ArticleBMC genomics2009
Identification and characterization of pseudogenes in the rice gene complement.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed, 63 citations in OpenAlex.
- A Genome-Wide Pseudogene Map Reveals the Asymmetric Evolution of the A, B, and D Subgenomes in Common Wheat.Plants (Basel, Switzerland) · 2026Article
- The subordinate role of pseudogenization to recombinative deletion following polyploidization in angiosperms.Nature communications · 2025Article
- Genome sequencing of three Polyscias species reveals common features in terpene synthase gene family evolution in these species.The plant genome · 2025Article
- Overexpression of theFrontiers in plant science · 2024Article
- Genome-wide identification ofPeerJ · 2023Article
- Identification of Pseudo-R genes in Vitis vinifera and characterization of their role as immunomodulators in host-pathogen interactions.Journal of advanced research · 2022Article
- Structural characterization and duplication modes of pseudogenes in plants.Scientific reports · 2021Article
- Computational Methods for Pseudogene Annotation Based on Sequence Homology.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C.GigaScience · 2019Article
- Article
- Origination and Function of Plant Pseudogenes.Plant signaling & behavior · 2019Article
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- Systematic analysis of DEMETER-like DNA glycosylase genes shows lineage-specific Smi-miR7972 involved in SmDML1 regulation in Salvia miltiorrhiza.Scientific reports · 2018Article
- A TRIM insertion in the promoter of Ms2 causes male sterility in wheat.Nature communications · 2017Article
- Pseudogenes and Their Genome-Wide Prediction in Plants.International journal of molecular sciences · 2016Review
- Evolution of Gene Duplication in Plants.Plant physiology · 2016Review
- Identification of a Dolabellane Type Diterpene Synthase and other Root-Expressed Diterpene Synthases inFrontiers in plant science · 2016Article
- Identification and analysis of unitary loss of long-established protein-coding genes in Poaceae shows evidences for biased gene loss and putatively functional transcription of relics.BMC evolutionary biology · 2015Article
- Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome.Genome biology · 2015Article
- The Rho GTPase Family Genes in Bivalvia Genomes: Sequence, Evolution and Expression Analysis.PloS one · 2015Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe Osa1 Genome Annotation of rice (Oryza sativa L. ssp. japonica cv. Nipponbare) is the product of a semi-automated pipeline that does not explicitly predict pseudogenes. As such, it is likely to mis-annotate pseudogenes as functional genes. A total of 22,033 gene models within the Osa1 Release 5 were investigated as potential pseudogenes as these genes exhibit at least one feature potentially indicative of pseudogenes: lack of transcript support, short coding region, long untranslated region, or, for genes residing within a segmentally duplicated region, lack of a paralog or significantly shorter corresponding paralog.
resultsA total of 1,439 pseudogenes, identified among genes with pseudogene features, were characterized by similarity to fully-supported gene models and the presence of frameshifts or premature translational stop codons. Significant difference in the length of duplicated genes within segmentally-duplicated regions was the optimal indicator of pseudogenization. Among the 816 pseudogenes for which a probable origin could be determined, 75% originated from gene duplication events while 25% were the result of retrotransposition events. A total of 12% of the pseudogenes were expressed. Finally, F-box proteins, BTB/POZ proteins, terpene synthases, chalcone synthases and cytochrome P450 protein families were found to harbor large numbers of pseudogenes.
conclusionThese pseudogenes still have a detectable open reading frame and are thus distinct from pseudogenes detected within intergenic regions which typically lack definable open reading frames. Families containing the highest number of pseudogenes are fast-evolving families involved in ubiquitination and secondary metabolism.
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