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Revisiting avian 'missing' genes from de novo assembled transcripts.

Zhong-Tao Yin1, Feng Zhu1, Fang-Bin Lin1

  • 1National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.

BMC Genomics
|January 7, 2019
PubMed
Summary

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Many avian genes presumed lost are actually present but hard to detect. This study recovers these hidden genes using extensive transcriptomic data, improving avian genome annotation.

Area of Science:

  • Genomics
  • Comparative genomics
  • Bioinformatics

Background:

  • The presence or absence of genes in birds compared to other vertebrates is debated.
  • High-quality gene sets are crucial for accurate gene gain/loss analysis.
  • Exploring new transcripts from de novo assembled transcriptomes can reveal hidden avian genes.

Purpose of the Study:

  • To reconstruct avian transcripts and discover potentially hidden genes in bird genomes.
  • To improve the completeness and accuracy of avian gene annotation.

Main Methods:

  • Analysis of 196 high-quality transcriptomic datasets from five bird species.
  • Construction of a comprehensive bird transcript database.
  • Identification and characterization of previously undetected avian genes.
Keywords:
Avian genomeEvolutionMissing genede novo assembly

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Main Results:

  • A database of 1,623,045 transcripts was created, recovering 83.2% of presumed missing avian genes.
  • Most recovered genes were identified in birds for the first time.
  • Recovered genes often exhibit high GC content and strong tissue-specific expression, with lower Ka/Ks values than average.

Conclusions:

  • Poor reference genome quality is a primary cause of erroneously inferred missing avian genes.
  • Many "missing" genes show significant tissue-specific expression.
  • Multi-tissue transcriptomic data are essential for accurate gene family evolution studies in species with draft genomes.