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植物研究 ›› 2020, Vol. 40 ›› Issue (4): 613-622.doi: 10.7525/j.issn.1673-5102.2020.04.016

• 研究报告 • 上一篇    

闽楠转录组分析及基因功能注释

刘丹, 曾钦朦, 刘斌, 李煜, 陈世品   

  1. 福建农林大学林学院, 福州 350002
  • 收稿日期:2019-04-16 发布日期:2020-06-12
  • 通讯作者: 陈世品,E-mail:312084828@qq.com E-mail:312084828@qq.com
  • 作者简介:刘丹(1993-),女,硕士研究生,主要从事植物地理学方面的研究。
  • 基金资助:
    福建省林业厅林木种苗科技攻关五期项目(闽林[2016]9号);福建省科技厅引导性项目(2016N0001)

Transcriptome Analysis and Gene Functional Annotation in Phoebe bournei

LIU Dan, ZENG Qin-Meng, LIU Bin, LI Yu, CHEN Shi-Pin   

  1. College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002
  • Received:2019-04-16 Published:2020-06-12
  • Supported by:
    Fujian provincial forestry department forest seedling Science and Technology research project of the fifth phase(Minlin[2016] No.9);Fujian provincial department of Science and Technology guiding project(2016N0001)

摘要: 采用第二代Illumina HiSeq测序技术对闽楠的木质部、韧皮部、叶片进行转录组测序,分别获得Clean Reads片段41 383 707条、43 343 922条、44 191 586条,经转录本拼接后得到序列总长度达120 535 288 bp的383 331条Conting片段,进一步组装得到平均长度为542 bp的151 729条Unigenes。将闽楠转录组Unigenes进行基因功能注释,与NR数据库比对发现,其与葡萄的相似序列最多(34%),与黄瓜、野草莓、大豆的同源性较低(各占3%);进行GO功能注释,可将其划分为生物过程、细胞成分、分子功能3大类共计52个分支,与eggNOG数据库比对可分为25类,通过KEGG功能注释可知转录组中涉及的基因共参与了176条代谢通路,其中核糖体和碳代谢获得的注释较多。另外通过MISA软件分析,共获得35 972个SSR位点。其中,单核苷酸、二核苷酸和三核苷酸为优势重复类型,SSR位点数分别为21 762(60.50%),8 931(24.83%),4 924(13.69%)。闽楠转录组分析及基因功能注释为深入开展闽楠遗传育种及分子生物学相关研究奠定基础。

关键词: 闽楠, 转录组, 基因, 功能注释

Abstract: The second generation Illumina HiSeq sequencing technology was used to sequence the xylem, phloem and leaves of Phoebe bournei, and 41 383 707, 43 343 922, 44 191 586 clean reads fragments were obtained, respectively. After transcript splicing, the total length of the sequence was 120 535 288 bp, including 383 331 contings. The contings were further assembled to obtain 151 729 Unigenes with an average length of 542 bp. The gene function of the transcriptome unigenes was annotated with the NR database. It was found to have the most similar sequence with grape(34%) and low homology with cucumber, wild strawberry and soybean(3% each). The GO function annotation showed that it can be divided into 52 branches of biological process, cell component and molecular function. Using eggNOG, it can be divided into 25 categories. The KEGG function annotation indicates that the genes involved in the transcriptome are involved. There are 176 metabolic pathways, most of the notes on ribosome and carbon metabolism are obtained. In addition, through the MISA software analysis, a total of 35 972 SSR sites were obtained. Among them, single nucleotide, dinucleotide and trinucleotide were dominant repeat types, and the number of SSR sites was 21 762(60.50%), 8 931(24.83%) and 4 924(13.69%), respectively. It laid a foundation for further research on genetics, breeding and molecular biology.

Key words: Phoebe bournei, transcriptome, gene, function annotation

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