基于高通量测序的菜头肾叶绿体基因组的组装及序列分析

目的以药用植物菜头肾Championella sarcorrhiza为材料,对其叶绿体基因组进行组装和序列分析,为进一步开展菜头肾遗传与鉴定学研究奠定基础。方法采用高通量测序技术首次对菜头肾叶绿体基因组进行测序,以板蓝叶绿体基因组为参考,进行特征分析和聚类关系研究。结果生物信息学分析表明,菜头肾叶绿体基因组总长为144 713 bp,具有典型的被子植物叶绿体基因组环状四分体结构,GC含量为38.35%;共注释得到129个基因,包括84个蛋白编码基因,37个tRNA基因和8个rRNA基因;蛋白编码基因对应的密码子偏好使用A/T碱基。系统发育研究表明,菜头肾与板蓝亲缘关系最近,提示它们在进化上具有共线性。结论建立了适于菜头肾植物完整叶绿体基因组组装及其特征分析的方法,为菜头肾的鉴定、系统发育研究奠定了基础。

Assembly and sequence analysis of chloroplast genome of Championella sarcorrhiza based on high-throughput sequencing

Objective The chloroplast genome of Championella sarcorrhiza was assembled and sequenced, laying a foundation for the further development of the genetics and identification of C. sarcorrhiza. Methods The chloroplast genome of C. sarcorrhiza was sequenced using high-throughput sequencing technology for the first time, taking the chloroplast genome of Strobilanthes cusia as a reference, the feature analysis and clustering relationship study were carried out. Results Bioinformatics analysis showed that the total length of the chloroplast genome of C. sarcorrhiza is 144,713bp, containing a typical angiosperm chloroplast genome circular tetrad structure, with a GC content of 38.35%. A total of 129 genes were annotated, including 84 protein-coding genes, 37 tRNA genes and eight rRNA genes. The codons corresponding to protein coding genes are preferred with A/T bases. Phylogenetic studies showed that the relationship between C. sarcorrhiza and S. cusia was the closest, suggesting that they were evolutionarily co-linear. Conclusion The research provided a method suitable for the assembly of the complete chloroplast genome and the analysis of characteristics of the whole chloroplast genome of the C. sarcorrhiza, which also could lay the foundation for the research on the identification and phylogeny of C. sarcorrhiza.