Revisiting avian ‘missing’ genes from de novo assembled transcripts

Background
Argument remains as to whether birds have lost genes compared with mammals and non-avian vertebrates during speciation. High quality-reference gene sets are necessary for precisely evaluating gene gain and loss. It is essential to explore new reference transcripts from large-scale de novo assembled transcriptomes to recover the potential hidden genes in avian genomes.
Results
We explored 196 high quality transcriptomic datasets from five bird species to reconstruct transcripts for the purpose of discovering potential hidden genes in the avian genomes. We constructed a relatively complete and high-quality bird transcript database from a large amount of avian transcriptomic data, and recovered most of the presumed missing genes. Most of these genes have been identified for the first time in birds, and some incorrectly annotated genes were also corrected. Our results clearly demonstrate most of those presumed missing genes (about 63~77%) could be recovered in all five bird species.
Conclusion
Insufficient reference genome quality is the major reason for wrongly inferring missing genes in birds. Those presumably missing genes often have a very strong tissue-specific expression pattern. We show multi-tissue transcriptomic data from various species are necessary for inferring gene family evolution for species with only draft reference genomes. This study supports the fact that avians share similar genes with mammals and non-avian vertebrates.