基于全基因组从头测序技术盐肤木叶绿体基因组的测序分析

Analysis of the chloroplast genome characteristics of Rhus chinensis by de novo sequencing

摘要:

盐肤木是一种重要的经济树种，可为医药和工业染料提供原料。盐肤木具有较强的抗旱、耐寒、耐盐，可在温带、暖温带和亚热带地区生长。本研究首次对盐肤木叶绿体基因组进行从头测序 (de novo sequencing) 组装研究。结果表明，盐肤木叶绿体基因组长度为159 082 bp，具有典型的四部分结构，两个单拷贝区被一对反向重复区分隔。LSC和SSC的长度分别为85 394 bp和18 663 bp。叶绿体基因组总共编码126个基因，其中包括88个蛋白编码基因，8个rRNA基因，30个tRNA基因。在叶绿体基因组中，61.97%的序列为基因编码区。在盐肤木叶绿体基因组中，只有8个基因含有内含子，除ycf3基因 (2个内含子) 外，其余均含有1个内含子。盐肤木叶绿体基因组总共存在755个SSR位点。SSR主要由二核苷酸和单核苷酸组成，分别占60% (453) 和28.74% (217)。聚类分析结果表明，漆树科与盐肤木最为接近，其次为槭树科和无患子科。本研究为盐肤木的分类提供了分子基础。本研究是关于盐肤木叶绿体基因组的首次报道，对了解其光合作用、进化和叶绿体转基因工程具有重要意义。

Abstract:

Rhus chinensis is an important economic species, which could provide raw materials for pharmaceutical and industrial dyes. Rhus chinensis is famous for its resistance to drought, cold, and salt. It grows in temperate, warm temperate, and subtropical regions. We report here Rhus chinensis chloroplast genomes by de novo sequencing. The results show that the length of Rhus chinensis was 159 082 bp, exhibiting a typical four-part structure with two single-copy regions (long single copy [LSC] and short single copy [SSC] sections) separated by a pair of inverted repeats (IRs). The length of LSC and SSC was 85 394 bp and 18 663 bp, respectively. The genomes contained 126 genes, including 88 protein encoding genes, 8 rRNA and 30 tRNA genes. In the chloroplast genome, 61.97% of the sequence were gene coding region. In the sequence of gene encoding region, the vast majority of sequences were protein encoding region, accounting for 86.65%, followed by rRNA (10 620 bp, 10.77%) and tRNA (2 540 bp, 2.58%). In Rhus chinensis chloroplast genome, only 8 genes contain introns, all containing 1 intron except ycf3 gene (2 introns). The Rhus chinensis chloroplast genome contains 755 SSR locies. SSR mainly consists of dinucleotide and mononucleotide, accounting for 60% (453) and 28.74% (217) respectively. The clustering results show that Anacardiaceae were closest to Rhus chinensis, followed by Aceraceae and Sapindaceae. This study provides a molecular basis for the classification of Rhus chinensis.