苹果叶绿体基因组特征分析

doi:10.7677/ynzwyj201413188

摘要/Abstract

摘要：

苹果（Malus × domestica）是最重要的温带水果之一。为了能更好的了解本种的分子生物学基础，对已发布的苹果叶绿体全基因组序列进行了结构特征分析。结果显示苹果的叶绿体基因组全长为160068bp，具有典型的被子植物叶绿体基因组的环状四分体结构，包含大单拷贝区（LSC），小单拷贝区（SSC）和两个反向互补重复区（IRs），长度分别为88184bp，19180bp和26352bp。基因组共有135个基因（20个基因分布在反向互补重复区，因此整个基因组包含115个不同的基因）。按照功能进行分类，这115个基因包括81个蛋白质编码基因，4个rRNA编码基因和30个tRNA 基因。其中，ycf15，ycf68和infA三个基因包含多个终止密码子，推测可能为假基因。苹果的基因组结构，基因顺序，GC含量和密码子使用偏好均与典型的被子植物叶绿体基因组类似。在苹果的叶绿体基因组中，共检测到30个大于30bp的重复序列，其中包括21串联重复，6个正向重复和3个反向重复序列；并检测到237个简单重复序列（SSR）位点，大部分的SSR位点都偏向于A或者T组成。此外，每10000bp非编码区平均分布有24个SSR位点，而编码区平均有5个SSR位点，表明SSRs在叶绿体基因组上的分布是不均匀的。本文对苹果叶绿体基因组序列特征的报道，将有助于促进该种的居群遗传学、系统发育和叶绿体基因工程的研究。

关键词: 苹果, 叶绿体基因组, 重复分析, SSRs

Abstract:

Apple (Malus × domestica) is one of the most important temperate fruits. To better understand the molecular basis of this species, we characterized the complete chloroplast (cp) genome sequence downloaded from Genome Database for Rosaceae. The cp genome of apple is a circular molecule of 160068bp in length with a typical quadripartite structure of two inverted repeats (IRs) of 26352bp, separated by a small single copy region of 19180bp (SSC) and a large singlecopy region (LSC) of 88184bp. A total of 135 predicted genes (115 unique genes, and another 20 genes were duplicated in the IR) were identified, including 81 proteincoding genes, four rRNA genes and 30 tRNA genes. Three genes of ycf15, ycf68 and infA contain several internal stop codons, which were interpreted as pseudogenes. The genome structure, gene order, GC content and codon usage of apple are similar to the typical angiosperm cp genomes. Thirty repeat regions (≥30bp) were detected, twentyone of which are tandem, six are forward and three are inverted repeats. Two hundred thirtyseven simple sequence repeat (SSR) loci were revealed and most of them are composed of A or T, contributing to a distinct bias in base composition. Additionally, average 10000bp noncoding region contains 24 SSR sites, while proteincoding region contains five SSR sites, indicating an uneven distribution of SSRs. The complete cp genome sequence of apple reported in this paper will facilitate the future studies of its population genetics, phylogenetics and chloroplast genetic engineering.

Key words: Apple, Chloroplast genome, Repeat analysis, SSRs

中图分类号:

Q 75

金桂花, 陈斯云, 伊廷双, 张书东. 苹果叶绿体基因组特征分析[J]. Plant Diversity, 2014, 36(04): 468-484.

JIN Gui-Hua, CHEN Shi-Yun, YI Ting-Shuang, ZHANG Shu-Dong. Characterization of the Complete Chloroplast Genome of Apple (Malus × domestica, Rosaceae)*[J]. Plant Diversity, 2014, 36(04): 468-484.

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