博罗红豆叶绿体基因组测序与特征分析

Sequencing and Characterization of Chloroplast Genome of Ormosia boluoensis

为丰富惠州市特有极小种群植物博罗红豆Ormosia boluoensis的叶绿体基因组资料,进一步为其种质资源鉴定,分子标记开发提供参考依据,文章基于高通量测序方法完成了博罗红豆不同分布点的叶绿体基因组测序,并运用生物信息学和系统基因组学方法分析其结构、基因构成的特征。结果表明:(1)4个采样点博罗红豆的基因组长度分别为174713、174694、174695、174861 bp,基因组总GC含量分别为36.22%、35.76%、36.42%、36.07%,都具有典型的环状四分体结构;(2)博罗红豆叶绿体基因组包含有142个基因,包括97个蛋白质编码基因(PCG),8个核糖体RNA基因(rRNA),37个转运RNA基因(tRNA);(3)博罗红豆叶绿体基因组中共检测到28225个密码子,这些密码子中编码亮氨酸(Leu)、丝氨酸(Ser)和精氨酸(Arg)的种类最多且均达到6种,使用频率最多的是编码异亮氨酸(Ile)的AUU(1241个)密码子;(4)进一步对其简单重复序列(SSR)及核苷酸多样性分析结果表明,博罗红豆叶绿体基因组具有较高的单核苷酸重复类型SSR,并在LSC区域检测到4个核苷酸多态性变异热点区域。

The Ormosia boluoensis is one of the second-class protected plants in China.The aim of this study is to enrich the data of chloroplast genome,and provide a reference for further research on exploitation of the germplasm resources and molecular marker development.This study sequenced the chloroplast genome of O.boluoensis using high-throughput sequencing methods,analyzed its structural and genetic characteristics using bioinformatics methods,and explored its phylogenetic relationships.The results showed that:(1)The genome length ratios of NKS01,XTS01,XTS02,and XTS03 were 174713 bp,174694 bp,174695 bp,174861 bp,and the total GC content of the genome was 36.22%,35.76%,36.42%,and 36.07%,respectively,in four different populations of Borneo beans,exhibiting a typical circular tetrad structure;(2)The chloroplast genome of Borneo red bean contains 142 genes,including 97 protein coding genes(PCG),8 ribosomal RNA genes(rRNA),and 37 transport RNA genes(tRNA);(3)A total of 28225 codons were detected in the chloroplast genome of Borneo red beans,with the highest number of codons encoding leucine(Leu),serine(Ser),and arginine(Arg),all of which reached 6 types.The most frequently used codon was the AUU(1241)codon encoding isoleucine(Ile);(4)The nucleotide diversity analysis results indicate that the nucleotide diversity levels of the four populations of Borneo red beans are relatively low.