四倍体海岛棉LTR反转录转座子的数量与分布

doi:10.13560/j.cnki.biotech.bull.1985.2017-0940

生物技术通报 ›› 2018, Vol. 34 ›› Issue (5): 124-130.doi: 10.13560/j.cnki.biotech.bull.1985.2017-0940

四倍体海岛棉LTR反转录转座子的数量与分布

刘震,张树林,史莹慧,彭仁海

安阳工学院生物与食品工程学院,安阳 455000

收稿日期:2017-11-03 出版日期:2018-05-26 发布日期:2018-06-07
作者简介:刘震,男,博士,研究方向：生物信息学;E-mail：liuzhen378@163.com
基金资助:
国家自然科学基金项目（31471548）,河南省科技发展计划（152300410009）,河南省高等学校重点科研项目（18A180010）,安阳工学院校科研基金（YJJ2017007）,棉花生物学国家重点实验室开放课题（CB2015A21）

Quantitative and Distribution Characteristics of LTR Retrotransposons in Tetraploid Gossypium barbadense

LIU Zhen ZHANG, Shu-lin, SHI Ying-hui, PENG Ren-hai

School of Biotechnology and Food Science,Anyang Institute of Technology,Anyang 455000

Received:2017-11-03 Published:2018-05-26 Online:2018-06-07

摘要/Abstract

摘要： 棉花是重要的纤维作物,在四个栽培棉种中,海岛棉纤维品质最优,了解LTR反转录转座子的数量与分布,可以促进海岛棉基因组的研究。通过综合不同方法挖掘海岛棉基因组中的LTR反转录转座子序列,并进行家族归类和数据分析。结果表明海岛棉A亚组和D亚组共有的LTR反转录转座子家族占全部家族的95%,LTR反转录转座子的Copia超家族和Gypsy超家族的分布特征有明显的不同,但相同超家族在相同亚组染色体上则表现出相似的特征。LTR反转录转座子周边基因的GO注释主要富集在结合活性、催化活性和代谢过程等方面。研究结果揭示了LTR反转录转座子在海岛棉染色体上的分布特征及其周边基因的功能富集。

关键词: 海岛棉, LTR反转录转座子, 分布, 基因组

Abstract: Cotton is leading natural fiber-producing crop in the world. The fiber quality of Gossypium barbadense is the best among the four cultivated species of cotton. Understanding the number and distribution of LTR retrotransposons will promote the genome study of G. barbadense. In this study,we searched,classified and analyzed the LTR retrotransposon sequences from the genome of G. barbadense by many different methods. The results showed that LTR retrotransposon families shared by both of subgenome A and D accounted for 95% of all families,and the copy number and specific families of LTR retrotransposons in subgenome A were more than that in the subgenome D. The distribution characteristics of LTR retrotransposons superfamily Copia and Gypsy were significantly different;however,the same superfamily showed similar characteristics on the same subgenome chromosomes. In addition,the GO annotations of genes around LTR retrotransposons were mainly enriched in binding,catalytic,metabolic process,etc. In summary,the distribution characteristics of LTR retrotransposons on G. barbadense chromosomes and the functional enrichment of their surrounding genes are revealed in this paper.

Key words: Gossypium barbadense, LTR retrotransposon, distribution, genome

刘震,张树林,史莹慧,彭仁海. 四倍体海岛棉LTR反转录转座子的数量与分布[J]. 生物技术通报, 2018, 34(5): 124-130.

LIU Zhen ZHANG, Shu-lin, SHI Ying-hui, PENG Ren-hai. Quantitative and Distribution Characteristics of LTR Retrotransposons in Tetraploid Gossypium barbadense[J]. Biotechnology Bulletin, 2018, 34(5): 124-130.

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四倍体海岛棉LTR反转录转座子的数量与分布

Quantitative and Distribution Characteristics of LTR Retrotransposons in Tetraploid Gossypium barbadense

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