{"doi":"10.1186/1471-2164-14-652","title":"Different patterns of gene structure divergence following gene duplication in Arabidopsis","abstract":"<jats:title>Abstract</jats:title>\n          <jats:sec>\n            <jats:title>Background</jats:title>\n            <jats:p>Divergence in gene structure following gene duplication is not well understood. Gene duplication can occur via whole-genome duplication (WGD) and single-gene duplications including tandem, proximal and transposed duplications. Different modes of gene duplication may be associated with different types, levels, and patterns of structural divergence.</jats:p>\n          </jats:sec>\n          <jats:sec>\n            <jats:title>Results</jats:title>\n            <jats:p>In <jats:italic>Arabidopsis thaliana</jats:italic>, we denote levels of structural divergence between duplicated genes by differences in coding-region lengths and average exon lengths, and the number of insertions/deletions (indels) and maximum indel length in their protein sequence alignment. Among recent duplicates of different modes, transposed duplicates diverge most dramatically in gene structure. In transposed duplications, parental loci tend to have longer coding-regions and exons, and smaller numbers of indels and maximum indel lengths than transposed loci, reflecting biased structural changes in transposed duplications. Structural divergence increases with evolutionary time for WGDs, but not transposed duplications, possibly because of biased gene losses following transposed duplications. Structural divergence has heterogeneous relationships with nucleotide substitution rates, but is consistently positively correlated with gene expression divergence. The NBS-LRR gene family shows higher-than-average levels of structural divergence.</jats:p>\n          </jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions</jats:title>\n            <jats:p>Our study suggests that structural divergence between duplicated genes is greatly affected by the mechanisms of gene duplication and may be not proportional to evolutionary time, and that certain gene families are under selection on rapid evolution of gene structure.</jats:p>\n          </jats:sec>","journal":"BMC Genomics","year":2013,"id":589602,"datarank":3.4457102621140034,"base_score":4.6913478822291435,"endowment":4.6913478822291435,"self_citation_contribution":0.7037021823343717,"citation_network_contribution":2.742008079779632,"self_endowment_contribution":0.7037021823343717,"citer_contribution":2.742008079779632,"corpus_percentile":null,"corpus_rank":null,"citation_count":108,"citer_count":103,"citers_with_citation_signal":75,"citers_with_endowment":75,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":268514,"name":"Xu Tan","orcid":"0009-0007-6126-6549","position":1,"is_corresponding":false},{"id":207284,"name":"Andrew H Paterson","orcid":null,"position":2,"is_corresponding":false},{"id":218523,"name":"Yupeng Wang","orcid":"0000-0003-3061-0611","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Different patterns of gene structure divergence following gene duplication in Arabidopsis","abstract":"<jats:title>Abstract</jats:title>\n          <jats:sec>\n            <jats:title>Background</jats:title>\n            <jats:p>Divergence in gene structure following gene duplication is not well understood. Gene duplication can occur via whole-genome duplication (WGD) and single-gene duplications including tandem, proximal and transposed duplications. Different modes of gene duplication may be associated with different types, levels, and patterns of structural divergence.</jats:p>\n          </jats:sec>\n          <jats:sec>\n            <jats:title>Results</jats:title>\n            <jats:p>In <jats:italic>Arabidopsis thaliana</jats:italic>, we denote levels of structural divergence between duplicated genes by differences in coding-region lengths and average exon lengths, and the number of insertions/deletions (indels) and maximum indel length in their protein sequence alignment. Among recent duplicates of different modes, transposed duplicates diverge most dramatically in gene structure. In transposed duplications, parental loci tend to have longer coding-regions and exons, and smaller numbers of indels and maximum indel lengths than transposed loci, reflecting biased structural changes in transposed duplications. Structural divergence increases with evolutionary time for WGDs, but not transposed duplications, possibly because of biased gene losses following transposed duplications. Structural divergence has heterogeneous relationships with nucleotide substitution rates, but is consistently positively correlated with gene expression divergence. The NBS-LRR gene family shows higher-than-average levels of structural divergence.</jats:p>\n          </jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions</jats:title>\n            <jats:p>Our study suggests that structural divergence between duplicated genes is greatly affected by the mechanisms of gene duplication and may be not proportional to evolutionary time, and that certain gene families are under selection on rapid evolution of gene structure.</jats:p>\n          </jats:sec>","is_dataset_classified":null,"base_score":4.6913478822291435,"endowment":4.6913478822291435,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"24063813","pmcid":"PMC3848917","openalex_id":"https://openalex.org/W2150845008","authors":[],"funders":[{"funder_name":"National Science Foundation","grant_id":"1127017","title":"A Systems Approach to the Development and Function of C4 Photosynthesis"},{"funder_name":"National Science Foundation","grant_id":"0821096","title":"Arabidopsis 2010: Collaborative Research: Evolution of gene position and function in Arabidopsis using outgroup genomes"},{"funder_name":"National Science Foundation","grant_id":"0849896","title":"A Plant Genome Duplication Database"},{"funder_name":"National Science Foundation","grant_id":"1021718","title":"Adapting to a Duplicated Genome"}],"total_grants":4,"fwci":6.4259,"citation_percentile":0.96105669,"influential_citations":0,"citation_trend":[{"year":2014,"count":6},{"year":2015,"count":3},{"year":2016,"count":6},{"year":2017,"count":7},{"year":2018,"count":7},{"year":2019,"count":10},{"year":2020,"count":15},{"year":2021,"count":7},{"year":2022,"count":19},{"year":2023,"count":3},{"year":2024,"count":15},{"year":2025,"count":7},{"year":2026,"count":3}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/1471-2164-14-652","host_type":"journal"},{"url":"https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/1471-2164-14-652","host_type":"publisher"},{"url":"https://link.springer.com/content/pdf/10.1186/1471-2164-14-652.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1186/1471-2164-14-652","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/24063813","host_type":"repository"},{"url":"http://europepmc.org/articles/PMC3848917","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3848917","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC3848917","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC3848917?pdf=render","host_type":"Europe_PMC"},{"url":"https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-14-652","host_type":""},{"url":"http://dx.doi.org/10.1186/1471-2164-14-652","host_type":""},{"url":"https://dx.doi.org/10.1186/1471-2164-14-652","host_type":""}],"fields_of_study":["Plant Molecular Biology Research","Chromosomal and Genetic Variations","Genomic variations and chromosomal abnormalities","0301 basic medicine","0303 health sciences","03 medical and health sciences","Arabidopsis","Arabidopsis Proteins","DNA Transposable Elements","Gene Dosage","Gene Duplication","Gene Expression Regulation, Plant","Genes, Duplicate","Genes, Plant","Genetic Variation","Multigene Family","Nucleotides"],"mesh_terms":["DNA Transposable Elements","Multigene Family","Nucleotides","Genetic Variation","Genes, Plant","Arabidopsis","Gene Expression Regulation, Plant","Gene Dosage","Genes, Duplicate","Gene Duplication","Arabidopsis Proteins"],"keywords":["Gene duplication","Biology","Indel","Tandem exon duplication","Functional divergence","Gene","Segmental duplication","Genetics","Gene family","Gene dosage","Copy-number variation","Exon","Coding region","Genome","Gene expression","Single-nucleotide polymorphism","Genotype","Arabidopsis Proteins","Nucleotides","Arabidopsis","Genetic Variation","Genes, Plant","Gene Expression Regulation, Plant","Genes, Duplicate","Multigene Family","DNA Transposable Elements","Biotechnology","Research Article"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"geo"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-23T23:11:14.583264Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}