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Annotation and analysis of low-complexity protein families of Anopheles gambiae that are associated with cuticle.

ABSTRACT: We have characterized four new families of homologous genes of the mosquito, Anopheles gambiae, all of which include members shown by previous work to be cuticular in nature. The CPLCG, CPLCW, CPLCP, and CPLCA families (where CPLC is 'cuticular protein of low complexity') encode proteins with a high proportion of low-complexity sequence. We have also annotated the An. gambiae Tweedle genes, a family of cuticular protein genes first described in Drosophila, and additional ungrouped An. gambiae cuticular proteins identified by proteomics. Our annotations reveal multiple gene-family expansions that are specific to Diptera or Culicidae. The CPLCG and CPLCW families occur within a large and dynamic tandem array on chromosome 3R that includes sets of concertedly evolving genes. Most gene families exhibit two or more different expression profiles during development.

SUBMITTER: Cornman RS

PROVIDER: S-EPMC3701952 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature

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Annotation and analysis of low-complexity protein families of Anopheles gambiae that are associated with cuticle.

Cornman R S RS Willis J H JH

Insect molecular biology 20091001 5

We have characterized four new families of homologous genes of the mosquito, Anopheles gambiae, all of which include members shown by previous work to be cuticular in nature. The CPLCG, CPLCW, CPLCP, and CPLCA families (where CPLC is 'cuticular protein of low complexity') encode proteins with a high proportion of low-complexity sequence. We have also annotated the An. gambiae Tweedle genes, a family of cuticular protein genes first described in Drosophila, and additional ungrouped An. gambiae cu ...[more]

PMID: 19754739

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Project description:BackgroundGenome sequencing of Anopheles gambiae was completed more than ten years ago and has accelerated research on malaria transmission. However, annotation needs to be refined and verified experimentally, as most predicted transcripts have been identified by comparative analysis with genomes from other species. The mosquito midgut-the first organ to interact with Plasmodium parasites-mounts effective antiplasmodial responses that limit parasite survival and disease transmission. High-throughput Illumina sequencing of the midgut transcriptome was used to identify new genes and transcripts, contributing to the refinement of An. gambiae genome annotation.ResultsWe sequenced ~223 million reads from An. gambiae midgut cDNA libraries generated from susceptible (G3) and refractory (L35) mosquito strains. Mosquitoes were infected with either Plasmodium berghei or Plasmodium falciparum, and midguts were collected after the first or second Plasmodium infection. In total, 22,889 unique midgut transcript models were generated from both An. gambiae strain sequences combined, and 76% are potentially novel. Of these novel transcripts, 49.5% aligned with annotated genes and appear to be isoforms or pre-mRNAs of reference transcripts, while 50.5% mapped to regions between annotated genes and represent novel intergenic transcripts (NITs). Predicted models were validated for midgut expression using qRT-PCR and microarray analysis, and novel isoforms were confirmed by sequencing predicted intron-exon boundaries. Coding potential analysis revealed that 43% of total midgut transcripts appear to be long non-coding RNA (lncRNA), and functional annotation of NITs showed that 68% had no homology to current databases from other species. Reads were also analyzed using de novo assembly and predicted transcripts compared with genome mapping-based models. Finally, variant analysis of G3 and L35 midgut transcripts detected 160,742 variants with respect to the An. gambiae PEST genome, and 74% were new variants. Intergenic transcripts had a higher frequency of variation compared with non-intergenic transcripts.ConclusionThis in-depth Illumina sequencing and assembly of the An. gambiae midgut transcriptome doubled the number of known transcripts and tripled the number of variants known in this mosquito species. It also revealed existence of a large number of lncRNA and opens new possibilities for investigating the biological function of many newly discovered transcripts.

Dataset Information

Annotation and analysis of low-complexity protein families of Anopheles gambiae that are associated with cuticle.

Publications

Annotation and analysis of low-complexity protein families of Anopheles gambiae that are associated with cuticle.

Similar Datasets

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