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

Abstract

BackgroundOnly 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).ResultsOur 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.ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1038) contains supplementary material, which is available to authorized users.

Analysis of microRNA profile of Anopheles sinensis by deep sequencing and bioinformatic approaches

“…More than one hundred transcripts were targeted by two or more miRNAs. Meanwhile, 50 transcripts were regulated by miRNAs in different regions, suggesting that miRNAs are involved in complicated regulatory networks as suggested by other studies [ 8 , 36 , 50 ]. The conserved miRNAs in An.…”

“…Compared with miRNA genes predicted from the genome of An. sinensis by Dritsou et al [ 36 ] (Additional file 4 : Table S4), 19 miRNAs (asi-miR-252, asi-miR-10, asi-miR-927, asi-miR-8, asi-miR-996, asi-miR-1, asi-miR-276, asi-miR-305, asi-miR-277, asi-let-7, asi-miR-283, asi-miR-210, asi-miR-133, asi-miR-988, asi-miR-275, asi-miR-315, asi-miR-14, asi-miR-31 and asi-miR-999) in the An. sinensis were shared within three databases as shown in Fig.…”

A draft genome sequence of an invasive mosquito: an ItalianAedes albopictus

“…Interestingly, 22 contigs in the assembly were found to contain rDNA sequences, a family of genes that is known to be extremely difficult to be assembled correctly in WGS (Whole Genome Sequence) projects. 60 The most abundant elements of the 'Other' class of Table 4 includes (but is not limited to) the fruit fly elements 17.6, S, Doc, Bari1, piwi, F, TART and Asterix as well as the rice gypsy-type retrotransposon; these are listed in decreasing order of frequency identified, which, in no case, was higher that 0.2%. A recent publication reported the assembly of the 'repeatome' of A. albopictus.…”

The role of microRNAs in Anopheles biology—an emerging research field

“…The major drawback of the homology‐based analysis is that by definition, it detects only broadly conserved miRNA genes. This limitation was partially overcome by a conservative ab initio prediction coupled with homology searches of 16 Anopheles genomes . This study validated 58 previously identified miRNAs, discovered five new genes and revealed 21 miRNAs common to all species within the Anopheles complex.…”

“…Studies in late larval stages confirmed high levels of expression of these miRNA and revealed stage‐specific enrichment of miR‐11, miR‐276 and miR‐306 . Conservation of miR‐8 and miR‐10 in all Anopheles species indicates a conserved role of these abundantly expressed miRNAs in mosquito biology . Interestingly, sequences of the 20 most abundant miRNAs make up for 96% of all RNAseq reads, highlighting a dramatic difference in expression levels of miRNAs .…”