生物多样性 ›› 2016, Vol. 24 ›› Issue (12): 1325-1334.DOI: 10.17520/biods.2016231

• 数据论文 • 上一篇    下一篇

东亚特有珍稀蕨类植物岩穴蕨(碗蕨科)高通量转录组测序及分析

刘莉1,3, 舒江平1,3, 韦宏金1, 张锐1, 沈慧1,*(), 严岳鸿1,2   

  1. 1 上海辰山植物园, 中国科学院上海辰山植物科学研究中心, 上海 201602
    2 华东野生濒危资源植物保育中心, 上海 201602
    3 上海师范大学生命与环境科学学院, 上海 200234
  • 收稿日期:2016-08-23 接受日期:2016-11-09 出版日期:2016-12-20 发布日期:2017-01-10
  • 通讯作者: 沈慧
  • 作者简介:* 通讯作者 E-mail: shenhui@sibs.ac.cn
  • 基金资助:
    上海市绿化和市容管理局科学技术项目(G142433)和中国科学院战略生物资源科技支撑体系运行专项(ZSZY-001)

De novo transcriptome analysis of the rare fern Monachosorum maximowiczii (Dennstaedtiaceae) endemic to East Asia

Li Liu1,3, Jiangping Shu1,3, Hongjin Wei1, Rui Zhang1, Hui Shen1,*(), Yuehong Yan1,2   

  1. 1 Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai 201602
    2 National Conservation Center for Endangered Useful Plants in East China, Shanghai 201602
    3 College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234
  • Received:2016-08-23 Accepted:2016-11-09 Online:2016-12-20 Published:2017-01-10
  • Contact: Hui Shen

摘要:

岩穴蕨(Monachosorum maximowiczii)隶属于碗蕨科稀子蕨属, 是东亚中高海拔地区所特有的珍稀濒危植物。为了在分子水平对该物种有进一步的认识, 本文首次利用二代高通量测序技术(RNA-seq)对岩穴蕨进行了转录组测序分析。通过Illumina Hiseq 2500测序平台, 共计获得4.95 Gb原始数据(raw data), 经过滤后得到4.83 Gb有效数据(clean reads), 并进行从头组装得到了101,448条unigene。其中, 54,106条unigene预测到完整的开放阅读框。我们利用目前已知的51个植物基因组数据, 对岩穴蕨的unigene进行了详尽的功能注释, 并通过GO、COG、KEGG注释进一步了解了这些编码基因的作用方式、特征以及所参与的代谢通路。同时, 转录因子分析结果也为岩穴蕨的环境适应机制研究提供了初步线索。

关键词: 蕨类植物, 转录组学, 高通量测序, 生物多样性, 适应性

Abstract

Monachosorum maximowiczii, which belongs to the family Dennstaedtiaceae, is a unique fern rarely distributed in the middle-high altitudinal areas in East Asia. In order to identify the molecular basis of this species at the transcriptome level, a second generation sequencing technology (RNA-seq) was employed here for the first time. Using Illumina Hiseq 2500 platform, a total of 4.95 Gb raw data were obtained. After filtration, 4.83 Gb clean reads were kept and 101,448 unigene were generated using de novo assembly. Among them, 54,106 unigene were predicted to have a complete open reading frame. The functional annotation of the unigene obtained here was carried out using the Phytozome v11.0 databases. The gene function pattern and participated pathway were further explored based on GO, COG and KEGG annotation. Meanwhile, transcription factors prediction and analysis will provide preliminary insights into mechanisms of Monachosorum maximowiczii for environmental adaptation.

Key words: ferns, transcriptomics, high-throughput sequencing, biodiversity, adaptation