ArticleGenome research2012
Positionally biased gene loss after whole genome duplication: evidence from human, yeast, and plant.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
27 citing papers in PubMed, 48 citations in OpenAlex.
- Phylogenomic synteny reveals paleohexaploid-derived genomic blocks across Asteraceae.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A Class of Allopolyploidy Showing High Duplicate Retention and Continued Homoeologous Exchanges.Genome biology and evolution · 2025Article
- Evolution and function of galectins inBBA advances · 2025Article
- Dosage sensitivity shapes balanced expression and gene longevity of homoeologs after whole-genome duplications in angiosperms.The Plant cell · 2024Article
- Comparative transcriptome analysis of persimmon somatic mutants (Frontiers in plant science · 2024Article
- Comparative Analysis Reveals Different Evolutionary Fates and Biological Functions in Wheat Duplicated Genes (Plants (Basel, Switzerland) · 2023Article
- Parallel evolution of amphioxus and vertebrate small-scale gene duplications.Genome biology · 2022Article
- Species Tree Estimation and the Impact of Gene Loss Following Whole-Genome Duplication.Systematic biology · 2022Article
- Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution.Nature communications · 2021Article
- The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible.Genome research · 2021Article
- Comparative analysis ofPeerJ · 2021Article
- Review
- The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization.Nature ecology & evolution · 2020Article
- Article
- Ancestry of the AUTS2 family-A novel group of polycomb-complex proteins involved in human neurological disease.PloS one · 2020Article
- The Evolution of Gene Duplicates in Angiosperms and the Impact of Protein-Protein Interactions and the Mechanism of Duplication.Genome biology and evolution · 2019Article
- Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants.Genome biology · 2019Article
- Rapid functional and evolutionary changes follow gene duplication in yeast.Proceedings. Biological sciences · 2017Article
- Evolution of Gene Duplication in Plants.Plant physiology · 2016Review
- Evolution by gene loss.Nature reviews. Genetics · 2016Review
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole genome duplication (WGD) has made a significant contribution to many eukaryotic genomes including yeast, plants, and vertebrates. Following WGD, some ohnologs (WGD paralogs) remain in the genome arranged in blocks of conserved gene order and content (paralogons). However, the most common outcome is loss of one of the ohnolog pair. It is unclear what factors, if any, govern gene loss from paralogons. Recent studies have reported physical clustering (genetic linkage) of functionally linked (interacting) genes in the human genome and propose a biological significance for the clustering of interacting genes such as coexpression or preservation of epistatic interactions. Here we conduct a novel test of a hypothesis that functionally linked genes in the same paralogon are preferentially retained in cis after WGD. We compare the number of protein-protein interactions (PPIs) between linked singletons within a paralogon (defined as cis-PPIs) with that of PPIs between singletons across paralogon pairs (defined as trans-PPIs). We find that paralogons in which the number of cis-PPIs is greater than that of trans-PPIs are significantly enriched in human and yeast. The trend is similar in plants, but it is difficult to assess statistical significance due to multiple, overlapping WGD events. Interestingly, human singletons participating in cis-PPIs tend to be classified into "response to stimulus." We uncover strong evidence of biased gene loss after WGD, which further supports the hypothesis of biologically significant gene clusters in eukaryotic genomes. These observations give us new insight for understanding the evolution of genome structure and of protein interaction networks.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.