2022年1月21日 星期五
节瓜 Ty1-copia 类逆转座子逆转录酶序列的克隆及比对
Cloning and alignment of sequence of reverse transcriptase of Ty1-copia-like retrotransposon from Benincasa hispida var. chieh-qua
2014年 第23卷 第4期 页码[17-26]    下载全文[2.1MB]  
摘要

对8 个节瓜(Benincasa hispida var. chieh-qua How)品系基因组 DNA 中的 Ty1-copia 类逆转座子逆转录酶核苷酸序列进行扩增,并对品系 A39FA 的 29 个克隆产物的核苷酸序列及翻译的氨基酸序列的系统进化和同源性进行了分析,还对 29 条氨基酸序列进行了比对。 扩增结果表明:8 个节瓜品系的基因组 DNA 中均包含长度约 260 bp 的逆转录酶核苷酸片段;从品系 A39FA 中获得的 29 条 Ty1 - copia 类逆转座子逆转录酶核苷酸序列( CqRt1 至CqRt29)的长度为 247 ~ 267 bp,同源率为 46. 2% ~ 98. 1% ,而它们的氨基酸序列同源率为 26. 7% ~ 98. 8% 。 序列分析结果表明:节瓜 Ty1-copia 类逆转座子逆转录酶核苷酸序列中碱基 A、T、G 和 C 的数量分别为 65 ~ 96、47 ~ 92、45 ~ 74 和 32 ~ 49,所有序列均富含碱基 A 和 T,AT / GC 比为 1. 35 ~ 2. 33;缺失突变是造成节瓜 Ty1-copia 类逆转座子逆转录酶核苷酸序列长度差异的主要因素,在序列长度和碱基组成方面的明显差异表明节瓜 Ty1-copia 类逆转座子逆转录酶核苷酸序列具有高度异质性。 翻译后的氨基酸序列中有 21 条序列存在终止密码子突变、12 条序列存在移框突变,表明Ty1-copia 类逆转座子是节瓜基因组内序列重组的热点。 通过聚类分析可将 29 个逆转录酶核苷酸序列分为 5 个家族(Family),分别包括 16、4、4、4 和 1 条序列,其中 Family 1 可能是具有转座活性的逆转座子家族,但存在转录活性的逆转录酶序列仅占全部序列数量的 20. 69% 。 将每一家族中的 1 ~ 2 条序列与其他 15 种植物的Ty1-copia类逆转座子逆转录酶的氨基酸序列进行比对,显示出较高的同源性。 研究结果表明:节瓜与其他植物的Ty1-copia类逆转座子可能有相同起源,而且 Ty1-copia 类逆转座子可在不同类群间横向传递。

 

Abstract

Nucleotide sequence of reverse transcriptase of Ty1-copia -like retrotransposon in genomic DNA from eight lines of Benincasa hispida var. chieh-qua How was amplified, system evolution and homology of nucleotide sequence and translated amino acid sequence of 29 cloning products obtained from line A39FA were analyzed, and 29 amino acid sequences were aligned. The amplification results show that genomic DNA from eight lines of B. hispida var. chieh-qua all includes reverse transcriptase nucleotide fragment with length about 260 bp. Length of 29 nucleotide sequences (from CqRt1 to CqRt29)of reverse transcriptase of Ty1-copia-like retrotransposon obtained from line A39FA is 247-267 bp with homologous rate of 46. 2% -98. 1% , while homologous rate of their amino acid sequences is 26. 7% -98. 8% . The sequence analysis results show that number of base A, T, G and C in nucleotide sequence of reverse transcriptase of Ty1-copia -like retrotransposon from B. hispida var. chieh-qua is 65-96, 47-92, 45-74 and 32 - 49, respectively. All sequences are rich in base A and T, and AT / GC ratio is 1. 35 - 2. 33. Deletion mutation is the main reason inducing differences in length of nucleotide sequence of reverse transcriptase of Ty1-copia-like retrotransposon from B. hispida var. chieh-qua, and obvious differences in sequence length and base composition indicate that there is high heterogeneity in nucleotide sequence of reverse transcriptase of Ty1-copia -like retrotransposon from B. hispida var. chieh-qua. There is stop codon mutation in 21 sequences and frame. shift mutation in 12 sequences from translated amino acid sequence, which indicates that Ty1-copia -like retrotransposon is the hot spot in sequence recombination within B. hispida var. chieh-qua genome. 29 nucleotide sequences of reverse transcriptase can be divided into 5 families, containing 16, 4, 4, 4 and 1 sequences, respectively. Family 1 might be a retrotransposon family with transposition activity, while number of reverse transcriptase sequence with transposition activity only accounts for 20. 69% of total number of sequences . The alignment result on 1-2 amino acid sequences in each family of Ty1-copia -like retrotransposons from B. hispida var. chieh-qua and that of other 15 species shows higher homology. It is indicated that B. hispida var. chieh-qua and other species may possess the same origin, and Ty1-copia -like retrotransposon can be horizontally transferred among different taxa.

关键词节瓜; Ty1-copia 类逆转座子; 逆转录酶; 序列分析; 同源性; 系统发育
Key wordsBenincasa hispida var. chieh-qua How; Ty1-copia-like retrotransposon; reverse transcriptase; sequence analysis; homology; system evolution
作者赵芹,谢大森, 江彪, 罗少波, 彭庆务, 李明珠
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); 广州市珠江科技新星专项资助项目(2013086)