Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera

Abstract

The Hymenoptera Genome Database (HGD) is a comprehensive model organism database that caters to the needs of scientists working on insect species of the order Hymenoptera. This system implements open-source software and relational databases providing access to curated data contributed by an extensive, active research community. HGD contains data from 9 different species across ∼200 million years in the phylogeny of Hymenoptera, allowing researchers to leverage genetic, genome sequence and gene expression data, as well as the biological knowledge of related model organisms. The availability of resources across an order greatly facilitates comparative genomics and enhances our understanding of the biology of agriculturally important Hymenoptera species through genomics. Curated data at HGD includes predicted and annotated gene sets supported with evidence tracks such as ESTs/cDNAs, small RNA sequences and GC composition domains. Data at HGD can be queried using genome browsers and/or BLAST/PSI-BLAST servers, and it may also be downloaded to perform local searches. We encourage the public to access and contribute data to HGD at: http://HymenopteraGenome.org.

Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality

“…Additional supplemental files are freely available for download from the Hymenoptera Genome Database (http://hymenopteragenome. org/ant_genomes/?q=consortium_datasets) (Munoz-Torres et al 2011).…”

Comparative genomics of chemosensory protein genes reveals rapid evolution and positive selection in ant-specific duplicates

“…We identified a total of 11-21 functional CSP genes per ant species (Table 1, Supplementary Table S1, Supplementary Table S2, Supplementary Data set 1), the predicted length of the produced protein ranging from 100 to 130 amino acids with a signal peptide. Three of the 97 annotated genes were unusually short (length 60-80 amino acids) but they were classified as functional based on support from gene models in the Hymenoptera Genome Database (Munoz-Torres et al, 2011). Additionally, we detected several pseudogenes (0-6 per species, the highest numbers being in the leafcutting ants A. echinatior and A. cephalotes) marked by inframe stop codon mutations or frame shifts or usually both, and several partial gene fragments (length o20 amino acids).…”

Unraveling the venom proteome of the bumblebee (Bombus terrestris) by integrating a combinatorial peptide ligand library approach with FT-ICR MS

“…As not all sequences are correct in prediction datasets, we tried to determine the correct protein sequence for each identification by searching for B. terrestris EST data and homologs of well-annotated species (Drosophila melanogaster, Mus musculus and Homo sapiens). B. terrestris EST sequences were searched by Blasts of each prediction against the Bter_1.0 genome scaffolds on Beebase (Munoz-Torres et al, 2011), while homologs were searched against the Uniprot database using the Blast algorithm (The Uniprot Consortium, 2012). A database containing all correct(ed) sequences was constructed and was used for performing bioinformatics analyses: the presence of secretion signal peptides, protein domains, protease and protease inhibitor families and GO-terms, and the existence of similar proteins in exosomes and venoms of other species were determined as previously described (Van Vaerenbergh et al, 2013b).…”