[1]李阳,袁娜,刘大亮,等.绿豆Copia类反转座子全基因组注释及进化分析[J].江苏农业学报,2020,(04):858-867.[doi:doi:10.3969/j.issn.1000-4440.2020.04.008]
 LI Yang,YUAN Na,LIU Da-liang,et al.Annotation and evolutionary analysis of the Copia retrotransposons in mung bean[J].,2020,(04):858-867.[doi:doi:10.3969/j.issn.1000-4440.2020.04.008]
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绿豆Copia类反转座子全基因组注释及进化分析()
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江苏农业学报[ISSN:1006-6977/CN:61-1281/TN]

卷:
期数:
2020年04期
页码:
858-867
栏目:
遗传育种·生理生化
出版日期:
2020-08-31

文章信息/Info

Title:
Annotation and evolutionary analysis of the Copia retrotransposons in mung bean
作者:
李阳12袁娜2刘大亮12翟小杰12徐照龙2程静12杜建厂12
(1.南京农业大学园艺学院/作物遗传与种质创新国家重点实验室,江苏南京210095;2.江苏省农业科学院种质资源与生物技术研究所/江苏省农业生物学重点实验室,江苏南京210014)
Author(s):
LI Yang12YUAN Na2LIU Da-liang12ZHAI Xiao-jie12XU Zhao-long2CHENG Jing12DU Jian-chang12
(1.College of Horticulture, Nanjing Agricultural University/State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing 210095,China;2.Institute of Germplasm Resoueces and Biotechnology, Jiangsu Academy of Agricultural Sciences/Jiangsu Provincial Key Laboratory of Agrobiology, Nanjing 210014, China)
关键词:
Copia类反转座子插入时间进化树绿豆
Keywords:
Copia retrotransposonsinsertion timephylogenetic treemung bean
分类号:
Q754
DOI:
doi:10.3969/j.issn.1000-4440.2020.04.008
文献标志码:
A
摘要:
利用基于结构从头寻找和同源比对的方法,从绿豆基因组中鉴定出插入位置明确的1 198个完整的Copia类反转座子和1 038个solo LTR转座子元件。这些元件不均匀分布在绿豆的22条染色体上,并和功能基因的分布呈现显著的负相关关系。绝大部分Copia类反转座子(91.8%)在最近5.0 MYA内插入到寄主基因组中,并在1.0~2.0 MYA呈现1个明显的活跃峰值。此外,每个家族的solo LTR转座元件数量与完整转座元件数量的比值与进化时间无关,而与LTR的长度呈现显著的正相关关系。尽管这些Copia类反转座子可划分为Angela、Ale、Bianca、Ivana、Maximus和TAR等6个谱系,但各谱系内所包含的家族数和元件数差异较大。通过染色体上的位置比较,发现67个Copia类反转座子家族的713个元件插入到629个功能基因的内部或附近区域(<1 kb),提示这些元件可能对基因的结构、表达和功能产生一定的影响。
Abstract:
Using structure-based and homology search approaches, 1 198 intact Copia retrotransposons and 1 038 solo LTR retrotransposons with well-defined insertion positions were identified from the mung bean genome. These elements were unevenly distributed along 22 chromosomes of mung bean, and showed a significant negative correlation with the distribution of functional genes. The vast majority of Copia retrotransposons (91.8%) were inserted into the host genome in the last 5.0 MYA, and showed a significant active peak during 1.0-2.0 MYA. In addition, the ratio of the number of solo LTRs to the number of intact elements in each family had no correlation with the evolutionary time,but had a significant positive correlation with the size of the LTR. Although these Copia retrotransposons could be divided into six lineages, such as Angela, Ale, Bianca, Ivana, Maximus and TAR, the number of families and elements in each lineage varied greatly. By comparing the positions on the chromosomes, it was found that 713 elements of 67 Copia retrotransposon families were inserted into or close to the 629 functional genes (<1 kb), suggesting that these elements may affect the structure, expression and function of genes.

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备注/Memo

备注/Memo:
收稿日期:2020-01-04基金项目:国家自然科学基金项目(31370266);江苏省农业科技自主创新基金项目(CX17-3004)作者简介:李阳(1993-),男,河南焦作人,硕士研究生,主要从事生物信息学研究。(E-mail)yliroot@163.com通讯作者:杜建厂, (E-mail)dujianchang@hotmail.com
更新日期/Last Update: 2020-09-08