Rezende Victor Borges, Congrains Carlos, Lima André Luís A, Campanini Emeline Boni, Nakamura Aline Minali, Oliveira Janaína Lima de, Chahad-Ehlers Samira, Junior Iderval Sobrinho, Alves de Brito Reinaldo
Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo 13565-905, Brazil.
Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo 13565-905, Brazil
G3 (Bethesda). 2016 Oct 13;6(10):3283-3295. doi: 10.1534/g3.116.030486.
Several fruit flies species of the Anastrepha fraterculus group are of great economic importance for the damage they cause to a variety of fleshy fruits. Some species in this group have diverged recently, with evidence of introgression, showing similar morphological attributes that render their identification difficult, reinforcing the relevance of identifying new molecular markers that may differentiate species. We investigated genes expressed in head tissues from two closely related species: A. obliqua and A. fraterculus, aiming to identify fixed single nucleotide polymorphisms (SNPs) and highly differentiated transcripts, which, considering that these species still experience some level of gene flow, could indicate potential candidate genes involved in their differentiation process. We generated multiple libraries from head tissues of these two species, at different reproductive stages, for both sexes. Our analyses indicate that the de novo transcriptome assemblies are fairly complete. We also produced a hybrid assembly to map each species' reads, and identified 67,470 SNPs in A. fraterculus, 39,252 in A. obliqua, and 6386 that were common to both species. We identified 164 highly differentiated unigenes that had a mean interspecific index ([Formula: see text]) of at least 0.94. We selected unigenes that had Ka/Ks higher than 0.5, or had at least three or more highly differentiated SNPs as potential candidate genes for species differentiation. Among these candidates, we identified proteases, regulators of redox homeostasis, and an odorant-binding protein (Obp99c), among other genes. The head transcriptomes described here enabled the identification of thousands of genes hitherto unavailable for these species, and generated a set of candidate genes that are potentially important to genetically identify species and understand the speciation process in the presence of gene flow of A. obliqua and A. fraterculus.
果实蝇属的一些果蝇物种对多种肉质果实造成损害，具有重大经济意义。该类群中的一些物种最近出现了分化，存在基因渗入的证据，表现出相似的形态特征，这使得它们的鉴别变得困难，这进一步凸显了识别可能区分物种的新分子标记的重要性。我们研究了两个近缘物种：斜带果实蝇（A. obliqua）和巴西果实蝇（A. fraterculus）头部组织中表达的基因，旨在识别固定的单核苷酸多态性（SNP）和高度分化的转录本。考虑到这些物种仍存在一定程度的基因流动，这些基因可能指示参与其分化过程的潜在候选基因。我们从这两个物种不同生殖阶段的头部组织中为雌雄两性生成了多个文库。我们的分析表明，从头转录组组装相当完整。我们还进行了混合组装以映射每个物种的 reads，并在巴西果实蝇中鉴定出67470个SNP，在斜带果实蝇中鉴定出39252个SNP，以及6386个两个物种共有的SNP。我们鉴定出164个高度分化的单基因，其平均种间指数（[公式：见正文]）至少为0.94。我们选择Ka/Ks高于0.5或至少有三个或更多高度分化SNP的单基因作为物种分化的潜在候选基因。在这些候选基因中，我们鉴定出了蛋白酶、氧化还原稳态调节剂和一种气味结合蛋白（Obp99c）等基因。这里描述的头部转录组使得能够识别出数千个此前这些物种未知的基因，并产生了一组候选基因，这些基因对于从基因层面识别物种以及理解在斜带果实蝇和巴西果实蝇存在基因流动情况下的物种形成过程可能具有重要意义。
