PubMed Health⌕ Search
Home/Archive/PubMed

PubMed · 10605109

Statistical methods for testing functional divergence after gene duplication.

X Gu
View original source ↗Export metadata ↓

Abstract

Functional innovations after gene duplication may result in altered functional constraints between member gene clusters of a gene family. This type (type I) of functional divergence is measured by the coefficient of functional divergence (theta lambda), which can be interpreted as the decrease in rate correlation between gene clusters, or the probability that the evolutionary rate at a site is statistically independent between two gene clusters. A simple stochastic model has been developed for estimating theta lambda and testing its statistical significance. The current model includes the model of rate variation among sites as a special case when theta lambda = 0. Moreover, we have developed a site-specific profile based on the hidden Markov model to identify critical amino acid residues that are responsible for these functional differences between two gene clusters, which may have great potential in functional genomics.

Explore related subjects

Gene DuplicationGenetic VariationModels, GeneticModels, StatisticalMultigene FamilyPhylogenyStochastic ProcessesJournal ArticleResearch Support, Non-U.S. Gov't

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

X Gu. 1999. Statistical methods for testing functional divergence after gene duplication.. https://doi.org/10.1093/oxfordjournals.molbev.a026080

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2025

Primulina pan-genome reveals differential gene retention following whole-genome duplications and provides insights into edaphic specialization.

Primulina, a genus of >200 species specialized to extreme soils, provides a model for edaphic adaptation. We assemble seven genomes and construct a pan-genome spanning nine species from karst, Danxia, and acidic soils. Comparative analyses reveal that karst-adapted species have smaller genomes. Two lineage-specific whole-genome duplications (WGDs) exhibit biased duplicate loss in large gene families but preferential retention of transcription factors, indicating combined adaptive and nonadaptive forces. Pan-genome analyses identify ion channel and transporter genes enriched in variant hotspots and under positive selection in karst lineages. Candidate genes for drought and salt stress tolerance include ABC transporters and ion channels. Notably, an ABC transporter shows positive selection in karst species and unique structural variation in non-karst species. Together, our findings show that genome downsizing, biased post-WGD retention, and evolution of ion-transport pathways shape adaptation to extreme soils. The Primulina pan-genome provides a resource for dissecting mechanisms underlying edaphic specialization.

Gene Duplication↗
PubMed2025

ERCnet: Phylogenomic Prediction of Interaction Networks in the Presence of Gene Duplication.

Assigning gene function from genome sequences is a rate-limiting step in molecular biology research. A protein's position within an interaction network can potentially provide insights into its molecular mechanisms. Phylogenetic analysis of evolutionary rate covariation (ERC) in protein sequence has been shown to be effective for large-scale prediction of functional relationships and interactions. However, gene duplication, gene loss, and other sources of phylogenetic incongruence are barriers for analyzing ERC on a genome-wide basis. Here, we developed ERCnet, a bioinformatic program designed to overcome these challenges, facilitating efficient all-versus-all ERC analyses for large protein sequence datasets. We simulated proteome datasets and found that ERCnet achieves combined false positive and negative error rates well below 10% and that our novel "branch-by-branch" length measurements outperforms "root-to-tip" approaches in most cases, offering a valuable new strategy for performing ERC. We also compiled a sample set of 35 angiosperm genomes to test the performance of ERCnet on empirical data, including its sensitivity to user-defined analysis parameters such as input dataset size and branch-length measurement strategy. We investigated the overlap between ERCnet runs with different species samples to understand how species number and composition affect predicted interactions and to identify the protein sets that consistently exhibit ERC across angiosperms. Our systematic exploration of the performance of ERCnet provides a roadmap for design of future ERC analyses to predict functional interactions in a wide array of genomic datasets. ERCnet code is freely available at https://github.com/EvanForsythe/ERCnet.

Gene Duplication↗
PubMed2025

Comprehensive identification and analysis of clusters of tandemly duplicated genes reveal their contributions to adaptive evolution of green plants.

Tandem gene duplication occurred more frequently compared with the episodic whole-genome duplication (WGD), providing a continuous supply of genetic material for evolutionary innovation and adaptation to changing environments. The rising roles of clusters of tandemly duplicated genes (CTDGs) in the evolution of phenotypic diversity have been unraveled in mammals. However, the content and biological roles of CTDGs remain largely unknown in plants. Here, we comprehensively identified CTDGs in 220 published plant genomes representing major lineages of green plants. The number of CTDGs showed great variation across taxa, ranging from 0 to 6028. The size of CTDGs varied from 2 to 47 genes, with small clusters containing two members predominating. Interestingly, significant expansion of CTDGs was found in early-diverging land plants and is closely associated with the evolution of key traits (e.g., ABA response, plant cuticle, UV-B resistance) required for plants to conquer terrestrial environments. Functional enrichment analysis revealed conserved and specialized functional profiles among different sizes of CTDGs in both Arabidopsis thaliana and the bryophyte Physcomitrium patens. Small CTDGs were enriched in fundamental stress responses, including protein modification, signal transduction, and responses to diverse stress stimuli, while large CTDGs were enriched in more sophisticated processes such as plant hormone biosynthesis and signaling, plant-microbe interactions, and reproductive processes. Expression pattern analyses of CTDGs under different stress conditions in A. thaliana and P. patens revealed that the highest number of CTDGs showed differential expression under drought stress, suggesting important roles of CTDGs in the evolution of desiccation tolerance in early land plants. The results of this study provide new additions to our knowledge about the abundance of CTDGs across green plants and reveal their important contributions to enable plants to overcome stressful environments on land.

Gene Duplication↗