Yang Yong, Zhang Ying, Chen Yukai, Gul Juma, Zhang Jingwen, Liu Qiang, Chen Qing
Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China.
Life Sciences and Technology School, Lingnan Normal University, Zhanjiang, China.
PeerJ. 2019 Sep 20;7:e7713. doi: 10.7717/peerj.7713. eCollection 2019.
As one of the most cold and salt-tolerant mangrove species, is widely distributed in China. Here, we report the complete chloroplast genome sequence (Rhizophoraceae) obtained via next-generation sequencing, compare the general features of the sampled plastomes of this species to those of other sequenced mangrove species, and perform a phylogenetic analysis based on the protein-coding genes of these plastomes. The complete chloroplast genome of is 160,325 bp in size and has a 35.22% GC content. The genome has a typical circular quadripartite structure, with a pair of inverted repeat (IR) regions 26,670 bp in length separating a large single-copy (LSC) region (91,156 bp) and a small single-cope (SSC) region (15,829 bp). The chloroplast genome of contains 128 unique genes, including 80 protein-coding genes, 38 tRNA genes, 8 rRNA genes and 2 pseudogenes ( in the IRA region and in the IRB region). In addition, a simple sequence repeat (SSR) analysis found 108 SSR loci in the chloroplast genome of , most of which are A/T rich. IR expansion and contraction regions were compared between and five related species: two from Malpighiales and three mangrove species from different orders. The mVISTA results indicated that the genome structure, gene order and gene content are highly conserved among the analyzed species. The phylogenetic analysis using 54 common protein-coding genes from the chloroplast genome showed that the plant most closely related to is of Rhizophoraceae. The results of this study provide useful molecular information about the evolution and molecular biology of these mangrove trees.
作为最耐寒冷和耐盐的红树林物种之一，在中国广泛分布。在此，我们报告通过下一代测序获得的秋茄（红树科）完整叶绿体基因组序列，将该物种采样叶绿体基因组的一般特征与其他已测序红树林物种的进行比较，并基于这些叶绿体基因组的蛋白质编码基因进行系统发育分析。秋茄的完整叶绿体基因组大小为160,325 bp，GC含量为35.22%。该基因组具有典型的环状四分体结构，一对长度为26,670 bp的反向重复（IR）区域将一个大单拷贝（LSC）区域（91,156 bp）和一个小单拷贝（SSC）区域（15,829 bp）分开。秋茄的叶绿体基因组包含128个独特基因，包括80个蛋白质编码基因、38个tRNA基因、8个rRNA基因和2个假基因（一个在IRA区域，一个在IRB区域）。此外，简单序列重复（SSR）分析在秋茄的叶绿体基因组中发现了108个SSR位点，其中大多数富含A/T。比较了秋茄与五个相关物种之间的IR扩展和收缩区域：两个来自金虎尾目，三个来自不同目级别的红树林物种。mVISTA结果表明，在所分析的物种中，基因组结构、基因顺序和基因含量高度保守。使用来自叶绿体基因组的54个常见蛋白质编码基因进行的系统发育分析表明，与秋茄关系最密切的植物是红树科的红海榄。本研究结果为这些红树林树木的进化和分子生物学提供了有用的分子信息。
