球状轮藻叶绿体全基因组的组装与特征分析

Assembly and characteristic analysis of Chara globularis chloroplast whole genome

摘要:

为揭示球状轮藻叶绿体全基因组的特征以及探究其在轮藻科内的系统发育关系，本研究基于高通量测序技术对其叶绿体全基因组进行组装和序列分析.结果表明：球状轮藻叶绿体基因组全长180 652 bp，GC含量26.6％，具有典型的四分体环状结构，与普生轮藻十分类似；球状轮藻叶绿体基因组共注释出137个基因，其中包括94个蛋白质编码基因、37个tRNA基因和6个rRNA基因，比无色丽藻多2个蛋白质编码基因和3个tRNA基因，与高等植物相比具有rpl12、trnL(gag)、rpl19、ycf20四个特殊基因；球状轮藻叶绿体全基因组共检测出87个SSR位点且绝大部分由A和T构成；此外，球状轮藻共包含24 989个密码子且密码子使用更偏好A和T，亮氨酸(Leu)是编码氨基酸最多的密码子；通过邻近法(NJ)对包括球状轮藻在内的5个种的叶绿体全基因组构建系统发育树显示，球状轮藻的亲缘关系与普生轮藻更为接近.本研究对球状轮藻叶绿体全基因组进行了解析，利用现有数据确立其系统发育学地位.

Abstract:

In order to reveal the characteristics of the entire chloroplast genome of Chara globularis and explore its phylogenetic relationship in Characeae, highthroughput sequencing technology was used to assemble and sequence the entire chloroplast genome. The study showed that C. gloublaris is a circular molecule of 180 652 bp in length with a typical quadripartite structure and a 26.6% GC-content. 137 chloroplast genes were successfully annotated, including 94 protein-coding genes, 37 tRNA genes and 6 rRNA genes. There are 2 more protein-coding genes and 3 more tRNA genes than Nitella hyalina. Compared to land plants, C. globularis has four special genes: rpl12, trnL(gag), rpl19, and ycf20. A total of 87 SSR loci were detected in the genome, and most of them were composed of A and T. In addition, C. gloublaris contains a total of 24 989 codons and the codon usage prefers A and T. Leucine (Leu) is the codon that encodes the most amino acids. The phylogenetic tree constructed by the Neighbor Joining(NJ) on the entire chloroplast genomes of 5 species including C. gloublaris. showed that the phylogenetic relationship of C.gloublaris was closer to that of Chara vulgairs. This study analyzed the entire chloroplast genome of Chara globularis, and established its phylogenetic status by using the existing data.