AphidBase: A database for aphid genomic resources

INRA, Agrocampus Rennes, UMR 1099 BiO3P (Biology of Organisms and Populations applied to Plant Protection), F-35653 LE RHEU, France.
Bioinformatics (Impact Factor: 4.98). 04/2007; 23(6):783-4. DOI: 10.1093/bioinformatics/btl682
Source: PubMed


AphidBase aims to (i) store recently acquired genomic resources on aphids and (ii) compare them to other insect resources as functional annotation tools. For that, the Drosophila melanogaster genome has been loaded in the database using the GMOD open source software for a comparison with the 17 069 pea aphid unique transcripts (contigs) and the 13 639 gene transcripts of the Anopheles gambiae. Links to FlyBase and A.gambiae Entrez databases allow a rapid characterization of the putative functions of the aphid sequences. Text mining of the D.melanogaster literature was performed to construct a network of co-cited gene or protein names, which should facilitate functional annotation of aphid homolog sequences. AphidBase represents one of the first genomic databases for a hemipteran insect. AVAILABILITY: http://w3.rennes.inra.fr/AphidBase.

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Available from: Claude Rispe,
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    • "Available genomes analyzed in the present study were retrieved from the FlyBase [47], AphidBase [48], VectorBase [49], Ensembl [50] and GenBank (WGS division, [51]) databases as well as from the JGI [52], the OIST Marine Genomics Unit, the Broad Institute of Harvard and MIT, the Elephant shark genome sequencing Project and the FUGU Genome Project websites. In order to determine the hsp90 gene copy number of each species, BLAST [53] searches were performed against the corresponding genomes using as queries known Hsp90 sequences of the same or closely related species (accepted E-value was zero). "
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    ABSTRACT: Hsp90s, members of the Heat Shock Protein class, protect the structure and function of proteins and play a significant task in cellular homeostasis and signal transduction. In order to determine the number of hsp90 gene copies and encoded proteins in fungal and animal lineages and through that key duplication events that this family has undergone, we collected and evaluated Hsp90 protein sequences and corresponding Expressed Sequence Tags and analyzed available genomes from various taxa. We provide evidence for duplication events affecting either single species or wider taxonomic groups. With regard to Fungi, duplicated genes have been detected in several lineages. In invertebrates, we demonstrate key duplication events in certain clades of Arthropoda and Mollusca, and a possible gene loss event in a hymenopteran family. Finally, we infer that the duplication event responsible for the two (a and b) isoforms in vertebrates occurred probably shortly after the split of Hyperoartia and Gnathostomata.
    PLoS ONE 09/2013; 8(9):e73217. DOI:10.1371/journal.pone.0073217 · 3.23 Impact Factor
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    • "A BLAST search of the A. americanum EST library was also performed against a combined database of the predicted peptides of nine insect species, Acyrthosiphon pisum (pea aphid), Aedes aegypti (yellow fever mosquito), Anopheles gambiae (African malaria mosquito), Apis mellifera (honey bee), Bombyx mori (silkmoth), Culex quinquefasciatus (Southern house mosquito), Drosophila melanogaster (common fruit fly), Pediculus humanus (human louse), and Tribolium castaneum (red flour beetle), one crustacean, Daphnia pulex (water flea), and two chelicerates, I. scapularis (black-legged deer tick) and the recently sequenced Tetranychus urticae (two-spotted spider mite). These datasets were obtained, respectively, from AphidBase [71], VectorBase (VectorBase [72], http://www.vectorbase.org, A. aegypti Liverpool LVP annotation, Aaegl1), VectorBase (A. gambiae PEST annotation, AgamP3.5), "
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    ABSTRACT: Background Genomic resources within the phylum Arthropoda are largely limited to the true insects but are beginning to include unexplored subphyla, such as the Crustacea and Chelicerata. Investigations of these understudied taxa uncover high frequencies of orphan genes, which lack detectable sequence homology to genes in pre-existing databases. The ticks (Acari: Chelicerata) are one such understudied taxon for which genomic resources are urgently needed. Ticks are obligate blood-feeders that vector major diseases of humans, domesticated animals, and wildlife. In analyzing a transcriptome of the lone star tick Amblyomma americanum, one of the most abundant disease vectors in the United States, we find a high representation of unannotated sequences. We apply a general framework for quantifying the origin and true representation of unannotated sequences in a dataset and for evaluating the biological significance of orphan genes. Results Expressed sequence tags (ESTs) were derived from different life stages and populations of A. americanum and combined with ESTs available from GenBank to produce 14,310 ESTs, over twice the number previously available. The vast majority (71%) has no sequence homology to proteins archived in UniProtKB. We show that poor sequence or assembly quality is not a major contributor to this high representation by orphan genes. Moreover, most unannotated sequences are functional: a microarray experiment demonstrates that 59% of functional ESTs are unannotated. Lastly, we attempt to further annotate our EST dataset using genomic datasets from other members of the Acari, including Ixodes scapularis, four other tick species and the mite Tetranychus urticae. We find low homology with these species, consistent with significant divergence within this subclass. Conclusions We conclude that the abundance of orphan genes in A. americanum likely results from 1) taxonomic isolation stemming from divergence within the tick lineage and limited genomic resources for ticks and 2) lineage-specific genes needing functional genomic studies to evaluate their association with the unique biology of ticks. The EST sequences described here will contribute substantially to the development of tick genomics. Moreover, the framework provided for the evaluation of orphan genes can guide analyses of future transcriptome sequencing projects.
    BMC Genomics 02/2013; 14(1):135. DOI:10.1186/1471-2164-14-135 · 3.99 Impact Factor
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    • "Official gene sets and assembled genome sequences for 23 arthropod species were retrieved from publically available resources including AphidBase [36], BeetleBase [37], FlyBase [38], Hymenoptera Genome Database [39], SilkDB [40], VectorBase [41], and wFleaBase [42]; see Additional file 1, Table S2 for full details. The examined arthropod species include: Diptera - Drosophila melanogaster (Dmela) [43] and 11 other fruit flies [44]: Drosophila sechellia (Dsech), Drosophila simulans (Dsimu), Drosophila erecta (Derec), Drosophila yakuba (Dyaku), Drosophila ananassae (Danan), Drosophila persimilis (Dpers), Drosophila pseudoobscura (Dpseu), Drosophila willistoni (Dwill), Drosophila mojavensis (Dmoja), Drosophila virilis (Dviri), Drosophila grimshawi (Dgrim), as well as three mosquitoes: Anopheles gambiae (Agamb) [45], Aedes aegypti (Aaegy) [46], Culex quinquefasciatus (Cquin) [47]; Lepidoptera - the silk moth, Bombyx mori (Bmori) [48]; Coleoptera - the flour beetle, Tribolium castaneum (Tcast) [49]; Hymenoptera - the honey bee, Apis mellifera (Amell) [50] and the parasitoid wasp, Nasonia vitripennis (Nvitr) [51]; Hemiptera - the pea aphid, Acyrthosiphon pisum (Apisu) [52]; Phthiraptera - the human body louse, Pediculus humanus (Phuma) [25]; Crustacea - the water flea, Daphnia pulex (Dpule) [53]; and Arachnida - the deer tick, Ixodes scapularis (Iscap). "
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    ABSTRACT: First identified in fruit flies with temperature-sensitive paralysis phenotypes, the Drosophila melanogaster TipE locus encodes four voltage-gated sodium (NaV) channel auxiliary subunits. This cluster of TipE-like genes on chromosome 3L, and a fifth family member on chromosome 3R, are important for the optional expression and functionality of the Para NaV channel but appear quite distinct from auxiliary subunits in vertebrates. Here, we exploited available arthropod genomic resources to trace the origin of TipE-like genes by mapping their evolutionary histories and examining their genomic architectures. We identified a remarkably conserved synteny block of TipE-like orthologues with well-maintained local gene arrangements from 21 insect species. Homologues in the water flea, Daphnia pulex, suggest an ancestral pancrustacean repertoire of four TipE-like genes; a subsequent gene duplication may have generated functional redundancy allowing gene losses in the silk moth and mosquitoes. Intronic nesting of the insect TipE gene cluster probably occurred following the divergence from crustaceans, but in the flour beetle and silk moth genomes the clusters apparently escaped from nesting. Across Pancrustacea, TipE gene family members have experienced intronic nesting, escape from nesting, retrotransposition, translocation, and gene loss events while generally maintaining their local gene neighbourhoods. D. melanogaster TipE-like genes exhibit coordinated spatial and temporal regulation of expression distinct from their host gene but well-correlated with their regulatory target, the Para NaV channel, suggesting that functional constraints may preserve the TipE gene cluster. We identified homology between TipE-like NaV channel regulators and vertebrate Slo-beta auxiliary subunits of big-conductance calcium-activated potassium (BKCa) channels, which suggests that ion channel regulatory partners have evolved distinct lineage-specific characteristics. TipE-like genes form a remarkably conserved genomic cluster across all examined insect genomes. This study reveals likely structural and functional constraints on the genomic evolution of insect TipE gene family members maintained in synteny over hundreds of millions of years of evolution. The likely common origin of these NaV channel regulators with BKCa auxiliary subunits highlights the evolutionary plasticity of ion channel regulatory mechanisms.
    BMC Evolutionary Biology 11/2011; 11(1):337. DOI:10.1186/1471-2148-11-337 · 3.37 Impact Factor
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