苦豆子叶绿体基因组密码子偏好性分析及系统发育研究

Codon usage bias and phylogenetic analysis of chloroplast genome in Sophora alopecuroides (Fabaceae)

关键词:  苦豆子, 叶绿体基因组, 密码子偏好性, 系统发育, 选择压力

Key words:  Sophora alopecuroides, chloroplast genome, codon usage bias, phylogeny, selective pressure

摘要:

为明确苦豆子(Sophora alopecuroides)的叶绿体基因组特征及其系统发育位置,该研究利用Illumina平台对苦豆子叶绿体基因组进行测序,并通过生物信息学方法进行叶绿体基因组装、注释和特征分析,基于叶绿体基因组和单拷贝直系同源基因分别对苦豆子进行系统发育研究及分歧时间估计。结果表明:(1)苦豆子叶绿体基因组全长154 399 bp,呈典型的四分体结构,GC含量36.6%,编码84个蛋白基因,37个tRNA基因和8个rRNA基因。(2)共检测到94个以单核苷酸A/T重复类型为主的简单重复序列(simple sequence repeats, SSR)位点,主要分布于基因间隔区。(3)亮氨酸(Leu)是苦豆子叶绿体基因组使用频率最高的氨基酸(10.39%),相对同义密码子使用频率(relative synonymous codon usage, RSCU)大于1且ΔRSCU≥0.08的密码子有21个,均以A/U结尾,偏好性受突变与自然选择的综合作用。(4)选择压力分析结果显示,苦豆子叶绿体基因组中ycf2基因受到正选择作用。(5)基于叶绿体基因组序列和利用转录组/基因组筛选出的单拷贝直系同源基因序列构建的系统发育树拓扑结构并非完全相同,但结果均显示苦豆子与白刺花(Sophora davidii)具有较近的亲缘关系; 分歧时间估计结果显示,以叶绿体基因组为参考估计出的苦豆子分化时间(8.05 Mya)远小于以单拷贝直系同源基因为参考(18.28 Mya)。该研究结果明晰了苦豆子的叶绿体基因组特征,并获得了苦豆子较为合理的系统发育位置和分化时间,为后续探讨苦参属系统发育关系、遗传多样性、种质资源筛选与利用等提供了基础数据和参考价值。

Abstract:

In order to comprehensively investigate the characteristics of the chloroplast genome and phylogenetic location of Sophora alopecuroides, we sequenced the chloroplast genome of S. alopecuroides using Illumina platform, and performed assembly, annotation and characteristic analysis by bioinformatics methods, conducting phylogenetic studies and divergence time estimation of S. alopecuroides based on chloroplast genomes and single-copy orthologous genes. The results were as follows:(1)The chloroplast genome of S. alopecuroides was 154 399 bp in length, with a typical quadripartite structure and 36.6% GC content, which contained 84 protein-coding genes, 37 tRNA genes and eight rRNA genes.(2)A total of 94 simple sequence repeat(SSR)sites were detected in the chloroplast genome, which were mainly distributed in the intergenic regions and dominated by single nucleotide A/T repeats.(3)Simultaneously, codon bias analysis indicated that leucine(Leu)was the most frequent amino acid used(10.39%). There were 21 codons whose relative synonymous codon usage(RSCU)was greater than 1 and ΔRSCU≥0.08, all of which mainly ended in A/U. Their preferences are influenced by the combined effects of mutation and natural selection.(4)We also found that the ycf2 gene of the chloroplast genome in S. alopecuroides were under positive selection through selective pressure analysis.(5)Additionally, due to the different evolutionary rates of organelle genes and nuclear genes, the topological structures of phylogenetic trees constructed based on chloroplast genome sequences and single-copy orthologous gene sequences screened from transcriptome/genome were not exactly the same, but the results showed that S. alopecuroides and S. davidii were closely related. Estimates of divergence times indicated that the estimated differentiation time of S. alopecuroides based on chloroplast genome(8.05 Mya)was much smaller than that based on single-copy of orthologous gene(18.28 Mya). This study clarified the chloroplast genome characteristics and obtained reasonable phylogenetic position and differentiation time of S. alopecuroide. It provides fundamental data and reference value for subsequent discussions on the phylogeny, genetic diversity, and selection and utilization of germplasm resources of Sophora in the future.