2024年3月29日 星期五
瓠瓜LINE 逆转座子RT 序列的克隆与特征分析
Cloning and characteristic analysis on RT sequence of LINE retrotransposon from Lagenaria siceraria
2015年 第24卷 第1期 页码[1-11]    下载全文[2.2MB]  
摘要

以瓠瓜[Lagenaria siceraria (Molina) Standl.]品种‘大籽葫芦’(‘Dazihulu’)和‘杂交瓠瓜’(‘Hybrid bottlegourd’)为供试材料,对其基因组总DNA 中的LINE 逆转座子RT 序列进行扩增,并对30 个克隆产物的核苷酸序列及其编码的氨基酸序列进行比对、同源性分析和系统进化分析。结果表明:瓠瓜品种‘大籽葫芦’与‘杂交瓠瓜’的基因组总DNA 均包含长度约580 bp 的RT 序列片段。从2 个瓠瓜品种中获得的30 条LINE 逆转座子RT 核苷酸序列(编号为LsRT1 至LsRT30)长度为564 ~599 bp,碱基A、T、G 和C 的数量分别为143 ~ 193、157 ~ 205、104 ~ 139和83 ~134,AT/ GC 比为1. 29 ~1. 76,表现出高度异质性。缺失突变和终止密码子突变是造成瓠瓜LINE 逆转座子RT 核苷酸序列长度差异的主要因素。30 条瓠瓜LINE 逆转座子RT 核苷酸序列的相似性为47. 1% ~99. 5%,其编码的氨基酸序列相似性为26. 7% ~100. 0%。根据核苷酸替代值,30 条瓠瓜LINE 逆转座子RT 核苷酸序列可分为4 个家族(family),分别包含14、8、1 和7 条序列。氨基酸序列分析结果显示:瓠瓜LINE 逆转座子RT 氨基酸序列包含20 个保守氨基酸残基和多个半保守氨基酸残基;有14 条氨基酸序列具有终止密码子突变。Family 1、Family 2和Family 4 是可能具有转座活性的逆转座子家族,分别包含8、3 和5 条无终止密码子的RT 氨基酸序列。根据瓠瓜与其他15 种植物的LINE 逆转座子RT 氨基酸序列构建的系统进化树,瓠瓜与葡萄(Vitis vinifera Linn.)和黄瓜(Cucumis sativus Linn.)等种类的LINE 逆转座子RT 氨基酸序列有较高同源性。研究结果表明:瓠瓜LINE 逆转座子是一类较古老元件,LINE 逆转座子可在瓠瓜与其他种类的基因组间横向传递。

Abstract

Taking cultivars ‘Dazihulu’ and ‘Hybrid bottle gourd’ of Lagenaria siceraria (Molina) Standl. as tested materials, RT sequence of LINE retrotransposon in their genomic total DNA was amplified, and alignment, homology analysis and phylogeny analysis of nucleotide sequence of 30 cloning products and their amino acid sequences encoded were carried out. The results show that genomic total DNA of both ‘Dazihulu’ and ‘Hybrid bottle gourd’ includes RT sequence fragment with length about 580 bp. Length of 30 RT nucleotide sequences (Nos. from LsRT1 to LsRT30) of LINE retrotransposon obtained from the two cultivars is 564-599 bp, base number of A, T, G and C is 143-193, 157-205, 104-139 and 83-134, respectively and AT/ GC ratio is 1. 29-1. 76, which shows high heterogeneity. The main factors inducing difference in length of RT nucleotide sequence of LINE retrotransposon from L. siceraria are deletion mutation and stop codon mutation. Similarity of 30 RT nucleotide sequences of LINE retrotransposon from L. siceraria is 47. 1% -99. 5%, and that of amino acid sequence encoded is 26. 7% -100. 0%. Based on nucleotide substitution, 30 RT nucleotide sequences of LINE retrotransposon from L. siceraria can be divided into four families, which contains 14, 8, 1 and 7 sequences, respectively. The analysis result on amino acid sequence shows that RT amino acid sequence of LINE retrotransposon from L. siceraria contains 20 conservative amino acid residues and many semi-conservative amino acid residues, and 14 amino acid sequences possess stop codon mutation. Family 1, Family 2 and Family 4 may be the retrotransposon families with transposition activity, and include 8, 3 and 5 RT amino acid sequences without stop codon, respectively. According to phylogenetic tree constructed on RT amino acid sequence of LINE retrotransposon from L. siceraria and other 15 species, there is higher homology in RT amino acid sequence of LINE retrotransposon from L. siceraria with those from Vitis vinifera Linn., Cucumis sativus Linn. and other species. It is suggested that LINE retrotransposon from L. siceraria is a more ancient element, and can be horizontally transferred among genome of L. siceraria and other species.

 

关键词瓠瓜; LINE 逆转座子; RT 序列; 序列分析; 相似性; 系统进化
Key wordsLagenaria siceraria ( Molina) Standl.; LINE retrotransposon; RT sequence; sequence analysis; similarity; phylogeny
作者赵芹, 谢大森, 何晓明, 罗少波, 彭庆务, 陈俊秋
所在单位广东省农业科学院蔬菜研究所, 广东广州510640
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基金项目国家自然科学基金资助项目(31311643); 广东省自然科学基金博士科研启动基金资助项目(10451064001006063); 广州市珠江科技新星专项资助项目(2013086)