ArticleThe Plant cell2012
Pericentromeric effects shape the patterns of divergence, retention, and expression of duplicated genes in the paleopolyploid soybean.
Article in The Plant cell, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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55 citing papers in PubMed, 122 citations in OpenAlex.
- Recurrent sex chromosome turnover mediated by distinct ARR17 and PISTILLATA duplications in willows.Genome biology · 2026Article
- Molecular polymorphisms that underlie trait variation in crops: Lessons learned from soybean.The plant genome · 2026Review
- From duplication to divergence: Single-cell insights into transcriptional and cis-regulatory landscapes in soybean.The Plant cell · 2025Article
- Global identification and characterization of soybean TPR genes with expression analysis under photoperiod variations.Scientific reports · 2025Article
- Genome-Wide Analysis ofInternational journal of molecular sciences · 2025Article
- Comprehensive genome-wide analysis of the GmFRIGIDA gene family in soybean: identification, characterization, and expression dynamics.Frontiers in plant science · 2025Article
- Noncanonical transcription initiation is primarily tissue specific and epigenetically tuned in paleopolyploid plants.The Plant cell · 2024Article
- Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce.GigaScience · 2024Article
- Comparative Analysis Reveals Different Evolutionary Fates and Biological Functions in Wheat Duplicated Genes (Plants (Basel, Switzerland) · 2023Article
- Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet.Nature communications · 2023Article
- Polyploidy and diploidization in soybean.Molecular breeding : new strategies in plant improvement · 2023Article
- Conserved noncoding sequences and de novo Mutator insertion alleles are imprinted in maize.Plant physiology · 2023Article
- The evolutionary patterns, expression profiles, and genetic diversity of expanded genes in barley.Frontiers in plant science · 2023Article
- The genome sequence of Hirschfeldia incana, a new Brassicaceae model to improve photosynthetic light-use efficiency.The Plant journal : for cell and molecular biology · 2022Article
- The Heterogeneity in the Landscape of Gene Dominance in Maize is Accompanied by Unique Chromatin Environments.Molecular biology and evolution · 2022Article
- The multiple fates of gene duplications: Deletion, hypofunctionalization, subfunctionalization, neofunctionalization, dosage balance constraints, and neutral variation.The Plant cell · 2022Article
- Genomic insights into positive selection during barley domestication.BMC plant biology · 2022Article
- Progress in soybean functional genomics over the past decade.Plant biotechnology journal · 2022Review
- The CCCH zinc finger family of soybean (Glycine max L.): genome-wide identification, expression, domestication, GWAS and haplotype analysis.BMC genomics · 2021Article
- Altered chromatin architecture and gene expression during polyploidization and domestication of soybean.The Plant cell · 2021Article
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Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The evolutionary forces that govern the divergence and retention of duplicated genes in polyploids are poorly understood. In this study, we first investigated the rates of nonsynonymous substitution (Ka) and the rates of synonymous substitution (Ks) for a nearly complete set of genes in the paleopolyploid soybean (Glycine max) by comparing the orthologs between soybean and its progenitor species Glycine soja and then compared the patterns of gene divergence and expression between pericentromeric regions and chromosomal arms in different gene categories. Our results reveal strong associations between duplication status and Ka and gene expression levels and overall low Ks and low levels of gene expression in pericentromeric regions. It is theorized that deleterious mutations can easily accumulate in recombination-suppressed regions, because of Hill-Robertson effects. Intriguingly, the genes in pericentromeric regions-the cold spots for meiotic recombination in soybean-showed significantly lower Ka and higher levels of expression than their homoeologs in chromosomal arms. This asymmetric evolution of two members of individual whole genome duplication (WGD)-derived gene pairs, echoing the biased accumulation of singletons in pericentromeric regions, suggests that distinct genomic features between the two distinct chromatin types are important determinants shaping the patterns of divergence and retention of WGD-derived genes.
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