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

Dritsou V, Deligianni E, Dialynas E, Allen J, Poulakakis N, Louis C, Lawson D, Topalis P - BMC Genomics (2014)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Greece. topalis@imbb.forth.gr.

ABSTRACT

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.

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Related in: MedlinePlus

Bayesian Inference tree inferred by the concatenated dataset. The numbers on the branches indicate posterior probabilities and bootstrap supports (BI/ML/NJ).
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Fig3: Bayesian Inference tree inferred by the concatenated dataset. The numbers on the branches indicate posterior probabilities and bootstrap supports (BI/ML/NJ).

Mentions: The absence of complete rDNA sequences for some of the species combined with the fact that the alignment procedure led to remove a large part of them as unaligned (the alignment was ambiguous) made us decide to restrict our analysis to a concatenated sequence that included a portion of the nuclear ribosomal sequences produced in this study and segments of the mitochondrial 16S rDNA gene and the COI genes. Our aim was to identify the origin of these ribosomal sequences and also to evaluate the produced phylogenetic relationships based on the previously published data. A total of 5,145 base pairs (bp) for all loci (5S rRNA: 170 bp, 18S rRNA: 1332 bp, 28SrRNA: 826 bp, 16SrRNA: 1338 bp, and COI: 1479 bp) were analyzed for 18 taxa (17 ingroup taxa of the genus Anopheles and one outgroup taxon D. melanogaster). The ingroup alignment contained 921 variable and 395 parsimony informative sites, while when the outgroup taxon were included they were raised to 1229 and 472, respectively. Maximum Likelihood (-lnL = 16177.91), Bayesian Inference (-lnL = 16201.02) and Neighbor Joining analyses of the concatenated data produced similar topologies (see Figure 3). Although without very good statistical support (posterior probabilities in BI and bootstrap values in ML and NJ), the produced tree revealed several groups of species. One of them is the Anopheles gambiae complex that includes A. gambiae that branched off first, A. merus, A. arabiensis, A. melas, and A. quadriannulatus, which is in agreement with previous published analyses [45]. The other major group comprises 7 species in which A. maculatus seems to be sister taxon to A. stephensi (1.00/95/59) and A. culicifacies to A. minimus (0.99/77/<50).Figure 3


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

Dritsou V, Deligianni E, Dialynas E, Allen J, Poulakakis N, Louis C, Lawson D, Topalis P - BMC Genomics (2014)

Bayesian Inference tree inferred by the concatenated dataset. The numbers on the branches indicate posterior probabilities and bootstrap supports (BI/ML/NJ).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4300560&req=5

Fig3: Bayesian Inference tree inferred by the concatenated dataset. The numbers on the branches indicate posterior probabilities and bootstrap supports (BI/ML/NJ).
Mentions: The absence of complete rDNA sequences for some of the species combined with the fact that the alignment procedure led to remove a large part of them as unaligned (the alignment was ambiguous) made us decide to restrict our analysis to a concatenated sequence that included a portion of the nuclear ribosomal sequences produced in this study and segments of the mitochondrial 16S rDNA gene and the COI genes. Our aim was to identify the origin of these ribosomal sequences and also to evaluate the produced phylogenetic relationships based on the previously published data. A total of 5,145 base pairs (bp) for all loci (5S rRNA: 170 bp, 18S rRNA: 1332 bp, 28SrRNA: 826 bp, 16SrRNA: 1338 bp, and COI: 1479 bp) were analyzed for 18 taxa (17 ingroup taxa of the genus Anopheles and one outgroup taxon D. melanogaster). The ingroup alignment contained 921 variable and 395 parsimony informative sites, while when the outgroup taxon were included they were raised to 1229 and 472, respectively. Maximum Likelihood (-lnL = 16177.91), Bayesian Inference (-lnL = 16201.02) and Neighbor Joining analyses of the concatenated data produced similar topologies (see Figure 3). Although without very good statistical support (posterior probabilities in BI and bootstrap values in ML and NJ), the produced tree revealed several groups of species. One of them is the Anopheles gambiae complex that includes A. gambiae that branched off first, A. merus, A. arabiensis, A. melas, and A. quadriannulatus, which is in agreement with previous published analyses [45]. The other major group comprises 7 species in which A. maculatus seems to be sister taxon to A. stephensi (1.00/95/59) and A. culicifacies to A. minimus (0.99/77/<50).Figure 3

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Greece. topalis@imbb.forth.gr.

ABSTRACT

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.

Show MeSH
Related in: MedlinePlus