{"doi":"10.1073/pnas.0307827100","title":"Codon usage between genomes is constrained by genome-wide mutational processes","abstract":"<jats:p>Analysis of genome-wide codon bias shows that only two parameters effectively differentiate the genome-wide codon bias of 100 eubacterial and archaeal organisms. The first parameter correlates with genome GC content, and the second parameter correlates with context-dependent nucleotide bias. Both of these parameters may be calculated from intergenic sequences. Therefore, genome-wide codon bias in eubacteria and archaea may be predicted from intergenic sequences that are not translated. When these two parameters are calculated for genes from nonmammalian eukaryotic organisms, genes from the same organism again have similar values, and genome-wide codon bias may also be predicted from intergenic sequences. In mammals, genes from the same organism are similar only in the second parameter, because GC content varies widely among isochores. Our results suggest that, in general, genome-wide codon bias is determined primarily by mutational processes that act throughout the genome, and only secondarily by selective forces acting on translated sequences.</jats:p>","journal":"Proceedings of the National Academy of Sciences","year":2004,"id":40008,"datarank":12.11620893866012,"base_score":5.934894195619588,"endowment":5.934894195619588,"self_citation_contribution":0.8902341293429383,"citation_network_contribution":11.225974809317183,"self_endowment_contribution":0.8902341293429383,"citer_contribution":11.225974809317183,"corpus_percentile":null,"corpus_rank":null,"citation_count":377,"citer_count":200,"citers_with_citation_signal":200,"citers_with_endowment":200,"datacite_reuse_total":20,"is_dataset":false,"is_dataset_confidence":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":4491,"name":"William Lee","orcid":"0000-0002-0650-1442","position":1,"is_corresponding":false},{"id":195168,"name":"Alison K. Hottes","orcid":null,"position":2,"is_corresponding":false},{"id":195169,"name":"Lucy Shapiro","orcid":null,"position":3,"is_corresponding":false},{"id":195170,"name":"Harley H. McAdams","orcid":null,"position":4,"is_corresponding":false},{"id":195167,"name":"Swaine L. Chen","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":5.934894195619588,"endowment":5.934894195619588,"datacite_reuse_total":20,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"14990797","pmcid":"PMC373487","openalex_id":"https://openalex.org/W1967656821","authors":[],"funders":[{"funder_name":"NHGRI NIH HHS","grant_id":"HG00044","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"R01 GM051426","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"T32 GM007365","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"2T32GM07365","title":null},{"funder_name":"NHGRI NIH HHS","grant_id":"T32 HG000044","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"GM51426","title":null},{"funder_name":"NHGRI NIH HHS","grant_id":"K22 HG000044","title":null}],"total_grants":7,"fwci":5.0649,"citation_percentile":0.96202829,"influential_citations":7,"citation_trend":[{"year":2012,"count":15},{"year":2013,"count":14},{"year":2014,"count":13},{"year":2015,"count":15},{"year":2016,"count":25},{"year":2017,"count":28},{"year":2018,"count":21},{"year":2019,"count":24},{"year":2020,"count":18},{"year":2021,"count":25},{"year":2022,"count":15},{"year":2023,"count":18},{"year":2024,"count":19},{"year":2025,"count":18},{"year":2026,"count":2}],"oa_status":"green","license":null,"oa_locations":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/373487","host_type":"repository"},{"url":"https://europepmc.org/articles/pmc373487?pdf=render","host_type":"GREEN"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/373487","host_type":"repository"},{"url":"https://pnas.org/doi/pdf/10.1073/pnas.0307827100","host_type":"publisher"},{"url":"https://doi.org/10.1073/pnas.0307827100","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/14990797","host_type":"repository"}],"fields_of_study":["RNA and protein synthesis mechanisms","Genomics and Phylogenetic Studies","Bacterial Genetics and Biotechnology","Biology","Medicine","Animals","Archaea","Bacteria","Base Composition","Codon","DNA, Intergenic","Genome","Genome, Archaeal","Genome, Bacterial","Genomics","Mammals","Mutation","Protein Biosynthesis","RNA, Archaeal","RNA, Bacterial"],"mesh_terms":["Animals","Archaea","Bacteria","Base Composition","Codon","Mammals","Mutation","RNA, Bacterial","Protein Biosynthesis","Genome","Genome, Bacterial","RNA, Archaeal","Genome, Archaeal","DNA, Intergenic","Genomics"],"keywords":["Intergenic region","Codon usage bias","Genome","Biology","Genetics","GC-content","Gene","Bacterial genome size","Genome evolution","Context (archaeology)","Computational biology"],"sdg_mappings":[],"linked_datasets":[{"doi":"10.6084/m9.figshare.14385267.v1","title":"Additional file 1 of Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.14385267","title":"Additional file 1 of Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.14385270.v1","title":"Additional file 2 of Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.14385270","title":"Additional file 2 of Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.14385273.v1","title":"Additional file 3 of Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.14385273","title":"Additional file 3 of Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.14385276.v1","title":"Additional file 4 of Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.14385276","title":"Additional file 4 of Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.14385279.v1","title":"Additional file 5 of Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.14385279","title":"Additional file 5 of Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.14385282.v1","title":"Additional file 6 of Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.14385282","title":"Additional file 6 of Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.14385285.v1","title":"Additional file 7 of Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.14385285","title":"Additional file 7 of Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.25067233.v1","title":"Additional file 1 of Decoding the complete organelle genomic architecture of Stewartia gemmata: an early-diverging species in Theaceae","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.25067233","title":"Additional file 1 of Decoding the complete organelle genomic architecture of Stewartia gemmata: an early-diverging species in Theaceae","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.25067339","title":"Additional file 2 of Decoding the complete organelle genomic architecture of Stewartia gemmata: an early-diverging species in Theaceae","publisher":"figshare","resource_type":"Dataset"},{"doi":"10.6084/m9.figshare.25067339.v1","title":"Additional file 2 of Decoding the complete organelle genomic architecture of Stewartia gemmata: an early-diverging species in Theaceae","publisher":"figshare","resource_type":"Dataset"},{"doi":"10.6084/m9.figshare.21069380","title":"Additional file 1 of Newly reported chloroplast genome of Sinosenecio albonervius Y. Liu &amp; Q. E. Yang and comparative analyses with other Sinosenecio species","publisher":"figshare","resource_type":"Dataset"},{"doi":"10.6084/m9.figshare.21069380.v1","title":"Additional file 1 of Newly reported chloroplast genome of Sinosenecio albonervius Y. Liu &amp; Q. E. Yang and comparative analyses with other Sinosenecio species","publisher":"figshare","resource_type":"Dataset"}],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-06-12T00:20:46.044929Z","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":[]}