滇黄精叶绿体全基因组序列及其密码子使用偏性分析

Analysis of Chloroplast Genome Characteristics and Codon Usage Bias of Polygonatum kingianum

摘要:

为探究滇黄精(Polygonatum kingianum)叶绿体全基因组特征和密码子使用偏性，利用第二代测序技术对滇黄精嫩叶进行测序，再经组装与注释后得到其叶绿体基因组全序列，通过MISA、EMBOSS和CodonW等软件对滇黄精叶绿体全基因组的SSR位点、系统发育及密码子偏好性进行分析。结果表明，滇黄精完整叶绿体基因组长度为155 852 bp，基因组平均GC含量为37.7%，其大、小单拷贝区(LSC)长度分别为84 633和185 25 bp，反向重复区长度为26 347 bp，注释了132个基因，包括86个蛋白编码基因、38个tRNA基因和8个核糖rRNA基因。叶绿体基因组中共有69个SSR位点，绝大多数属于单碱基重复的A/T类型。系统发育分析表明滇黄精与格脉黄精(P. tessellatum)亲缘关系近，可能与分布地域有关。密码子偏好性分析表明，滇黄精叶绿体基因组密码子使用模式受到自然选择影响大于突变因素，最终确定9个最优密码子。因此, 滇黄精叶绿体基因组遗传结构和系统发育位置及其密码子偏倚的分析，为叶绿体基因工程研究提供理论依据。

Abstract:

In order to explore the chloroplast genome characteristics and codon bias of Polygonatum kingianum, the next generation sequencing technology was utilized to sequence the young leaves, and the complete chloroplast genome sequence was obtained after assembly and annotation. SSR loci, phylogeny and codon preference of the chloroplast genome were analyzed by MISA, Emboss and Codonw software. The results showed that the length of complete chloroplast genome sequence of P. kingianum was 155 852 bp, including a pair of inverted repeats of 26 347 bp that were separated by large and small single copy regions (LSC, 84 633 bp and SSC, 18 525 bp). A total of 132 genes were annotated in the chloroplast genome, including 86 protein-coding genes, 8 rRNA genes and 38 tRNA genes. The average GC content of chloroplast genomes was 37.7%. A total of 69 SSR loci were detected, most of which belonged to single-base repeat A/T type. Phylogenetic analysis showed that P. kingianum was closer to P. tessellatum than other species, which may be related to their geographical distribution. The chloroplast genome codon usage pattern was more influenced by natural selection than mutation, and 9 codons were identified as the optimal codon. Therefore, these would provide important reference information for exploring the genetic relationship and the improvement of exogenous genes in P. kingianum.