红锥叶绿体基因组特征及系统发育分析

Chloroplast genomic characterization and phylogenetic analysis of Castanopsis hystrix

摘要:

为确定红锥（Castanopsis hystrix）叶绿体基因组的结构组成情况，判定其在锥属中的进化位置及与同锥属叶绿体基因组的区别，为锥属物种鉴定、遗传多样性分析和资源保护提供相关依据。使用Illumina HiSeq 2500测序平台对红锥叶绿体基因组进行测序，通过生物信息学分析方法进行序列组装、注释和特征分析，并利用R、Python、MISA、CodonW和MEGA 6等生物信息学软件对其基因组结构和数目、密码子偏好性、序列重复、简单重复序列（simple sequence repeat，SSR）位点和系统发育进行分析。结果表明红锥叶绿体基因组大小为153 754 bp，呈现四分体结构；共拥有130个基因，包含85个编码基因、37个tRNA基因和8个rRNA基因；通过密码子偏好性分析，平均有效密码子数为55.5，说明其密码子随机性强、偏好性低；通过SSR及长重复片段分析，检测到45个重复序列及111个SSR位点；与近缘种比较，发现其叶绿体基因组序列高度保守，尤其蛋白质编码序列相似度极高；此外，系统发育分析发现红锥与海南锥聚为一支，关系密切。本研究得到了红锥的叶绿体基因组基本情况与系统发育位置，为红锥的物种辨别、天然种群遗传多样性与功能基因组学提供前期研究铺垫。

关键词:红锥;叶绿体基因组;密码子偏好性;系统发育

Abstract:

The structure and size of the chloroplast genome of Castanopsis hystrix was determined by Illumina HiSeq 2500 sequencing platform to understand the difference between C. hystrix and the chloroplast genome of the same genus, and the evolutionary position of C. hystrix in the genus, so as to facilitate species identification, genetic diversity analysis and resource conservation of the genus. Bioinformatics analysis was used to perform sequence assembly, annotation and characteristic analysis. R, Python, MISA, CodonW and MEGA 6 bioinformatics software were used to analyze the genome structure and number, codon bias, sequence repeats, simple sequence repeat (SSR) loci and phylogeny. The genome size of C. hystrix chloroplast was 153 754 bp, showing tetrad structure. A total of 130 genes were identified, including 85 coding genes, 37 tRNA genes and 8 rRNA genes. According to codon bias analysis, the average number of effective codons was 55.5, indicating that the codons were highly random and low in bias. Forty-five repeats and 111 SSR loci were detected by SSR and long repeat fragment analysis. Compared with the related species, chloroplast genome sequences were highly conserved, especially the protein coding sequences. Phylogenetic analysis showed that C. hystrix is closely related to the Hainanese cone. In summary, we obtained the basic information and phylogenetic position of the chloroplast genome of red cone, which will provide a preliminary basis for species identification, genetic diversity of natural populations and functional genomics research of C. hystrix.

Key words:Castanopsis hystrix;chloroplast genome;codon bias;phylogeny