Table 1 Evidence for a loss of protein coding genes in birds
From: Conserved syntenic clusters of protein coding genes are missing in birds
| A. Identification of protein coding gene orthologs in lizard, human, chicken, and zebra finch a | |
|---|---|
| Genes/Models | Category |
| 21,122 | Lizard gene models (Ensembl; AnoCar2.0) |
| 18,596 | Lizard protein coding gene models |
| 12,113 | Lizard models with 1-to-1 or apparent 1-to-1 orthologs in humans (GRH37) |
| 10,554 | Lizard models with 1-to-1 or apparent 1-to-1 orthologs in chicken (WASHUC2) and/or zebra finch (taeGut3.2.4) |
| 1,559 | Lizard models with no apparent orthologs in birds |
| B. Confirming gene loss in missing syntenic blocks in birds | |
| 537 | Initial set of candidate avian missing genes that are present in human/lizard syntenic blocks |
| +25 | Additional candidate missing genes that were not predicted by Ensembl, but were identified in lizard genome (‘no model’ entries on Tables S1A and S6) |
| +50 | Additional candidate missing genes with incorrectly annotated lizard model (‘†’ entries on Table S1) |
| - 89 | Genes found in birds based on Entrez gene, RefSeq, and cloned mRNA databases (Table S4A) |
| - 75 | Genes found in birds based on lizard/human mRNA and protein BLAT/BLAST searches of avian genomes, trace archives, and EST/mRNA databases (Table S4B) |
| −174 | Genes found in birds based on alligator/lizard/human protein tBLASTn searches of 60 avian whole genome shotgun contigs or evidence based on Refseqs in these species (Table S6) |
| 274 | Final set of avian missing genes (Table S1) |
| C. Final breakdown of curated set of genes missing in birds | |
| 162 | Genes that are part of missing syntenic blocks (Table S1A) |
| 112 | Genes that are in close proximity to missing syntenic blocks (Table S1B) |
| 274 | Total avian missing genes |