ArticleGenome biology and evolution2014
Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.
Article in Genome biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed, 72 citations in OpenAlex.
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- Phylogenomic analyses across land plants reveals motifs and coexpression patterns useful for functional prediction in the BAHD acyltransferase family.Frontiers in plant science · 2023Article
- Genetic Divergence of Lineage-Specific Tandemly Duplicated Gene Clusters in Four Diploid Potato Genotypes.Frontiers in plant science · 2022Article
- Comparisons within the Rice GA 2-Oxidase Gene Family Revealed Three Dominant Paralogs and a Functional Attenuated Gene that Led to the Identification of Four Amino Acid Variants Associated with GA Deactivation Capability.Rice (New York, N.Y.) · 2021Article
- Multi-responses of O-methyltransferase genes to salt stress and fiber development of Gossypium species.BMC plant biology · 2021Article
- CottonGVD: A Comprehensive Genomic Variation Database for Cultivated Cottons.Frontiers in plant science · 2021Article
- Expression of several Phytophthora cinnamomi putative RxLRs provides evidence for virulence roles in avocado.PloS one · 2021Article
- VviERF6Ls: an expanded clade in Vitis responds transcriptionally to abiotic and biotic stresses and berry development.BMC genomics · 2020Article
- Expression Partitioning of Duplicate Genes at Single Cell Resolution inFrontiers in genetics · 2020Article
- Centromere Satellite Repeats Have Undergone Rapid Changes in Polyploid Wheat Subgenomes.The Plant cell · 2019Article
- Genome wide identification and comparative analysis of glutathione transferases (GST) family genes in Brassica napus.Scientific reports · 2019Article
- Expression and regulatory asymmetry of retained Arabidopsis thaliana transcription factor genes derived from whole genome duplication.BMC evolutionary biology · 2019Article
- Spatio-temporal expression dynamics differ between homologues of flowering time genes in the allopolyploid Brassica napus.The Plant journal : for cell and molecular biology · 2018Article
- The effects of repeated whole genome duplication events on the evolution of cytokinin signaling pathway.BMC evolutionary biology · 2018Article
- Article
- Different Modes of Gene Duplication Show Divergent Evolutionary Patterns and Contribute Differently to the Expansion of Gene Families Involved in Important Fruit Traits in Pear (Frontiers in plant science · 2018Article
- Gene-body CG methylation and divergent expression of duplicate genes in rice.Scientific reports · 2017Article
- Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum.BMC genomics · 2017Article
- ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium.Nucleic acids research · 2017Article
- Evolution of Gene Duplication in Plants.Plant physiology · 2016Review
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole genome duplication (WGD) is widespread in flowering plants and is a driving force in angiosperm diversification. The redundancy introduced by WGD allows the evolution of novel gene interactions and functions, although the patterns and processes of diversification are poorly understood. We identified ∼ 2,000 pairs of paralogous genes in Gossypium raimondii (cotton) resulting from an approximately 60 My old 5- to 6-fold ploidy increase. Gene expression analyses revealed that, in G. raimondii, 99.4% of the gene pairs exhibit differential expression in at least one of the three tissues (petal, leaf, and seed), with 93% to 94% exhibiting differential expression on a per-tissue basis. For 1,666 (85%) pairs, differential expression was observed in all tissues. These observations were mirrored in a time series of G. raimondii seed, and separately in leaf, petal, and seed of G. arboreum, indicating expression level diversification before species divergence. A generalized linear model revealed 92.4% of the paralog pairs exhibited expression divergence, with most exhibiting significant gene and tissue interactions indicating complementary expression patterns in different tissues. These data indicate massive, near-complete expression level neo- and/or subfunctionalization among ancient gene duplicates, suggesting these processes are essential in their maintenance over ∼ 60 Ma.
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