Comparative chloroplast genomes of Paris Sect. Marmorata: insights into repeat regions and evolutionary implications
Comparative chloroplast genomes of Paris Sect. Marmorata: insights into repeat regions and evolutionary implications
复制标题
巴黎教派叶绿体基因组比较。
DOI：
10.1186/s12864-018-5281-x
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发表时间：
2018-12-31
期刊：
影响因子：
4.4
通讯作者：
Liu, Changning
中科院分区：
文献类型：
--
作者：
Gao, Xiaoyang;Zhang, Xuan;Liu, Changning
背景：花锦组巴黎属植物是合成甾体皂苷类化合物的重要药用植物，具有良好的药理作用。然而，在分子遗传学研究揭示其基因组及其进化意义之前，该物种的野生资源受到掠夺性开发的威胁。因此，获得大理石组植物叶绿体全基因组序列，对于了解该组植物的质体组进化和促进未来的群体遗传学研究是必要的和关键的。本文测定了大理石组叶绿体基因组，并进行了全叶绿体基因组比较。结果：获得了大理石组叶绿体基因组的详细序列和结构变异。检测到超过40个大重复序列和大约130个简单重复序列以及一组基因组热点。通过与轮叶紫菜叶绿体基因组的比较，推测该片段为反向重复收缩。此外，几乎所有的质体蛋白编码基因都偏好以A/U结尾。大多数基因的密码子偏好性主要受突变偏好和选择压力的影响。结论：重复序列和热点区域的扫描可以检测种内和种间的变异，并选择性地推断大理石组与Daiswa亚属其他物种的系统发育关系。突变和自然选择是大多数质体蛋白编码基因密码子偏好模式的主要驱动力。因此，本研究从叶绿体基因组角度加深了对玉黍组植物进化的认识，为玉黍组植物的遗传分析提供了基因组学依据。
Background:Species of Paris Sect. Marmorata are valuable medicinal plants to synthesize steroidal saponins with effective pharmacological therapy. However, the wild resources of the species are threatened by plundering exploitation before the molecular genetics studies uncover the genomes and evolutionary significance. Thus, the availability of complete chloroplast genome sequences of Sect. Marmorata is necessary and crucial to the understanding the plastome evolution of this section and facilitating future population genetics studies. Here, we determined chloroplast genomes of Sect. Marmorata, and conducted the whole chloroplast genome comparison.Results:This study presented detailed sequences and structural variations of chloroplast genomes of Sect. Marmorata. Over 40 large repeats and approximately 130 simple sequence repeats as well as a group of genomic hotspots were detected. Inverted repeat contraction of this section was inferred via comparing the chloroplast genomes with the one of P. verticillata. Additionally, almost all the plastid protein coding genes were found to prefer ending with A/U. Mutation bias and selection pressure predominately shaped the codon bias of most genes. And most of the genes underwent purifying selection, whereas photosynthetic genes experienced a relatively relaxed purifying selection.Conclusions:Repeat sequences and hotspot regions can be scanned to detect the intraspecific and interspecific variability, and selected to infer the phylogenetic relationships of Sect. Marmorata and other species in subgenus Daiswa. Mutation and natural selection were the main forces to drive the codon bias pattern of most plastid protein coding genes. Therefore, this study enhances the understanding about evolution of Sect. Marmorata from the chloroplast genome, and provide genomic insights into genetic analyses of Sect. Marmorata.