title: Head Transcriptomes of Two Closely Related Species of Fruit Flies of the Anastrepha fraterculus Group Reveals Divergent Genes in Species with Extensive Gene Flow.
abstract: 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.
authors: Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo 13565-905, Brazil.
authors: Victor Borges
authors: VB
authors: Rezende
authors: Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo 13565-905, Brazil.
authors: Carlos
authors: 0000-0001-7506-6133
authors: C
authors: Congrains
authors: Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo 13565-905, Brazil.
authors: André Luís A
authors: AL
authors: Lima
authors: Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo 13565-905, Brazil.
authors: Emeline Boni
authors: 0000-0003-1014-5265
authors: EB
authors: Campanini
authors: Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo 13565-905, Brazil.
authors: Aline Minali
authors: AM
authors: Nakamura
authors: Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo 13565-905, Brazil.
authors: Janaína Lima de
authors: JL
authors: Oliveira
authors: Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo 13565-905, Brazil.
authors: Samira
authors: S
authors: Chahad-Ehlers
authors: Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo 13565-905, Brazil.
authors: Iderval Sobrinho
authors: IS
authors: Junior
authors: Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Paulo 13565-905, Brazil brito@ufscar.br.
authors: Reinaldo
authors: 0000-0002-9441-6255
authors: R
authors: Alves de Brito
mesh_terms: D000483:Alleles; D000818:Animals; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D051456:Gene Flow; D017344:Genes, Insect; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D009928:Organ Specificity / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D013045:Species Specificity; D033621:Tephritidae / Q000235:genetics*; D059467:Transcriptome
keywords: RNA-Seq; de novo assembly; fixed SNPs; fraterculus group; next generation sequencing; positive selection