Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil.
Department of Botany and Biodiversity Research, University of Vienna, Wien, Austria.
PLoS One. 2022 Jul 28;17(7):e0266304. doi: 10.1371/journal.pone.0266304. eCollection 2022.
The Brazilian palm fruits and hearts-of-palm of Euterpe edulis, E. oleracea and E. precatoria are an important source for agro-industrial production, due to overexploitation, conservation strategies are required to maintain genetic diversity. Chloroplast genomes have conserved sequences, which are useful to explore evolutionary questions. Besides the plastid DNA, genome skimming allows the identification of other genomic resources, such as single nucleotide polymorphisms (SNPs), providing information about the genetic diversity of species. We sequenced the chloroplast genome and identified gene content in the three Euterpe species. We performed comparative analyses, described the polymorphisms among the chloroplast genome sequences (repeats, indels and SNPs) and performed a phylogenomic inference based on 55 palm species chloroplast genomes. Finally, using the remaining data from genome skimming, the nuclear and mitochondrial reads, we identified SNPs and estimated the genetic diversity among these Euterpe species. The Euterpe chloroplast genomes varied from 159,232 to 159,275 bp and presented a conserved quadripartite structure with high synteny with other palms. In a pairwise comparison, we found a greater number of insertions/deletions (indels = 93 and 103) and SNPs (284 and 254) between E. edulis/E. oleracea and E. edulis/E. precatoria when compared to E. oleracea/E. precatoria (58 indels and 114 SNPs). Also, the phylogeny indicated a closer relationship between E. oleracea/E. precatoria. The nuclear and mitochondrial genome analyses identified 1,077 SNPs and high divergence among species (FST = 0.77), especially between E. edulis and E. precatoria (FST = 0.86). These results showed that, despite the few structural differences among the chloroplast genomes of these Euterpe palms, a differentiation between E. edulis and the other Euterpe species can be identified by point mutations. This study not only brings new knowledge about the evolution of Euterpe chloroplast genomes, but also these new resources open the way for future phylogenomic inferences and comparative analyses within Arecaceae.
巴西棕榈果实和心叶棕榈（Euterpe edulis、E. oleracea 和 E. precatoria）是农业产业生产的重要来源，但由于过度开发，需要采取保护策略来维持遗传多样性。叶绿体基因组具有保守序列，可用于探索进化问题。除了质体 DNA，基因组掠取还可以识别其他基因组资源，如单核苷酸多态性（SNP），提供有关物种遗传多样性的信息。我们对这三种 Euterpe 物种的叶绿体基因组进行了测序和基因内容鉴定。我们进行了比较分析，描述了叶绿体基因组序列（重复、插入缺失和 SNP）之间的多态性，并基于 55 种棕榈物种的叶绿体基因组进行了系统发育推断。最后，利用基因组掠取剩余的数据，即核和线粒体读数，我们鉴定了 SNP，并估计了这些 Euterpe 物种之间的遗传多样性。Euterpe 叶绿体基因组大小在 159,232 到 159,275bp 之间，呈现出与其他棕榈科植物高度同源的四部分结构。在两两比较中，我们发现 E. edulis/E. oleracea 和 E. edulis/E. precatoria 之间的插入/缺失（indels = 93 和 103）和 SNP（284 和 254）数量多于 E. oleracea/E. precatoria（58 个 indels 和 114 SNPs）。此外，系统发育分析表明 E. oleracea/E. precatoria 之间的亲缘关系更密切。核和线粒体基因组分析鉴定了 1,077 个 SNP，并发现物种之间存在高度分化（FST = 0.77），尤其是 E. edulis 和 E. precatoria 之间（FST = 0.86）。这些结果表明，尽管这些 Euterpe 棕榈的叶绿体基因组之间存在少数结构差异，但可以通过点突变来识别 E. edulis 和其他 Euterpe 物种之间的分化。这项研究不仅为 Euterpe 叶绿体基因组的进化带来了新的认识，而且这些新资源也为未来的系统发育推断和 Arecaceae 内的比较分析开辟了道路。
