密花豆叶绿体基因组序列特征及密码子偏好性分析

Sequence characteristics and codon bias analysis of chloroplast genome from Spatholobus suberectus Dunn

  • 摘要: 【目的】分析密花豆叶绿体基因组序列特征及密码子偏好性,为密花豆种质鉴定、分子育种及资源保护利用提供理论参考。【方法】利用高通量测序技术对密花豆的叶绿体基因组进行测序,结合生物信息学软件和工具对序列进行拼接、注释及序列特征和密码子偏好性分析,并通过构建系统发育进化树解析密花豆的进化地位。【结果】密花豆叶绿体基因组全长为152275 bp,是由83924 bp的大单拷贝(LSC)区、25113 bp的反向重复A(IRA)区、18125 bp的小单拷贝(SSC)区和25113 bp的反向重复B (IRB)依次排列而成的环状双链四分体分子。密花豆叶绿体基因组共注释到129个基因,包括84个蛋白编码基因(PCGs),8个rRNA和37个tRNA。密花豆叶绿体基因组在自然选择为主的多因素作用下,偏好使用以A或T结尾的密码子,最优密码子是GCT、AGA、CGA、AAT、TGT、CAA、GAA、GGT、CAT、ATA、TTA、AAA、TTT、CCT、TCA、ACT、TAT和GTT。从密花豆叶绿体基因组检测到117个SSR位点,由单、二、三、四核苷酸重复基元组成,其中以单、二核苷酸复基元数量较多,分别占SSR位点总数的50.4%和36.8%,且单、二、三、四核苷酸重复基元均以A或T及其组合为主。叶绿体基因组在密花豆属内和属间均存在较明显的碱基突变,密花豆与同属的美丽密花豆的叶绿体基因组序列相似性最高,说明二者亲缘关系最近。【结论】密花豆叶绿体基因组具有植物叶绿体基因组典型的结构特点,在密花豆属内及属间均有较好的鉴别效果,且其密码子偏好性是多因素共同作用的结果,其中自然选择是主要决定因素,但碱基突变以及其他因素对密码子使用偏好也有一定影响。

     

    Abstract: 【Objective】This work was aimed to clarify the sequence features and codon bias of chloroplast genome from Spatholobus suberectus Dunn, and provide theoretical reference for germplasm identification, molecular breeding and resource conservation and utilization of S. suberectus.【Method】 S. suberectus chloroplast genome was sequenced using high-throughput sequencing technology and then was assembled, annotated and analyzed by means of bioinformatics softwares and tools. A phylogenetic tree was also constructed to understanding the evolution status of S. suberectus.【Result】 The chloroplast genome of S. suberectus was an annular double-chain molecule with a size of 152275 bp, which was successively composed of a large single copy(LSC)with 83924 bp, an inverted repeat A(IRA)with 25113 bp, a small single copy(SSC)with 18125 bp and an inverted repeat B(IRB) with 25113 bp. The chloroplast genome annotated 129 genes, including 84 protein-coding genes(PCGs), 8 rRNA and 37 tRNA. The chloroplast genome of S. suberectus tended to use the codon ended with A or T under the action of multiple factors dominated by natural selection, and the preference codons were identified as GCT, AGA, CGA, AAT, TGT, CAA, GAA, GGT, CAT, ATA, TTA, AAA, TTT, CCT, TCA, ACT, TAT, GTT. A total of 117 SSR loci were detected from the chloroplast genome of S. suberectus, which were composed of mononucleotide, dinucleotide, trinucleotide and tetranucleotide repeat motifs. The number of mononucleotide and dinucleotide repeat motifs was higher, accounting for 50.4% and 36.8% of the total number of SSR loci respectively, and the mononucleotide, dinucleotide, trinucleotide and tetranucleotide repeat motifs were mainly A or T and their combinations. There were obvious base mutations in the chloroplast genome both within and among the genera Spatholobus. The chloroplast genome sequences of S. suberectus and S. pulcher were the most similar, and the two were most closely related. 【Conclusion】 The chloroplast genome of S. suberectus possesses typical structure of plant chloroplast genome and preferable identification capability among the Spatholobus and other genera. The codon bias of S. suberectus chloroplast genome is a synergistical result of multiple factors. Among them, natural selection contributes most, and the base mutation and others also have a certain impact.

     

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