'Summit'完整叶绿体基因组序列的特征分析与比较分析
Characterization and comparative analysis of the complete chloroplast genome sequence from 'Summit'.
作者信息
Zhao Xueqing, Yan Ming, Ding Yu, Huo Yan, Yuan Zhaohe
机构信息
Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China.
College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China.
出版信息
PeerJ. 2019 Dec 20;7:e8210. doi: 10.7717/peerj.8210. eCollection 2019.
BACKGROUND
Sweet cherry () is one of the most popular of the temperate fruits. Previous studies have demonstrated that there were several haplotypes in the chloroplast genome of sweet cherry cultivars. However, none of chloroplast genome of a sweet cherry cultivar were yet released, and the phylogenetic relationships among based on chloroplast genome data were unclear.
METHODS
In this study, we assembled and annotated the complete chloroplast genome of a sweet cherry cultivar 'Summit' from high-throughput sequencing data. Gene Ontology (GO) terms were assigned to classify the function of the annotated genes. Maximum likelihood (ML) trees were constructed to reveal the phylogenetic relationships within species, using LSC (large single-copy) regions, SSC (small single-copy) regions, IR (inverted repeats) regions, CDS (coding sequences), intergenic regions, and whole cp genome datasets, respectively.
RESULTS
The complete plastid genome was 157, 886 bp in length with a typical quadripartite structure of LSC (85,990 bp) and SSC (19,080 bp) regions, separated by a pair of IR regions (26,408 bp). It contained 131 genes, including 86 protein-coding genes, 37 transfer RNA genes and 8 ribosomal RNA genes. A total of 77 genes were assigned to three major GO categories, including molecular function, cellular component and biological process categories. Comparison with other species showed that 'Summit' was quite conserved in gene content and structure. The non-coding regions, -, - and - were the most variable sequences between wild Mazzard cherry and 'Summit' cherry. A total of 73 simple sequence repeats (SSRs) were identified in 'Summit' cherry and most of them were mononucleotide repeats. ML phylogenetic tree within species revealed four clades: , , , and . The SSC and IR trees were incongruent with results using other cp data partitions. These data provide valuable genetic resources for future research on sweet cherry and species.
背景
甜樱桃（）是最受欢迎的温带水果之一。先前的研究表明，甜樱桃品种的叶绿体基因组存在几种单倍型。然而，尚未公布任何甜樱桃品种的叶绿体基因组，基于叶绿体基因组数据的甜樱桃品种间系统发育关系尚不清楚。
方法
在本研究中，我们从高通量测序数据中组装并注释了甜樱桃品种‘Summit’的完整叶绿体基因组。使用基因本体论（GO）术语对注释基因的功能进行分类。分别使用大单拷贝（LSC）区域、小单拷贝（SSC）区域、反向重复（IR）区域、编码序列（CDS）、基因间区域和整个叶绿体基因组数据集构建最大似然（ML）树，以揭示甜樱桃品种内的系统发育关系。
结果
完整的质体基因组长度为157,886 bp，具有典型的四分体结构，包括LSC（85,990 bp）和SSC（19,080 bp）区域，由一对IR区域（26,408 bp）隔开。它包含131个基因，包括86个蛋白质编码基因、37个转运RNA基因和8个核糖体RNA基因。共有77个基因被归入三个主要的GO类别，包括分子功能、细胞成分和生物学过程类别。与其他甜樱桃品种比较表明，‘Summit’在基因含量和结构上相当保守。非编码区域、、和是野生马扎德樱桃和‘Summit’樱桃之间最可变的序列。在‘Summit’樱桃中总共鉴定出73个简单序列重复（SSR），其中大多数是单核苷酸重复。甜樱桃品种内的ML系统发育树显示有四个分支：、、、和。SSC和IR树的结果与使用其他叶绿体数据分区的结果不一致。这些数据为甜樱桃及相关品种的未来研究提供了宝贵的遗传资源。
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