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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
  1. aEnsembl release e71.