2021年4月22日 星期四
花生异型雄蕊转录组分析
Analysis on transcriptome from heteromorphic stamens of Arachis hypogaea
2020年 第29卷 第5期 页码[21-29]
摘要

 以花生(Arachis hypogaea Linn.)品种‘Florunner’为研究对象,利用RNA-seq技术对花生异型雄蕊进行转录组测序;在此基础上,运用Nr、KOG、GO和KEGG数据库进行同源序列比对和基因功能分析。结果显示:花生异型雄蕊转录组测序共获得数据量约31.46 G,其中,clean reads所占比例均在96.0%以上;经过组装和拼接后得到197 193个contigs,片段总长度240 463 900 bp,最长片段为15 810 bp,非冗余unigenes片段的平均长度为1 219 bp,GC含量为39.1%,片段长度N50为1 966 bp;长度大于等于1 000 bp的unigenes占unigenes总数的43.4%,表明组装完整性较高,可用于注释分析。与Nr数据库的比对结果显示:共有129 223个unigenes注释到Nr数据库,占unigenes总数的65.5%;其中,1×10-100<E≤1×10-5的unigenes占54.2%,说明注释的unigenes序列与Nr数据库的同源序列具有高度相似性;共有106 900个unigenes注释到已探明的同源序列中,占注释unigenes总数的82.7%,且与大豆〔Glycine max (Linn.) Merr.〕和蒺藜苜蓿(Medicago truncatula Gaertn.)等同科种类的序列同源性较高。基因功能分析结果显示:共有133 387个unigenes注释到25个KOG功能类别上,且功能明确的unigenes均与配子体发育功能相关,其中,注释到信号转导机制功能的unigenes数量最多(17 135)。共有48 497个unigenes注释到生物过程、细胞组分和分子功能3大类55个亚类的GO功能类别上,其中,与核酸代谢过程、磷酸化、转录调节、核、核糖体、ATP结合、转录因子和钙离子结合相关的亚类中unigenes高度富集。共有30 428个unigenes注释到2 708个酶功能,映射了354个KEGG代谢通路,可分为遗传信息处理、细胞过程、生物系统、环境信息处理和代谢5大类32个亚类,其中,与代谢相关通路的unigenes数量最多(14 231)。综合分析结果表明:在花生异型雄蕊转录组中,多数unigenes的功能与雄蕊产生雄配子的功能有关,且部分基因可参与不同的代谢途径,对花生异型雄蕊的器官发生和花药形成具有重要作用。

Abstract

 Taking cultivar ‘Florunner’ of Arachis hypogaea Linn. as research object, transcriptome sequencing was conducted on its heteromorphic stamens by using RNA-seq technology; on the basis, homologous sequence alignment and gene function analysis were conducted by using Nr, KOG, GO and KEGG databases. The results show that about 31.46 G of data are obtained by transcriptome sequencing of heteromorphic stamens of A. hypogaea, in which, clean reads account for above 96.0%; 197 193 contigs are obtained after assembling and splicing, and the total length of fragments is 240 463 900 bp, the longest fragment is 15 810 bp; the average length of non-redundant unigenes fragment is 1 219 bp, the GC content is 39.1%, and the fragment length N50 is 1 966 bp; unigenes with a length greater than or equal to 1 000 bp account for 43.4% of total unigenes number, indicating that the assembly integrity is relatively high, and can be used for annotation analysis. The alignment result with Nr database shows that there are 129 223 unigenes annotated in Nr database, accounting for 65.5% of total unigenes number; in which, unigenes of 1×10-100<E≤1×10-5 account for 54.2%, indicating that annotated unigenes sequences have high similarity with homologous sequences in Nr database; there are 106 900 unigenes annotated in known homologous sequences, accounting for 82.7% of total annotated unigenes number, and have high sequence homology with plants of the same family, such as Glycine max (Linn.) Merr. and Medicago truncatula Gaertn., etc. The gene function analysis result shows that there are 133 387 unigenes annotated in 25 KOG functional categories, and functional unigenes are all associated with gametophyte development function, in which, number of unigenes annotated in signal transduction mechanism function is the largest (17 135). There are 48 497 unigenes annotated in 55 subcategories belonging to 3 GO functional categories including biological process, cellular component and molecular function, in which, unigenes are highly enriched in subcategories related to nucleic acid metabolic process, phosphorylation, transcriptional regulation, nucleus, ribosome, ATP binding, transcription factor and calcium binding. There are 30 428 unigenes annotated in 2 708 enzyme function mapping to 354 KEGG metabolic pathways, which can be divided into 32 subcategories belonging to 5 categories including genetic information processing, cellular process, organismal system, environmental information processing and metabolism, in which, number of unigenes in pathway related to metabolism is the largest (14 231). The comprehensive analysis result shows that in the transcriptome from heteromorphic stamens of A. hypogaea, function of most unigenes is associated with the function of stamens producing male gametes, and some genes are involved in different metabolic pathways, and play an important role in the organogenesis of heteromorphic stamens and formation of anther of A. hypogaea.

关键词花生; 异型雄蕊; 转录组; 同源性; 功能注释
Key wordsArachis hypogaea Linn.; heteromorphic stamen; transcriptome; homology; functional annotation
作者王海霞1a,1b,2, 王铭伦2, 丁雨龙1a,1c
所在单位1. 南京林业大学: a. 南方现代林业协同创新中心, b. 生物与环境学院, c. 竹类研究所, 江苏 南京 210037; 2. 青岛农业大学, 山东 青岛 266109
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基金项目国家花生产业技术体系建设项目(CARS-14); 江苏高校优势学科建设工程(PAPD)