雷蒙德氏棉PIF-like转座元件鉴定与特征分析

doi:10.11963/issn.1002-7807.201602006

棉花学报 ›› 2016, Vol. 28 ›› Issue (2): 138-143.doi: 10.11963/issn.1002-7807.201602006

雷蒙德氏棉PIF-like转座元件鉴定与特征分析

徐珍珍¹，彭珍²，刘静²，沈新莲¹，杜建厂^2*

1. 江苏省农业科学院经济作物研究所/农业部长江下游棉花和油菜重点实验室，江苏南京 210014；2. 江苏省农业科学院生物技术研究所/江苏省农业生物学重点实验室，江苏南京 210014

收稿日期:2015-04-25 出版日期:2016-03-15 发布日期:2016-03-15
通讯作者: dujianchang@hotmail.com
作者简介:徐珍珍（1984―），女，博士，lele20032@163.com
基金资助:
江苏省农业科技自主创新[CX(14)5008]；棉花生物学国家重点实验室开放课题（CB2014A01）；江苏省333人才工程（BRA2013267）；江苏省科技项目（ BK20150540）

Genome-wide Identification and Characterization of PIF-like Elements in Gossypium raimondii

Xu Zhenzhen¹, Peng Zhen², Liu Jing², Shen Xinlian¹, Du Jianchang^2*

1. Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences / Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Nanjing, Jiangsu 210014, China; 2. Institute of Agro-biotechnology, Jiangsu Academy of Agricultural Sciences/Provincial Key Laboratory of Agrobiology, Nanjing, Jiangsu 210014, China

Received:2015-04-25 Online:2016-03-15 Published:2016-03-15

摘要/Abstract

摘要： PIF-like转座元件在植物基因组中含量丰富，是植物DNA转座子的重要组成部分。利用基因组学和生物信息学的研究手段，系统研究了雷蒙德氏棉全基因组水平PIF-like转座元件的数量、染色体分布、结构特征、表达模式及相邻基因的种类和功能等，共鉴定了440条包含转座酶且插入位置明确的PIF-like转座元件。这些元件几乎均匀地分布在13条染色体上，上下游2 kb内共有171个相邻编码蛋白的基因，其中132个基因注释到了GO数据库中，且这些基因的功能分布广泛；部分PIF-like转座元件表达，且具有组织特异性。这些遗传信息为深入研究棉花PIF-like转座元件介导的基因和基因组的进化规律以及棉花基因的功能奠定基础。

关键词: PIF-like转座元件; 雷蒙德氏棉; 生物信息学; 基因组

Abstract: PIF-like elements are abundant in plant genomes and make up an important part of DNA transposons. In this study, we systematically studied the number, chromosome distribution, characteristic structure, and expression pattern of PIF-like elements in the Gossypium raimondii genome using genomic and bioinformatic methods. We also studied the types and functions of their adjacent genes. Four hundred and forty PIF-like elements that carried transposase and had clear insert positions were detected. These were distributed almost evenly on 13 chromosomes. One hundred and seventy-one adjacent protein-encoding genes with distances of less than 2 kb to the PIF-like elements were identified, 132 of which were annotated to the Gene Ontology database with a wide variety of functions. Some of the 440 PIF-like elements were expressed, with the expression patterns varying among different tissues. These results will provide a firm foundation for studying the evolution of genes and genomes mediated by PIF-like elements and the functions of protein-encoding genes in cotton.

Key words: PIF-like elements; Gossypium raimondii; bioinformatics; genome

中图分类号:

S562.03

徐珍珍, 彭珍, 刘静, 沈新莲, 杜建厂. 雷蒙德氏棉PIF-like转座元件鉴定与特征分析[J]. 棉花学报, 2016, 28(2): 138-143.

Xu Zhenzhen, Peng Zhen, Liu Jing, Shen Xinlian, Du Jianchang. Genome-wide Identification and Characterization of PIF-like Elements in Gossypium raimondii[J]. Cotton Science, 2016, 28(2): 138-143.

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雷蒙德氏棉PIF-like转座元件鉴定与特征分析

Genome-wide Identification and Characterization of PIF-like Elements in Gossypium raimondii

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