{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:28:41Z","timestamp":1792787321860,"version":"4.5.0"},"reference-count":58,"publisher":"Canadian Science Publishing","license":[{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/deed.en_GB"}],"funder":[{"name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","award":["313174\/2022-9"],"award-info":[{"award-number":["313174\/2022-9"]}],"id":[{"id":"https:\/\/ror.org\/03swz6y49","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","award":["2023\/03353-3"],"award-info":[{"award-number":["2023\/03353-3"]}],"id":[{"id":"https:\/\/ror.org\/02ddkpn78","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","award":["2024\/14461-4"],"award-info":[{"award-number":["2024\/14461-4"]}],"id":[{"id":"https:\/\/ror.org\/02ddkpn78","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","award":["2025\/05520-0"],"award-info":[{"award-number":["2025\/05520-0"]}],"id":[{"id":"https:\/\/ror.org\/02ddkpn78","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":["cdnsciencepub.com"],"crossmark-restriction":false},"short-container-title":["Genome"],"published-print":{"date-parts":[[2026,1,1]]},"abstract":"<jats:p>Biosynthetic gene clusters (BGCs) are important for plant specialized metabolism, but remain poorly characterized in coffee. Given Brazil\u2019s importance in coffee production, we performed a comparative genomic analysis of BGCs across the allotetraploid Coffea arabica and its diploid progenitors Coffea eugenioides and Coffea canephora. Using standardized genome filtering, annotation, orthogroup inference, and cluster classification, we identified 472 BGCs comprising 3118 biosynthetic genes, which were grouped into 194 cluster families and integrated with 28\u2009280 orthogroups. Of these, 7091 orthogroups were shared across all species; Coffea canephora and subgenomes shared 10\u2009923, while Coffea eugenioides and subgenomes shared 11\u2009446. Most BGC-associated orthogroups (86.4%) link to a single pathway class. BGC-associated genes form a highly structured yet lineage-dynamic component of the Coffea pangenome. Coffea eugenioides and its derived subgenomes in Arabica contributed disproportionately to 14 BGC-associated orthogroups, including flavonoid-, lipid-, and stress-related functions. In contrast, Coffea canephora derivatives contributed only two terpene-related orthogroups. The parental species showed fewer secondary metabolism-related enriched Gene Ontology terms (3 and 1) than their subgenomes (53 and 56). Species-specific rearrangements, expansions, and subgenome retention indicate that hybridization and polyploidy shaped BGC diversification. These results advance understanding of specialized metabolism in Coffea and identify targets for coffee improvement and climate resilience.<\/jats:p>","DOI":"10.1139\/gen-2026-0007","type":"journal-article","created":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T21:36:34Z","timestamp":1787088994000},"page":"1-15","update-policy":"https:\/\/doi.org\/10.1139\/csp-crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["<i>Coffea<\/i>\n                    comparative genomics reveals subgenome-associated expansion and diversification of biosynthetic gene clusters"],"prefix":"10.1139","volume":"69","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1932-2301","authenticated-orcid":false,"given":"Daisy Sotero","family":"Chacon","sequence":"first","affiliation":[{"name":"University of S\u00e3o Paulo","place":["Piracicaba, Brazil"]},{"name":"State University of Londrina (UEL)","place":["Londrina, Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura Natalia","family":"Gonzalez-Garcia","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Montpellier, CIRAD UMR DIADE","place":["Montpellier, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vitor","family":"Trinca","sequence":"additional","affiliation":[{"name":"S\u00e3o Paulo State University (UNESP)","place":["Jaboticabal, Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alessandro M.","family":"Varani","sequence":"additional","affiliation":[{"name":"S\u00e3o Paulo State University (UNESP)","place":["Jaboticabal, Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Romain","family":"Guyot","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Montpellier, CIRAD UMR DIADE","place":["Montpellier, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1290-0853","authenticated-orcid":false,"given":"Douglas Silva","family":"Domingues","sequence":"additional","affiliation":[{"name":"University of S\u00e3o Paulo","place":["Piracicaba, Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"155","reference":[{"key":"refg1\/ref1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-018-1536-8"},{"key":"refg2\/ref2","doi-asserted-by":"publisher","DOI":"10.3390\/molecules27165126"},{"key":"refg3\/ref3","doi-asserted-by":"publisher","DOI":"10.1038\/s41477-020-0733-0"},{"key":"refg4\/ref4","doi-asserted-by":"publisher","DOI":"10.1016\/j.molp.2024.02.003"},{"key":"refg5\/ref5","doi-asserted-by":"publisher","DOI":"10.1111\/ijfs.16261"},{"key":"refg6\/ref6","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2022.947558"},{"key":"refg7\/ref7","doi-asserted-by":"publisher","DOI":"10.1007\/s11103-013-0166-5"},{"key":"refg8\/ref8","doi-asserted-by":"publisher","DOI":"10.1016\/j.phytochem.2013.01.005"},{"key":"refg9\/ref9","doi-asserted-by":"publisher","DOI":"10.3390\/ijms24043266"},{"key":"refg10\/ref10","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1832-y"},{"key":"refg11\/ref11","doi-asserted-by":"publisher","DOI":"10.1104\/pp.114.243246"},{"key":"refg12\/ref12","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2014.00524"},{"key":"refg13\/ref13","doi-asserted-by":"publisher","DOI":"10.1093\/database\/baaa069"},{"key":"refg14\/ref14","doi-asserted-by":"publisher","DOI":"10.1016\/B978-0-443-13868-3.00035-1"},{"key":"refg15\/ref15","doi-asserted-by":"publisher","DOI":"10.1016\/j.molp.2021.06.028"},{"key":"refg16\/ref16","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-30653-w"},{"key":"refg17\/ref17","unstructured":"International Coffee Organization (ICO). 2023. Available from https:\/\/icocoffee.org\/documents\/cy2023-24\/Coffee_Report_and_Outlook_December_2023_ICO.pdf [accessed 25 July 2025]."},{"key":"refg18\/ref18","unstructured":"International Coffee Organization (ICO). 2025. Available from https:\/\/ico.org\/ [accessed 16 June 2025]."},{"key":"refg19\/ref19","doi-asserted-by":"publisher","DOI":"10.1126\/science.1240230"},{"key":"refg20\/ref20","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jafc.2c09087"},{"key":"refg21\/ref21","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu031"},{"key":"refg22\/ref22","doi-asserted-by":"publisher","DOI":"10.1007\/s10142-023-01095-z"},{"key":"refg23\/ref23","doi-asserted-by":"publisher","DOI":"10.1016\/j.pbi.2025.102729"},{"key":"refg24\/ref24","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2023.11.034"},{"key":"refg25\/ref25","doi-asserted-by":"publisher","DOI":"10.1016\/j.tibs.2016.01.007"},{"key":"refg26\/ref26","doi-asserted-by":"publisher","DOI":"10.1016\/j.molp.2023.01.004"},{"key":"refg27\/ref27","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2019.00893"},{"key":"refg28\/ref28","doi-asserted-by":"publisher","DOI":"10.1002\/fsn3.3848"},{"key":"refg29\/ref29","doi-asserted-by":"publisher","DOI":"10.1002\/cpz1.323"},{"key":"refg30\/ref30","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2229-11-85"},{"key":"refg31\/ref31","doi-asserted-by":"publisher","DOI":"10.1093\/g3journal\/jkae262"},{"key":"refg32\/ref32","doi-asserted-by":"publisher","DOI":"10.1155\/2012\/580857"},{"key":"refg33\/ref33","doi-asserted-by":"publisher","DOI":"10.1038\/s41589-019-0400-9"},{"key":"refg34\/ref34","doi-asserted-by":"publisher","DOI":"10.21203\/rs.3.rs-7032019\/v1"},{"key":"refg35\/ref35","doi-asserted-by":"publisher","DOI":"10.1590\/1413-70542018424000118"},{"key":"refg36\/ref36","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2123299119"},{"key":"refg37\/ref37","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2019.00835"},{"key":"refg38\/ref38","doi-asserted-by":"publisher","DOI":"10.1093\/plcell\/koae030"},{"key":"refg39\/ref39","doi-asserted-by":"publisher","DOI":"10.1111\/pce.13428"},{"key":"refg40\/ref40","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-024-01695-w"},{"key":"refg41\/ref41","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2022.868581"},{"key":"refg42\/ref42","doi-asserted-by":"publisher","DOI":"10.1007\/s00425-022-03898-z"},{"key":"refg43\/ref43","doi-asserted-by":"publisher","DOI":"10.3390\/molecules26247634"},{"key":"refg44\/ref44","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-44449-8"},{"key":"refg45\/ref45","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-024-00691-4"},{"key":"refg46\/ref46","doi-asserted-by":"publisher","DOI":"10.1016\/j.molp.2022.12.009"},{"key":"refg47\/ref47","doi-asserted-by":"publisher","DOI":"10.3390\/plants11070979"},{"key":"refg48\/ref48","doi-asserted-by":"publisher","DOI":"10.1039\/d2np00005a"},{"key":"refg49\/ref49","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-313X.2011.04685.x"},{"key":"refg50\/ref50","doi-asserted-by":"publisher","DOI":"10.1016\/j.cbpa.2024.102462"},{"key":"refg51\/ref51","doi-asserted-by":"publisher","DOI":"10.1126\/science.1220757"},{"key":"refg52\/ref52","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msag117"},{"key":"refg53\/ref53","doi-asserted-by":"publisher","DOI":"10.1016\/j.jfca.2024.106570"},{"key":"refg54\/ref54","doi-asserted-by":"publisher","DOI":"10.1111\/nph.19150"},{"key":"refg55\/ref55","doi-asserted-by":"publisher","DOI":"10.1080\/09168451.2014.987207"},{"key":"refg56\/ref56","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2022.1001206"},{"key":"refg57\/ref57","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2020.06.003"},{"key":"refg58\/ref58","doi-asserted-by":"publisher","DOI":"10.1093\/hr\/uhac017"}],"container-title":["Genome"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/cdnsciencepub.com\/doi\/full-xml\/10.1139\/gen-2026-0007","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/cdnsciencepub.com\/doi\/pdf\/10.1139\/gen-2026-0007","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T11:00:28Z","timestamp":1791370828000},"score":1,"resource":{"primary":{"URL":"https:\/\/cdnsciencepub.com\/doi\/10.1139\/gen-2026-0007"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,1]]},"references-count":58,"alternative-id":["10.1139\/gen-2026-0007"],"URL":"https:\/\/doi.org\/10.1139\/gen-2026-0007","relation":{},"ISSN":["0831-2796","1480-3321"],"issn-type":[{"value":"0831-2796","type":"print"},{"value":"1480-3321","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,1]]},"assertion":[{"value":"2026-10-07","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}