Aecyo Paulo, Marques André, Huettel Bruno, Silva Ana, Esposito Tiago, Ribeiro Elâine, Leal Inara R, Gagnon Edeline, Souza Gustavo, Pedrosa-Harand Andrea
Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil.
Max Planck Institute for Plant Breeding Research, Cologne, Germany.
Planta. 2021 Jul 8;254(2):27. doi: 10.1007/s00425-021-03655-8.
The chloroplast genomes of Caesalpinia group species are structurally conserved, but sequence level variation is useful for both phylogenomic and population genetic analyses. Variation in chloroplast genomes (plastomes) has been an important source of information in plant biology. The Caesalpinia group has been used as a model in studies correlating ecological and genomic variables, yet its intergeneric and infrageneric relationships are not fully solved, despite densely sampled phylogenies including nuclear and plastid loci by Sanger sequencing. Here, we present the de novo assembly and characterization of plastomes from 13 species from the Caesalpinia group belonging to eight genera. A comparative analysis was carried out with 13 other plastomes previously available, totalizing 26 plastomes and representing 15 of the 26 known Caesalpinia group genera. All plastomes showed a conserved quadripartite structure and gene repertoire, except for the loss of four ndh genes in Erythrostemon gilliesii. Thirty polymorphic regions were identified for inter- or intrageneric analyses. The 26 aligned plastomes were used for phylogenetic reconstruction, revealing a well-resolved topology, and dividing the Caesalpinia group into two fully supported clades. Sixteen microsatellite (cpSSR) loci were selected from Cenostigma microphyllum for primer development and at least two were cross-amplified in different Leguminosae subfamilies by in vitro or in silico approaches. Four loci were used to assess the genetic diversity of C. microphyllum in the Brazilian Caatinga. Our results demonstrate the structural conservation of plastomes in the Caesalpinia group, offering insights into its systematics and evolution, and provides new genomic tools for future phylogenetic, population genetics, and phylogeographic studies.
云实亚科植物的叶绿体基因组在结构上是保守的，但序列水平的变异对系统发育基因组学和群体遗传学分析都很有用。叶绿体基因组（质体基因组）的变异一直是植物生物学中重要的信息来源。云实亚科已被用作关联生态和基因组变量研究的模型，然而，尽管通过桑格测序对包括核基因座和质体基因座在内的系统发育进行了密集采样，但其属间和属内关系仍未完全解决。在这里，我们展示了来自云实亚科八个属的13个物种的质体基因组的从头组装和特征分析。我们与之前可用的其他13个质体基因组进行了比较分析，总计26个质体基因组，代表了26个已知云实亚科属中的15个。除了红蕊苏木中四个ndh基因的缺失外，所有质体基因组都显示出保守的四分体结构和基因库。共鉴定出30个多态性区域用于属间或属内分析。这26个比对后的质体基因组用于系统发育重建，揭示了一个解析良好的拓扑结构，并将云实亚科分为两个得到充分支持的分支。从小叶苏木中选择了16个微卫星（cpSSR）位点用于引物开发，并且至少有两个位点通过体外或计算机模拟方法在不同豆科亚科中交叉扩增。四个位点用于评估巴西卡廷加地区小叶苏木的遗传多样性。我们的结果证明了云实亚科质体基因组的结构保守性，为其系统分类和进化提供了见解，并为未来的系统发育、群体遗传学和系统地理学研究提供了新的基因组工具。
