Non-coding RNA gene families in the genomes of anopheline mosquitoes

BMC Genomics

Pantelis Topalis³  Dan Lawson¹  Christos Louis⁴  Nikos Poulakakis⁵  James Allen¹  Emmanuel Dialynas³  Elena Deligianni³  Vicky Dritsou² 

[1]European Bioinformatics Institute, Hinxton, UK

[2]Centre for Functional Genomics, University of Perugia, Perugia, Italy

[3]Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Greece

[4]Department of Biology, University of Crete, Heraklion, Greece

[5]Natural History Museum of Crete, University of Crete, Heraklion, Greece

关键词: Whole Genome Sequencing;    tRNA;    Small nucleolar RNA;    Small nuclear RNA;    Ribosomal genes;    ncRNA;    microRNA;    Genome evolution;    Anopheles;   

Others  :  1090420
DOI  :  10.1186/1471-2164-15-1038

 received in 2014-08-18, accepted in 2014-11-19,  发布年份 2014

【 摘 要 】

Background

Only a small fraction of the mosquito species of the genus Anopheles are able to transmit malaria, one of the biggest killer diseases of poverty, which is mostly prevalent in the tropics. This diversity has genetic, yet unknown, causes. In a further attempt to contribute to the elucidation of these variances, the international “Anopheles Genomes Cluster Consortium” project (a.k.a. “16 Anopheles genomes project”) was established, aiming at a comprehensive genomic analysis of several anopheline species, most of which are malaria vectors. In the frame of the international consortium carrying out this project our team studied the genes encoding families of non-coding RNAs (ncRNAs), concentrating on four classes: microRNA (miRNA), ribosomal RNA (rRNA), small nuclear RNA (snRNA), and in particular small nucleolar RNA (snoRNA) and, finally, transfer RNA (tRNA).

Results

Our analysis was carried out using, exclusively, computational approaches, and evaluating both the primary NGS reads as well as the respective genome assemblies produced by the consortium and stored in VectorBase; moreover, the results of RNAseq surveys in cases in which these were available and meaningful were also accessed in order to obtain supplementary data, as were “pre-genomic era” sequence data stored in nucleic acid databases. The investigation included the identification and analysis, in most species studied, of ncRNA genes belonging to several families, as well as the analysis of the evolutionary relations of some of those genes in cross-comparisons to other members of the genus Anopheles.

Conclusions

Our study led to the identification of members of these gene families in the majority of twenty different anopheline taxa. A set of tools for the study of the evolution and molecular biology of important disease vectors has, thus, been obtained.

【 授权许可】

   
2014 Dritsou et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 2.

Figure 3.

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