Instituto Tecnológico Vale, Belém, Pará, Brazil.
Programa Interunidades de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
PLoS One. 2022 Mar 17;17(3):e0265449. doi: 10.1371/journal.pone.0265449. eCollection 2022.
Ipomoea is a large pantropical genus globally distributed, which importance goes beyond the economic value as food resources or ornamental crops. This highly diverse genus has been the focus of a great number of studies, enriching the plant genomics knowledge, and challenging the plant evolution models. In the Carajás mountain range, located in Eastern Amazon, the savannah-like ferruginous ecosystem known as canga harbors highly specialized plant and animal populations, and Ipomoea is substantially representative in such restrictive habitat. Thus, to provide genetic data and insights into whole plastome phylogenetic relationships among key Ipomoea species from Eastern Amazon with little to none previously available data, we present the complete plastome sequences of twelve lineages of the genus, including the canga microendemic I. cavalcantei, the closely related I. marabaensis, and their putative hybrids. The twelve plastomes presented similar gene content as most publicly available Ipomoea plastomes, although the putative hybrids were correctly placed as closely related to the two parental species. The cavalcantei-marabaensis group was consistently grouped between phylogenetic methods. The closer relationship of the I. carnea plastome with the cavalcantei-marabaensis group, as well as the branch formed by I. quamoclit, I. asarifolia and I. maurandioides, were probably a consequence of insufficient taxonomic representativity, instead of true genetic closeness, reinforcing the importance of new plastome assemblies to resolve inconsistencies and boost statistical confidence, especially the case for South American clades of Ipomoea. The search for k-mers presenting high dispersion among the frequency distributions pointed to highly variable coding and intergenic regions, which may potentially contribute to the genetic diversity observed at species level. Our results contribute to the resolution of uncertain clades within Ipomoea and future phylogenomic studies, bringing unprecedented results to Ipomoea species with restricted distribution, such as I. cavalcantei.
番薯属是一个全球性分布的大热带属，其重要性不仅在于作为食物资源或观赏作物的经济价值。这个高度多样化的属一直是大量研究的焦点，丰富了植物基因组学知识，挑战了植物进化模型。在卡雅拉山脉，位于东亚马逊地区，被称为铁矿的热带稀树草原铁矿区拥有高度专业化的动植物种群，番薯属在这种限制生境中具有显著的代表性。因此，为了提供遗传数据，并深入了解来自东亚马逊地区关键番薯属物种的全质体系统发育关系，而这些物种之前几乎没有可用的数据，我们呈现了该属的 12 个谱系的完整质体序列，包括铁矿微地方性种 I. cavalcantei、亲缘关系密切的 I. marabaensis 及其可能的杂种。这 12 个质体与大多数公开可用的番薯属质体具有相似的基因内容，尽管可能的杂种被正确地归为与两个亲本物种密切相关。cavalcantei-marabaensis 组在系统发育方法中始终分组在一起。I. carnea 质体与 cavalcantei-marabaensis 组的密切关系，以及 I. quamoclit、I. asarifolia 和 I. maurandioides 组成的分支，可能是由于分类代表性不足，而不是真正的遗传关系密切，这强调了新的质体组装对于解决不一致性和提高统计置信度的重要性，特别是对于南美洲番薯属的分支。寻找在频率分布中具有高分散性的 k-mer 表明编码和基因间区具有高度可变性，这可能有助于观察到的物种水平的遗传多样性。我们的研究结果有助于解决番薯属内不确定的分支，并为未来的系统基因组学研究提供参考，为分布受限的番薯属物种带来了前所未有的结果，如 I. cavalcantei。
