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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

Alignments of genes encoding the 5S ribosomal RNA. The species examined are shown at the left before the sequences. Nucleotides highlighted in green differ from those found at the corresponding position in the consensus sequence. Dashes refer to indels, periods to sequences that were not identified. The nucleotide corresponding to the most frequently used 3′ terminus (see section on 5S RNA) is underlined and highlighted in yellow in the Anopheles consensus sequence. The base numbering refers to the consensus sequence, excluding the dashes.
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Fig2: Alignments of genes encoding the 5S ribosomal RNA. The species examined are shown at the left before the sequences. Nucleotides highlighted in green differ from those found at the corresponding position in the consensus sequence. Dashes refer to indels, periods to sequences that were not identified. The nucleotide corresponding to the most frequently used 3′ terminus (see section on 5S RNA) is underlined and highlighted in yellow in the Anopheles consensus sequence. The base numbering refers to the consensus sequence, excluding the dashes.

Mentions: Little, so far, is known about 5S RNA genes in mosquitoes and no entry describing the complete or partial sequence of this RNA class is available in nucleic acid databases. To isolate the 5S rRNA gene we again used the D. melanogaster mature molecule to query the different genomes in BLAST searches of the SRAs. We succeeded in assembling the individual sequence of the mature 5S RNA genes in 19 genomes. A “consensus” sequence was also assembled for all species analyzed (Figure 2).Figure 2


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)

Alignments of genes encoding the 5S ribosomal RNA. The species examined are shown at the left before the sequences. Nucleotides highlighted in green differ from those found at the corresponding position in the consensus sequence. Dashes refer to indels, periods to sequences that were not identified. The nucleotide corresponding to the most frequently used 3′ terminus (see section on 5S RNA) is underlined and highlighted in yellow in the Anopheles consensus sequence. The base numbering refers to the consensus sequence, excluding the dashes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Alignments of genes encoding the 5S ribosomal RNA. The species examined are shown at the left before the sequences. Nucleotides highlighted in green differ from those found at the corresponding position in the consensus sequence. Dashes refer to indels, periods to sequences that were not identified. The nucleotide corresponding to the most frequently used 3′ terminus (see section on 5S RNA) is underlined and highlighted in yellow in the Anopheles consensus sequence. The base numbering refers to the consensus sequence, excluding the dashes.
Mentions: Little, so far, is known about 5S RNA genes in mosquitoes and no entry describing the complete or partial sequence of this RNA class is available in nucleic acid databases. To isolate the 5S rRNA gene we again used the D. melanogaster mature molecule to query the different genomes in BLAST searches of the SRAs. We succeeded in assembling the individual sequence of the mature 5S RNA genes in 19 genomes. A “consensus” sequence was also assembled for all species analyzed (Figure 2).Figure 2

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