Swiss-Prot注释。从梁山慈竹实生植株(对照)和体细胞突变体No.30这2个测序样本中,筛选出3572条差异表达unigenes,757条差异表达unigenes在COG分类体系中具有详细的蛋白功能释义,2213条差异表达unigenes在GO数据库具有功能定义,385条unigenes被注释到94条KEGGPathways中。纤维素合成相关纤维素合酶、过氧化物酶、泛素连接酶和热休克蛋白在梁山慈竹体细胞突变体No.30中表达量升高,木质素合成相关MYB4、4-香豆酸CoA连接酶、肉桂醇脱氢酶、肉桂酰-CoA还原酶和漆酶在突变体中表达量降低。提供了全面的梁山慈竹转录组信息,获得了一批在梁山慈竹纤维素和木质素生物合成过程中有重要功能的基因序列。

关键词: 梁山慈竹, 体细胞突变体, 转录组, 差异表达基因

Abstract: The transcriptome from the shoots of Dendrocalamus farinosus and its somatic mutant was sequenced using the RNA-Seq technology to elucidate its functional gene and analyze its differential expressed gene,providing a theoretical basis for its genetic improvement.The sequencing data was assembled by de novo assembly and the differential expressed gene screened was annotated in COG,GO and KEGG database.In addition,the differential expression of gene related to cellulose and lignin biosynthesis was analyzed,basing on the Swiss-Prot function annotation.The sequencing results showed that a total of 86 575 631 reads were produced and assembled into a total of 84 741 unigenes by de novo,among which 49 829 were annotated in Nonredundant protein,Cluster of Orthologous Groups of proteins,Gene Ontology,Kyoto Encyclopedia of Genes and Genomes and Swiss-Prot database.Besides,a total of 3 572 differential expressed unigenes were identified from the plant of seeds (CK) and the somatic mutant No.30.Of these differential expressed genes,757 unigenes had a detailed protein functions in the COG classification system,2 213 unigenes had the function definition in the GO database,385 unigenes were annotated to 94 KEGG Pathways.The expression of genes encoding CesA,Prx,Ubiquitin-conjugating enzyme and Heat shock proteins increased in somatic mutant No.30,while,the expression of genes encoding MYB4,4CL,CAD,CCR and LAC decreased.Our data provide the most comprehensive transcriptomic resource for Dendrocalamus farinosus and the transcript sequences with important function related to cellulose and lignin biosynthesis were found,which provide the most precious information resources for the further research on bamboo.

Key words: Dendrocalamus farinosus, Somatic mutant, Transcriptome, Differential expressed gene

中图分类号:

王身昌, 胡尚连, 曹颖, 徐刚. 梁山慈竹高通量转录组测序及差异表达基因分析[J]. 华北农学报, 2016, 31(3): 65-71. doi: 10.7668/hbnxb.2016.03.010.

WANG Shenchang, HU Shanglian, CAO Ying, XU Gang. High-throughput RNA-seq and Analysis on Differential Expressed Gene from Dendrocalamus farinosus[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2016, 31(3): 65-71. doi: 10.7668/hbnxb.2016.03.010.

http://www.hbnxb.net/CN/Y2016/V31/I3/65

参考文献

[1] 刘红亮,郑丽明,刘青青,等.非模式生物转录组研究[J].遗传,2013,35(8):955-970.
[2] Li X,Sun H,Pei J,et al.De novo sequencing and comparative analysis of the blueberry transcriptome to discover putative genes related to antioxidants[J].Gene,2012,511(1):54-61.
[3] Liu M,Qiao G,Jiang J,et al.Transcriptome sequencing and de novo analysis for Ma bamboo (Dendrocalamus latiflorus Munro) using the Illumina platform[J].PLoS One,2012,7(10):e46766.
[4] 熊壮,扶志宏,鄢武先,等.四川梁山慈竹纸浆林生产现状及培育技术初步研究[J].世界竹藤通讯,2012,10(5):7-11.
[5] 李永全,张安刚,龚兆全,等.梁山慈竹特性及育苗技术[J].四川林勘设计,2012(2):34-37.
[6] 胡尚连,蒋瑶,陈其兵,等.四川2种丛生竹理化特性及纤维形态研究[J].植物研究,2010,30(6):708-712.
[7] Yang X,Tian G L,Shang L L,et al.Variation in the cell wall mechanical properties of Dendrocalamus farinosus bamboo by nanoindentation[J].BioResources,2014,9(2):2289-2298.
[8] Hu S L,Jy Z,Cao Y,et al. In vitro callus induction and plant regeneration from mature seed embryo and young shoots in a giant sympodial bamboo,Dendrocalamus farinosus(Keng et Keng f.)Chia et HL Fung[J].African Journal of Biotechnology,2011,10(16):3120-3125.
[9] 郭鹏飞.梁山慈竹体细胞无性系再生植株变异研究[D].绵阳:西南科技大学,2013.
[10] Grabherr M G,Haas B J,Yassour M,et al.Full-length transcriptome assembly from RNA-Seq data without a reference genome[J].Nature Biotechnology,2011,29(7):644-652.
[11] Mortazavi A,Williams B A,Mccue K,et al.Mapping and quantifying mammalian transcriptomes by RNA-Seq[J].Nature Methods,2008,5(7):621-628.
[12] Kaul S,Koo H L,Jenkins J,et al.Analysis of the genome sequence of the flowering plant Arabidopsis thaliana [J].Nature,2000,408(6814):796-815.
[13] Goff S A,Ricke D,Lan T H,et al.A draft sequence of the rice genome ( Oryza sativa L.ssp.japonica)[ J].Science,2002,296(5565):92-100.
[14] Peng Z,Lu Y,Li L,et al.The draft genome of the fast-growing non-timber forest species moso bamboo ( Phyllostachys heterocycla )[ J].Nature Genetics,2013,45(4):456-461,461e1-2.
[15] Fullwood M J,Wei C L,Liu E T,et al.Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses[J].Genome Research,2009,19(4):521-532.
[16] Li C F,Wang X Q,Lu W X,et al.A poplar R2R3-MYB transcription factor,PtrMYB152,is involved in regulation of lignin biosynthesis during secondary cell wall formation[J].Plant Cell,Tissue and Organ Culture,2014,119(3):553-563.
[17] Patzlaff A,Mcinnis S,Courtenay A,et al.Characterisation of a pine MYB that regulates lignification[J].The Plant Journal,2003,36(6):743-754.
[18] Ma Q H,Wang C,Zhu H H. TaMYB4 cloned from wheat regulates lignin biosynthesis through negatively controlling the transcripts of both cinnamyl alcohol dehydrogenase and cinnamoyl-CoA reductase genes[J].Biochimie,2011,93(7):1179-1186.
[19] Li S F,Milliken O N,Pham H,et al.The Arabidopsis MYB5 transcription factor regulates mucilage synthesis,seed coat development,and trichome morphogenesis[J].The Plant Cell,2009,21(1):72-89.
[20] Taylor N G,Laurie S,Turner S R.Multiple cellulose synthase catalytic subunits are required for cellulose synthesis in Arabidopsis [J].The Plant Cell,2000,12(12):2529-2540.
[21] Hovav R,Udall J A,Chaudhary B,et al.The evolution of spinnable cotton fiber entailed prolonged development and a novel metabolism[J].PLOS Genetics,2008,4(2):e25.
[22] Sengar A S,Thind K S,Kumar B,et al. In vitro selection at cellular level for red rot resistance in sugarcane ( Saccharum sp.)[J].Plant Growth Regulation,2009,58(2):201-209.
[23] 梁芳,蒋素华,王洁琼,等.濒危植物太行菊组织培养及快繁技术研究[J].中国农学通报,2015,31(16):115-120.
[24] 王鹏姬.荞麦愈伤组织培养及其黄酮合成研究[D].杨凌:西北农林科技大学,2013.
[25] Sheidai M,Aminpoor H,Noormohammadi Z,et al.RAPD analysis of somaclonal variation in banana ( Musaacuminate L.) cultivar Valery[J].Acta Biol Szeged,2008,52:307-311.
[26] Carsono N,Yoshida T.Variation in spikelet-related traits of rice plants regenerated from mature seed-derived callus culture[J].Plant Production Science,2007,10(1):86-90.
[27] Mohanty S,Panda M K,Subudhi E,et al.Plant regeneration from callus culture of Curcuma aromatica and in vitro detection of somaclonal variation through cytophotometric analysis[J].Biologia Plantarum,2008,52(4):783-786.

选择文件类型/文献管理软件名称

选择包含的内容

梁山慈竹高通量转录组测序及差异表达基因分析

High-throughput RNA-seq and Analysis on Differential Expressed Gene from Dendrocalamus farinosus

PDF

可视化

被引次数

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics

本文评价

[1]	林静, 林建新, 张扬, 卢和顶, 陈山虎, 廖长见. 利用转录组解析鲜食玉米闽甜6855的耐寒机制[J]. 华北农学报, 2022, 37(5): 1-8.
[2]	王燕宁, 黄涛, 吴光亮, 黄诗颖, 钟奇, 王鹏, 杨朦朦, 李才敬, 程琴, 贺浩华, 金伟, 郭凌, 边建民. 水稻芽期响应镉胁迫的转录组分析[J]. 华北农学报, 2022, 37(5): 25-35.
[3]	梁鹏, 张稳, 冯登侦, 强浩, 荣轩, 孟科. 基于转录组学筛选绵羊肉质性状相关候选基因[J]. 华北农学报, 2022, 37(4): 220-231.
[4]	安清明, 王星, 吴震洋, 孟金柱, 赵园园, 宋兴超. 基于转录组挖掘不同性别贵州白山羊肌肉生长发育的关键基因及PI3K/ATK信号通路分析[J]. 华北农学报, 2022, 37(3): 213-222.
[5]	张敬敬, 李冰, 史宇凡, 高秀瑞, 潘秀清, 宋雪, 武彦荣. 不同硬度西瓜果皮的转录组测序及相关基因表达分析[J]. 华北农学报, 2022, 37(3): 44-52.
[6]	张宗祥, 黄峥嵘, 吴雪凡, 刘楠楠, 李笑笑, 董召荣, 宋贺. 土壤酸化对玉米产量、氮代谢及相关基因表达的影响[J]. 华北农学报, 2022, 37(3): 94-103.
[7]	史建磊, 熊自立, 苏世闻, 王克磊, 宰文珊. 基于RNA-seq的番茄青枯病响应基因鉴定与表达分析[J]. 华北农学报, 2022, 37(2): 171-182.
[8]	韩晓勇, 蒋璐, 殷剑美, 金林, 张培通. 山药品种苏蓣8号抗炭疽病基因的转录组测序与表达分析[J]. 华北农学报, 2022, 37(2): 211-222.
[9]	武悦, 陈阳, 王星哲, 单飞彪, 张勇, 孙鸿举. 扁茎黄芪转录组测序及生物信息学分析[J]. 华北农学报, 2022, 37(1): 42-49.
[10]	赵雅杰, 赵轩微, 田振东, 胡树平, 包海柱. 油用向日葵脱落酸代谢及差异基因表达对水分亏缺的响应[J]. 华北农学报, 2021, 36(6): 54-62.
[11]	国钰环, YAMAMOTO Naoki, 彭正松, 廖明莉, 魏淑红, 吴一超, 杨在君. 基于转录组数据的三雌蕊小麦中SNP/InDel位点的挖掘[J]. 华北农学报, 2021, 36(5): 35-42.
[12]	孟凡来, 白磊, 郭华春, 赵大伟, 余兴华, 王应梅, 李玉祥, 滕娟. 紫甘薯叶片响应UV-B辐射增强的转录组分析[J]. 华北农学报, 2021, 36(5): 135-142.
[13]	梅瑜, 李向荣, 蔡时可, 顾艳, 王继华. 药食同源植物甘葛藤的全长转录组分析[J]. 华北农学报, 2021, 36(5): 10-17.
[14]	代惠洁, 程琳, 曹慧, 竺晓平, 赵静. 烟粉虱取食ToCV侵染番茄对其解毒酶和保护酶基因表达的影响[J]. 华北农学报, 2021, 36(4): 172-183.
[15]	钱玉源, 刘祎, 张曦, 王燕, 王广恩, 崔淑芳, 李俊兰. 棉花种子质量突变体ims-15及其近等基因系种子发育期转录组分析[J]. 华北农学报, 2021, 36(3): 50-59.

模态框（Modal）标题

选择文件类型/文献管理软件名称

选择包含的内容

梁山慈竹高通量转录组测序及差异表达基因分析

High-throughput RNA-seq and Analysis on Differential Expressed Gene from Dendrocalamus farinosus

PDF

可视化

被引次数

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics

本文评价