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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160 068bp,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。
Malus × domestica is one of the most important temperate fruits. In order to better understand the molecular basis of this species, the published apple chloroplast genome sequence analysis of structural features. The results showed that the whole chloroplast genome of apple was 160 068 bp with the typical tetrad structure of the chloroplast genome of the angiosperms, including large single copy region (LSC), small single copy region (SSC) and two inverted complementary replicates Regions (IRs), with lengths of 88184 bp, 19180 bp and 26352 bp, respectively. There are a total of 135 genes in the genome (20 genes are located in the reverse complement repeat region, so the entire genome contains 115 different genes). Classified by function, these 115 genes include 81 protein-coding genes, 4 rRNA-encoding genes and 30 tRNA genes. Among them, ycf15, ycf68 and infA three genes contain multiple stop codons, presumably pseudogenes. Apple genome structure, gene order, GC content and codon usage preferences are similar to the typical angiosperm chloroplast genome. A total of 30 repeats> 30bp were detected in the chloroplast genome of apple, including 21 tandem repeats, 6 forward repeats and 3 inverted repeats. A total of 237 simple repeats (SSRs) were detected , Most of the SSR sites are biased toward A or T composition. In addition, an average of 24 SSR loci per 10,000 bp of non-coding region and an average of 5 SSR loci in the coding region indicate that the distribution of SSRs in the chloroplast genome is heterogeneous. In this paper, the report of apple chloroplast genome sequence features will help to promote the species of population genetics, phylogeny and chloroplast genetic engineering research.