Examinando por Autor "Henriques, Dora"

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From the popular tRNAleu-COX2 intergenic region to the mitogenome: insights from diverse honey bee populations of Europe and North Africa
(Springer Nature, 2019-03-01) Henriques, Dora; Chávez Galarza, Julio César; Quaresma, Andreia; Neves, Cátia José; Lopes, Ana Rita; Costa, Cecília; Costa, Filipe O.; Rufino, José; Pinto, María Alice
The tRNAleu-COX2 intergenic region of the mitochondrial DNA has been used for assessing diversity in honey bee (Apis mellifera L.) populations worldwide. However, differential mutation rates in different partitions of the mitogenome may produce incongruent results. In this study, we sequenced 123 mitogenomes of 7 subspecies from lineages A, M, and C. This allowed generating a comprehensive dataset to investigate the phylogenetic and phylogeographic congruence among the mitogenome, individual genes, and the tRNAleu-COX2 region. We showed that the diversity patterns inferred from the tRNAleu-COX2 marker are not fully paralleled by those obtained with the mitogenome and the individual genes; while the three lineages are supported by these, the African sub-lineages and the haplotypes are not. Thus, conclusions drawn from the tRNAleu-COX2 region need to be taken with caution and this marker may not be appropriate to infer phylogenetic relationships between honey bee colonies.
Mitochondrial DNA variation of Apis mellifera iberiensis further insights from a large-scale study using sequence data of the tRNAleu-cox2 intergenic region
(Springer Nature, 2017-02-15) Chávez Galarza, Julio César; Garnery, Lionel; Henriques, Dora; Neves, Cátia José; Loucif Ayad, Wahida; Johnston, J. Spencer; Pinto, María Alice
A large-scale survey of the Iberian honey bee (Apis mellifera iberiensis) diversity patterns, using sequence data of the tRNAleu-cox2 mitochondrial DNA (mtDNA) region, demonstrates that earlier studies based on the DraI test missed significant components of genetic variation. Based on results from this survey, existing haplotype names were revised and updated following a nomenclature system established earlier and extended herein for the intergenic region. A more complete picture of the complex diversity patterns of IHBs is revealed that includes 164 novel haplotypes, 113 belonging to lineage A and 51 to lineage M and within lineage A and 69 novel haplotypes that belong to sub-lineage AI, 13 to AII, and 31 to AIII. Within lineage M, two novel haplotypes show a striking architecture with features of lineages A and M, which based on sequence comparisons and relationships among haplotypes are seemingly ancestral. These data expand our knowledge of the complex architecture of the tRNAleu-cox2 intergenic region in Apis mellifera and re-emphasizes the importance of Iberia as a source of honey bee mtDNA diversity.
Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula
(Springer Nature, 2018-07-24) Henriques, Dora; Wallberg, Andreas; Chávez Galarza, Julio César; Johnston, J. Spencer; Webster, Matthew; Pinto, María Alice
The availability of powerful high-throughput genomic tools, combined with genome scans, has helped identifying genes and genetic changes responsible for environmental adaptation in many organisms, including the honeybee. Here, we resequenced 87 whole genomes of the honeybee native to Iberia and used conceptually different selection methods (Samβada, LFMM, PCAdapt, iHs) together with in sillico protein modelling to search for selection footprints along environmental gradients. We found 670 outlier SNPs, most of which associated with precipitation, longitude and latitude. Over 88.7% SNPs laid outside exons and there was a significant enrichment in regions adjacent to exons and UTRs. Enrichment was also detected in exonic regions. Furthermore, in silico protein modelling suggests that several non-synonymous SNPs are likely direct targets of selection, as they lead to amino acid replacements in functionally important sites of proteins. We identified genomic signatures of local adaptation in 140 genes, many of which are putatively implicated in fitness-related functions such as reproduction, immunity, olfaction, lipid biosynthesis and circadian clock. Our genome scan suggests that local adaptation in the Iberian honeybee involves variations in regions that might alter patterns of gene expression and in protein-coding genes, which are promising candidates to underpin adaptive change in the honeybee.