Abstract
G protein–coupled receptors (GPCRs) are one of the largest families of proteins, and here we scan the recently sequenced chicken genome for GPCRs. We use a homology-based approach, utilizing comparisons with all human GPCRs, to detect and verify chicken GPCRs from translated genomic alignments and Genscan predictions. We present 557 manually curated sequences for GPCRs from the chicken genome, of which 455 were previously not annotated. More than 60% of the chicken Genscan gene predictions with a human ortholog needed curation, which drastically changed the average percentage identity between the human–chicken orthologous pairs (from 56.3% to 72.9%). Of the non-olfactory chicken GPCRs, 79% had a one-to-one orthologous relationship to a human GPCR. The Frizzled, Secretin, and subgroups of the Rhodopsin families have high proportions of orthologous pairs, although the percentage of amino acid identity varies. Other groups show large differences, such as the Adhesion family and GPCRs that bind exogenous ligands. The chicken has only three bitter Taste 2 receptors, and it also lacks an ortholog to human TAS1R2 (one of three GPCRs in the human genome in the Taste 1 receptor family [TAS1R]), implying that the chicken's ability and mode of detecting both bitter and sweet taste may differ from the human's. The chicken genome contains at least 229 olfactory receptors, and the majority of these (218) originate from a chicken-specific expansion. To our knowledge, this dataset of chicken GPCRs is the largest curated dataset from a single gene family from a non-mammalian vertebrate. Both the updated human GPCR dataset, as well the chicken GPCR dataset, are available for download.
Highlights
Several vertebrate genomes have been sequenced since the release of the first draft sequence of the human genome in 2001 [1,2], but the first project to fill the large evolutionary gap between mammals and fish was the completion of the genome of the red jungle fowl, Gallus gallus, released in December 2004 [3]
In step 1, we created a Genscan dataset from the Ensembl February 2004 assembly of the chicken genome. This resulted in 30,165 Genscan predictions, and we used all human G protein–coupled receptor (GPCR) as baits in BLASTP searches to obtain, in total, 53,294 hits
We present a collection of 557 manually curated GPCR sequences from the chicken genome
Summary
Several vertebrate genomes have been sequenced since the release of the first draft sequence of the human genome in 2001 [1,2], but the first project to fill the large evolutionary gap between mammals and fish was the completion of the genome of the red jungle fowl, Gallus gallus, released in December 2004 [3]. The initial chicken genome annotation suggested between 20,000 and 23,000 protein-coding genes [3], which is similar to what has been estimated for the human genome [4,5] It is, well known that automatic annotations of new genomes are error-prone, and tremendous work is left in annotation of the different protein families. It has been estimated that the number of exons that have both splice sites correctly predicted by Genscan is as low as only 19% [6] This shows that the likelihood of correctly predicting multi-exon genes is fairly low. This has, a substantial impact on subsequent analysis such as phylogeny and calculations of evolutionary distances, when gene predictions are used instead of curated full-length genes
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