ArticlePloS one2013
Comparative genomic and transcriptomic analysis of tandemly and segmentally duplicated genes in rice.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed.
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- Comparative analysis of the LEA gene family in seven Ipomoea species, focuses on sweet potato (Ipomoea batatas L.).BMC plant biology · 2024Article
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- Comparative genomics points to tandem duplications of SAD gene clusters as drivers of increased α-linolenic (ω-3) content in S. hispanica seeds.The plant genome · 2024Article
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- Multi-algorithm cooperation research of WRKY genes under nitrogen stress in Panax notoginseng.Protoplasma · 2023Article
- Genome-wide comparative analysis of the valine glutamine motif containing genes in four Ipomoea species.BMC plant biology · 2023Article
- Comparative analysis of theFrontiers in plant science · 2023Article
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- Genetic Divergence of Lineage-Specific Tandemly Duplicated Gene Clusters in Four Diploid Potato Genotypes.Frontiers in plant science · 2022Article
- Genome-wide comparative analysis of the nucleotide-binding site-encoding genes in fourFrontiers in plant science · 2022Article
- Evolutionary history of the C-repeat binding factor/dehydration-responsive element-binding 1 (CBF/DREB1) protein family in 43 plant species and characterization of CBF/DREB1 proteins in Solanum tuberosum.BMC evolutionary biology · 2020Article
- Evolutionary history of the heat shock protein 90 (Hsp90) family of 43 plants and characterization of Hsp90s in Solanum tuberosum.Molecular biology reports · 2020Article
- Article
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3 authors.
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Abstract
Tandem and segmental duplications significantly contribute to gene family expansion and genome evolution. Genome-wide identification of tandem and segmental genes has been analyzed before in several plant genomes. However, comparative studies in functional bias, expression divergence and their roles in species domestication are still lacking. We have carried out a genome-wide identification and comparative analysis of tandem and segmental genes in the rice genome. A total of 3,646 and 3,633 pairs of tandem and segmental genes, respectively, were identified in the genome. They made up around 30% of total annotated rice genes (excluding transposon-coding genes). Both tandem and segmental duplicates showed different physical locations and exhibited a biased subset of functions. These two types of duplicated genes were also under different functional constrains as shown by nonsynonymous substitutions per site (Ka) and synonymous substitutions per site (Ks) analysis. They are also differently regulated depending on the tissues and abiotic and biotic stresses based on transcriptomics data. The expression divergence might be related to promoter differentiation and DNA methylation status after tandem or segmental duplications. Both tandem and segmental duplications differ in their contribution to genetic novelty but evidence suggests that they play their role in species domestication and genome evolution.
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