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Comparative genomics and phylogenomics of fruit fly species of the fraterculus group. III. The undiscovered country

Abstract

Though some species of the fraterculus group of true fruit flies involve some of the greatest threats to national fruit production, we still know very little about their biology and differentiation. In previous projects, we used genome and transcriptome sequencing data to identify thousands of regions in the genomes of different Anastrepha species with great potential to enable us to assess natural diversity of Anastrepha species and their association with different host fruits. Such procedures are especially important in the adaptation process of Anastrepha species, some of which experienced gene flow, especially in the fraterculus group. Differentiation with gene flow makes it difficult to identify regions in the genome involved in such differentiation, but here we will use strategies that can do so. In previous studies, we have identified phylogenetically informative regions for phylogenomic analysis at different hierarchical levels in Anastrepha. However, a better understanding of the limits of their usefulness requires more expanded sampling, both of species and of localities, and that will be accomplished by the resequencing of genes of interest and phylogenomic and selection analyses in these samples. The study of evolutionary forces involved in the differentiation of these regions will also involve the identification of their epigenetic marks, which may be associated with adaptation to different edaphic conditions, or even to different hosts. Thus, the identification of differently methylated regions can provide important information for the understanding of their role in ecological differentiation, since it can allow greater plasticity and facilitate both the adaptation to different hosts to be transferred to the progeny, but also between different species. The combination of the identification of regions in the genome that present epigenetic marks associated with different hosts with the identification of regions in the genome that differ between species promises to help both in the identification of the adaptive process to different hosts, as well as its role in the differentiation of species and identification of the main regions in the genome and evolutionary forces involved with this process. (AU)

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