生物技术通报 ›› 2021, Vol. 37 ›› Issue (8): 131-140.doi: 10.13560/j.cnki.biotech.bull.1985.2021-0191

• 研究报告 • 上一篇    下一篇

蒺藜苜蓿(Medicago truncatula)全长转录组测序及分析

尚骁尧(), 周玲芳, 尹芊芊, 晁跃辉()   

  1. 北京林业大学草业与草原学院,北京 100083
  • 收稿日期:2021-02-18 出版日期:2021-08-26 发布日期:2021-09-10
  • 作者简介:尚骁尧,女,硕士研究生,研究方向:草地植物生物技术;E-mail: sxy997987281@163.com
  • 基金资助:
    国家自然科学基金面上基金项目(31971770)

Sequencing and Analysis of Full-length Transcriptome from Medicago truncatula

SHANG Xiao-yao(), ZHOU Ling-fang, YIN Qian-qian, CHAO Yue-hui()   

  1. School of Grassland Science,Beijing Forestry University,Beijing 100083
  • Received:2021-02-18 Published:2021-08-26 Online:2021-09-10

摘要:

为了深入分析和探索豆科模式植物蒺藜苜蓿的mRNA完整结构,使用单分子长读数测序技术(single-molecule long-read sequencing technology,SMRT)对蒺藜苜蓿进行全长转录组测序及分析。共获得7 728 183个subread和509 014条全长非嵌合序列(full-length non-chimeric read,FLNC),通过比对分析发现,94.36%的序列与93.01%的序列分别与蒺藜苜蓿R108与A17参考基因组匹配。总计存在8 406种可变性剪接,其中主要的剪接方式为内含子保留(intron retention,RI)。共发现23 926个基因,其中12 049个基因存在295 545条转录本,在这些转录本中至少存在一个poly(A)位点。此外,共鉴定出3 223条转录因子,6 595条长非编码RNA(long non-coding RNA,lncRNA)和479条融合转录本。使用SMRT技术能够深入发掘蒺藜苜蓿转录数据,也为更好地利用蒺藜苜蓿基因组资源提供数据补充。

关键词: 蒺藜苜蓿, 单分子全长读数测序, 可变性剪接, 融合转录本

Abstract:

For deep analysis and exploring of the complete structure of mRNA from Medicago truncatula,a model plant in Leguminosae,the single-molecule long-read sequencing technology(SMRT)was used to sequence and analyze the full-length transcriptome of M. truncatula. A total of 7 728 183 subreads and 509 014 full-length non-chimeric reads(FLNC)were obtained. By comparing the reference genomes of R108 and A17,94.36% and 93.01% isoforms were identified as mapped reads,respectively. A total of 8 406 alternative splicing events was identified and the majority was intron retention(RI). The 23 926 genes were detected,of 12 049 genes had 295 545 transcripts,in which at least there was one poly(A)site. In addition,3 223 transcription factors,6 595 long non-coding RNAs(lncRNA)and 479 fusion transcripts were identified. The results showed the feasibility of deep sequencing M. truncatula transcriptome by SMRT,which provides data supplement for better utilizing the genome resource of M. truncatula.

Key words: Medicago truncatula, single-molecule long-read sequencing, alternative splice, fusion transcript