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Revisiting avian 'missing' genes from de novo assembled transcripts.
- Source :
-
BMC Genomics . 1/5/2019, Vol. 20 Issue 1, p1-10. 10p. 2 Diagrams, 1 Chart, 3 Graphs. - Publication Year :
- 2019
-
Abstract
- 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 (1,623,045 transcripts after quality control in five birds) from a large amount of avian transcriptomic data, and found most of the presumed missing genes (83.2%) could be recovered in at least one bird species. Most of these genes have been identified for the first time in birds. Our results demonstrate that 67.94% genes have GC content over 50%, while 2.91% genes are AT-rich (AT% > 60%). In our results, 239 (53.59%) genes had a tissue-specific expression index of more than 0.9 in chicken. The missing genes also have lower Ka/Ks values than average (genome-wide: Ka/Ks = 0.99; missing gene: Ka/Ks = 0.90; t-test = 1.25E-14). Among all presumed missing genes, there were 135 for which we did not find any meaningful orthologues in any of the 5 species studied. 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. [ABSTRACT FROM AUTHOR]
- Subjects :
- *GENETIC speciation
*BIRD evolution
*BIOLOGICAL evolution
*TRANSCRIPTOMES
*GENOMES
Subjects
Details
- Language :
- English
- ISSN :
- 14712164
- Volume :
- 20
- Issue :
- 1
- Database :
- Academic Search Index
- Journal :
- BMC Genomics
- Publication Type :
- Academic Journal
- Accession number :
- 133952450
- Full Text :
- https://doi.org/10.1186/s12864-018-5407-1