ArticleBMC genomics2019
Revisiting avian 'missing' genes from de novo assembled transcripts.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Article
- Decoding the Avian Missing Gene Mystery: Dot Chromosomes Unmask Extensive Gene Loss and Novel Genetic Instability.Genome biology and evolution · 2026Article
- Odorant-binding proteins (OBPs) in Ceratitis capitata Wiedemann (Diptera: Tephritidae): integrative analysis of a multigene family.Journal of insect science (Online) · 2025Article
- Divergence in expression of a singing-related neuroplasticity gene in the brains of 2 Ficedula flycatchers and their hybrids.G3 (Bethesda, Md.) · 2025Article
- Near telomere-to-telomere genome assemblies of Silkie Gallus gallus and Mallard Anas platyrhynchos restored the structure of chromosomes and "missing" genes in birds.Journal of animal science and biotechnology · 2025Article
- Genome of Russian Snow-White Chicken Reveals Genetic Features Associated with Adaptations to Cold and Diseases.International journal of molecular sciences · 2024Article
- Article
- The genome of a globally invasive passerine, the common myna, Acridotheres tristis.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Selection on the promoter regions plays an important role in complex traits during duck domestication.BMC biology · 2023Article
- A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes.Communications biology · 2023Article
- Genomic insights into metabolic flux in hummingbirds.Genome research · 2023Article
- New insights into the novel sequences of the chicken pan-genome by liquid chip.Journal of animal science · 2022Article
- De Novo Assembly of 20 Chicken Genomes Reveals the Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes and Subtelomeric Regions.Molecular biology and evolution · 2022Article
- Recurrent chromosome reshuffling and the evolution of neo-sex chromosomes in parrots.Nature communications · 2022Article
- Fourth Report on Chicken Genes and Chromosomes 2022.Cytogenetic and genome research · 2022Review
- Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication.Nature communications · 2021Article
- Sequencing refractory regions in bird genomes are hotspots for accelerated protein evolution.BMC ecology and evolution · 2021Article
- The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2021Article
- Article
- Connexins during 500 Million Years-From Cyclostomes to Mammals.International journal of molecular sciences · 2021Review
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11 authors.
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Abstract
backgroundArgument 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.
resultsWe 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.
conclusionInsufficient 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.
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