Head Transcriptomes of Two Closely Related Species of Fruit Flies of theAnastrepha fraterculusGroup 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 (Dtrue¯) 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.

Characterization of the Adult Head Transcriptome and Identification of Migration and Olfaction Genes in the Oriental Armyworm Mythimna separate

“…The distribution of the most general GO terms in biological processes, molecular functions, and cellular components in the M . separate head transcriptome were very similar to those in the head transcriptomes of the South American fruit fly Anastrepha fraterculus 26 and the subterranean termite Odontotermes formosanus 27 . Functional classification according to the KOG categories also exhibited an overall similarity between M .…”

Odorant-binding proteins expression patterns in recently diverged species of Anastrepha fruit flies

“…obliqua because, even though they may use common hosts, they have different host preferences and also because individuals seem to be able to recognize pheromones of their own species 22–24, 31 , which are two important ecological and reproductive attributes that may be involved in the species’ differentiation. We looked initially for differentially expressed OBP genes between these two species using RNA-seq data of head tissues 27 and found three OBP genes significantly differentially expressed (FDR < 0.001): OBP56a , OBP56d and OBP83cd in virgin females and OBP56d in virgin and post-mating males (Fig. 1; Table 1).…”

HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing

“…: Calla, Hall, Hou, and Geib (), Geib, Calla, Hall, Hou, and Manoukis (), Sim et al. ()] to genome assemblies from relatively low coverage re‐sequencing experiments or tissue‐specific RNA‐sequencing experiments (e.g., Rezende et al., ; Figure ; details for all data sources in Table S1). Later steps in our locus selection pipeline depend on trustworthy genome‐based annotations, specifically used to define exon/intron boundaries, so we identified four species ( B. dorsalis , B. oleae , C. capitata and Z. cucurbitae ) as having high‐quality genomic annotations based on the integration of homology‐based and evidence‐based predictions of gene function (e.g., Papanicolaou et al., ; Sim & Geib, ).…”