Dep. of Computational Biology and Bioinformatics, Univ. of Kerala, Thiruvananthapuram, Kerala, India.
Plant Genome. 2019 Nov;12(3):1-11. doi: 10.3835/plantgenome2019.04.0032.
We presents the first chloroplast genome from the genus Trichopus. Comparative analysis revealed that the IR regions are more conserved than the SC regions. Highly divergent sequence hot spots were identified, which could be used as molecular markers. Phylogenetic analysis gave insight into the evolutionary history of Trichopus zeylanicus. In this study, we determined the complete sequence of the chloroplast genome of an important, rare, and endangered medicinal plant, Trichopus zeylanicus. The analysis of the genome showed that the complete chloroplast genome of Trichopus zeylanicus is 153,497 bp in size, and has a quadripartite structure with a large single copy of 81,091 bp and a small single copy of 17,512 bp separated by inverted repeats of 27,447 bp. Sequence analysis revealed that the chloroplast genome encodes 112 unique genes, including 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. We also identified 95 simple sequence repeats and 54 long repeats including 34 forward repeats, seven inverted repeats, nine palindromes, three reverse repeats, and one complementary repeat within the chloroplast genome of Trichopus zeylanicus. Whole chloroplast genome comparison with those of other Dioscoreales indicated that the inverted regions are more conserved than large single copy and small single copy regions. In the phylogenetic trees based on complete chloroplast genome and 78 shared chloroplast protein-coding genes in 15 monocot species, including 14 Dioscoreales, Trichopus zeylanicus formed a distinct clade. In summary, the first chloroplast genome from the genus Trichopus reported in this study gave a better insight into the phylogenetic relationships of different genera within the order Dioscoreales. Moreover, the present data will be a valuable chloroplast genomic resource for population genetics.
我们呈现了 Trichopus 属的第一个叶绿体基因组。比较分析表明，IR 区比 SC 区更保守。鉴定出高度变异的序列热点，可作为分子标记。系统发育分析深入了解了 Trichopus zeylanicus 的进化历史。在这项研究中，我们确定了一种重要、稀有且濒危的药用植物 Trichopus zeylanicus 的完整叶绿体基因组序列。基因组分析表明， Trichopus zeylanicus 的完整叶绿体基因组大小为 153497 bp，具有四分体结构，大片段单拷贝为 81091 bp，小片段单拷贝为 17512 bp，由 27447 bp 的反向重复序列隔开。序列分析表明，叶绿体基因组编码 112 个独特基因，包括 78 个蛋白质编码基因、30 个 tRNA 基因和 4 个 rRNA 基因。我们还在 Trichopus zeylanicus 的叶绿体基因组中鉴定出 95 个简单序列重复和 54 个长重复，包括 34 个正向重复、7 个反向重复、9 个回文、3 个反转重复和 1 个互补重复。与其他薯蓣目植物的全叶绿体基因组比较表明，反向区域比大片段单拷贝和小片段单拷贝区域更保守。在基于完整叶绿体基因组和 15 种单子叶植物中的 78 个共享叶绿体蛋白质编码基因构建的系统发育树中，包括 14 种薯蓣目植物， Trichopus zeylanicus 形成了一个独特的分支。总之，本研究报告的 Trichopus 属的第一个叶绿体基因组为薯蓣目不同属之间的系统发育关系提供了更好的了解。此外，本研究的数据将为群体遗传学提供有价值的叶绿体基因组资源。
