蔓赤车叶绿体基因组结构及系统进化分析

Chloroplast genomic characterization and phylogenetic analysis of Pellionia scabra

摘要:

蔓赤车（Pellionia scabra）属于荨麻科赤车属，是一种具有高营养价值的优质野菜。本研究以蔓赤车为材料，基于高通量技术方法完成叶绿体基因组测序、组装注释、结构解析及构建系统发育树，以此深入研究蔓赤车叶绿体基因组特征。结果表明，蔓赤车叶绿体基因组大小为153 220 bp，GC含量为36.4%，属于典型的四分体结构。共注释到130个基因，其中85个蛋白编码基因，37个转运RNA基因，8个核糖体RNA基因；其中，有15个基因包含1个内含子，2个基因包含2个内含子，rps12存在反式剪接情况。蔓赤车叶绿体基因组可分为光合作用（43个）、自我复制（64个）、其他编码蛋白（7个）以及未知功能（4个）4大类基因。蔓赤车叶绿体基因组共检测出51 073个密码子，其中编码亮氨酸（Leu）的密码子占比最大，密码子偏向使用A和U两种碱基。检测到72个简单重复序列位点，其中有58个单核苷酸、12个二核苷酸、1个三核苷酸和1个四核苷酸4种不同类型的简单重复序列（simple sequence repeats，SSRs）。蔓赤车IRb/SSC边界存在ycf1基因扩张现象。系统进化树显示，蔓赤车（Pellionia scabra OL800583）与庐山楼梯草（Elatostema stewardii MZ292972）、盘托楼梯草（Elatostema dissectum MK227819）、光叶楼梯草（Elatostema laevissimumvar.laevissimum MN189961）亲缘关系最密切。基于蔓赤车叶绿体基因组的研究，旨在为蔓赤车物种鉴定、遗传进化及基因组学研究奠定理论基础。

Abstract:

Pellionia scabra belongs to the genus Pellionia in the family of Urticaceae, and is a high-quality wild vegetables with high nutritional value. In this study, high-throughput techniques were used to sequence, assemble and annotate the chloroplast genome. We also analyzed its structure, and construct the phylogenetic trees from the P. scabra to further study the chloroplast genome characteristics. The results showed that the chloroplast genome size was 153 220 bp, and the GC content was 36.4%, which belonged to the typical tetrad structure in P. scabra. The chloroplast genome encodes 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes in P. scabra. Among them, 15 genes contained 1 intron, 2 genes contained 2 introns, and rps12 had trans-splicing, respectively. In P. scabra, chloroplast genomes could be divided into four categories, including 43 photosynthesis, 64 self-replication, other 7 coding proteins, and 4 unknown functions. A total of 51 073 codons were detected in the chloroplast genome, among which the codon encoding leucine (Leu) accounted for the largest proportion, and the codon preferred to use A and U bases. There were 72 simple sequence repeats (SSRs) in the chloroplast genome of P. scabra, containing 58 single nucleotides, 12 dinucleotides, 1 trinucleotide, and 1 tetranucleotide. The ycf1 gene expansion was present at the IRb/SSC boundary. The phylogenetic trees showed that P. scabra (OL800583) was most closely related to Elatostema stewardii (MZ292972), Elatostema dissectum (MK227819) and Elatostema laevissimum var. laevissimum (MN189961). Taken together, our results provide worthwhile information for understanding the identification, genetic evolution, and genomics research of P. scabra species.