欧亚大陆分布的大花菟丝子叶绿体基因组插入缺失分析

doi:10.7677/ynzwyj201312070

摘要/Abstract

摘要：

运用鸟枪法在Illumina测序仪上对亚洲分布的大花菟丝子(Cuscuta reflexa)叶绿体基因组核苷酸全序列进行测定，并与已经发表的分布于欧洲的大花菟丝子进行了比较分析。研究结果表明亚洲分布的大花菟丝子叶绿体基因组总长度为120972bp，由79499bp的长单拷贝区，8369bp的短单拷贝区，以及两个16552bp的反向重复区组成，其长度比欧洲分布的大花菟丝子小了549bp；基因组总GC含量为38.3%，稍高于欧洲分布的大花菟丝子。两地区的大花菟丝子叶绿体全基因组编码的功能基因完全相同，且基因排列顺序也完全一致。另外，经过进一步序列比对后发现亚洲分布的大花菟丝子与欧洲分布的存在251个插入和210个缺失现象，总插入缺失及碱基替换长度分别为7649bp和3720bp，最大的插入和缺失长度分别为426bp和435bp。很多插入缺失都是单碱基，但仍然存在四个长度超过200bp的大突变，两个大的缺失发生在ycf2基因中，两个大的插入分别发生在trnFpsbE和matKtrnQ间隔区，详细的对比后发现大量的插入缺失都发生在大单拷贝区的基因间隔区，且插入缺失在反向重复区的发生频率较低。本研究首次报道不同大洲分布的同种异养植物的叶绿体全基因组比较分析，为研究这两个区域的居群多样性提供了基础资料。

关键词: 大花菟丝子, 叶绿体基因组, 插入缺失, 对比分析

Abstract:

We determined the complete nucleotide sequence of the chloroplast genome of Asian Cuscuta reflexa which is a world distributed dodder using shotgun method at Illumina’s Genome Analyzer, and then compared it with the corresponding published sequence of the same species that distributed in Europe. The chloroplast genome length was 120972bp, which was 549bp shorter than the European one, with a large single copy (LSC) region of 79499bp, a small single copy (SSC) region of 8369bp and two inverted repeats (IR) of 16552bp each. The overall GC content was 38.3%, which is slightly higher than European C.reflexa. The chloroplast genome of C.reflexa from both area encoded identical functional genes in the same order. On the other hand, detailed analyses revealed 251 insertions and 210 deletions. The length of indels substitution sum to 7649bp and the largest insertion and deletion reached 426bp and 435bp respectively. Meanwhile, 3720bp base substitution events were found in the entire chloroplast genome of Asian C.reflaxa. Majority of the indels observed were singlebase but four large length mutations longer than 200bp were also detected, including two deletions in ycf2 region, one insertion in trnFpsbE and another insertion in matKtrnQ. Most indels located in the intergenic regions of the LSC region while rare in the IR region. This research initially compared the whole chloroplast genome of same heterotrophic plants distributed in different continents.

Key words: Cuscuta reflexa, Chloroplast genome, Indels, Comparative analysis

中图分类号:

Q 75

王朝波1、2, 龚洵1. 欧亚大陆分布的大花菟丝子叶绿体基因组插入缺失分析[J]. Plant Diversity, 2013, 35(2): 158-164.

WANG Chao-Bo-, GONG Xun. Comparative Analyses of Indels Based on the Whole Chloroplast Genome of Cuscuta reflexa between European and Asian Populations[J]. Plant Diversity, 2013, 35(2): 158-164.

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