{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T05:28:43Z","timestamp":1790659723717,"version":"4.1.0"},"reference-count":102,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2024,4,16]],"date-time":"2024-04-16T00:00:00Z","timestamp":1713225600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32170351"],"award-info":[{"award-number":["32170351"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"General Research Projects of Zhejiang Provincial Department of Education","award":["Y202351039"],"award-info":[{"award-number":["Y202351039"]}]},{"name":"Huzhou Science and Technology Plan Project","award":["2023GZ44"],"award-info":[{"award-number":["2023GZ44"]}]},{"name":"Research Program of Huzhou College","award":["2023HXKM09"],"award-info":[{"award-number":["2023HXKM09"]}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>Proteins containing domain of unknown function (DUF) are prevalent in eukaryotic genome. The DUF1216 proteins possess a conserved DUF1216 domain resembling to the mediator protein of Arabidopsis RNA polymerase II transcriptional subunit-like protein. The DUF1216 family are specifically existed in <jats:italic>Brassicaceae<\/jats:italic>, however, no comprehensive evolutionary analysis of <jats:italic>DUF1216<\/jats:italic> genes have been performed. We performed a first comprehensive genome-wide analysis of DUF1216 proteins in <jats:italic>Brassicaceae<\/jats:italic>. Totally 284 <jats:italic>DUF1216<\/jats:italic> genes were identified in 27 <jats:italic>Brassicaceae<\/jats:italic> species and classified into four subfamilies on the basis of phylogenetic analysis. The analysis of gene structure and conserved motifs revealed that <jats:italic>DUF1216<\/jats:italic> genes within the same subfamily exhibited similar intron\/exon patterns and motif composition. The majority members of <jats:italic>DUF1216<\/jats:italic> genes contain a signal peptide in the N-terminal, and the ninth position of the signal peptide in most DUF1216 is cysteine. Synteny analysis revealed that segmental duplication is a major mechanism for expanding of <jats:italic>DUF1216<\/jats:italic> genes in <jats:italic>Brassica oleracea<\/jats:italic>, <jats:italic>Brassica juncea<\/jats:italic>, <jats:italic>Brassica napus<\/jats:italic>, <jats:italic>Lepidium meyneii<\/jats:italic>, and <jats:italic>Brassica carinata<\/jats:italic>, while in <jats:italic>Arabidopsis thaliana<\/jats:italic> and <jats:italic>Capsella rubella<\/jats:italic>, tandem duplication plays a major role in the expansion of the <jats:italic>DUF1216<\/jats:italic> gene family. The analysis of Ka\/Ks (non-synonymous substitution rate\/synonymous substitution rate) ratios for <jats:italic>DUF1216<\/jats:italic> paralogous indicated that most of gene pairs underwent purifying selection. <jats:italic>DUF1216<\/jats:italic> genes displayed a specifically high expression in reproductive tissues in most <jats:italic>Brassicaceae<\/jats:italic> species, while its expression in <jats:italic>Brassica juncea<\/jats:italic> was specifically high in root. Our studies offered new insights into the phylogenetic relationships, gene structures and expressional patterns of <jats:italic>DUF1216<\/jats:italic> members in <jats:italic>Brassicaceae<\/jats:italic>, which provides a foundation for future functional analysis.<\/jats:p>","DOI":"10.1371\/journal.pone.0302292","type":"journal-article","created":{"date-parts":[[2024,4,16]],"date-time":"2024-04-16T18:18:50Z","timestamp":1713291530000},"page":"e0302292","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":14,"title":["Lineage-specific gene duplication and expansion of DUF1216 gene family in Brassicaceae"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2278-0119","authenticated-orcid":true,"given":"Zai-Bao","family":"Zhang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4332-5433","authenticated-orcid":true,"given":"Tao","family":"Xiong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao-Jia","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu-Rui","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing-Lei","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cong-Li","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zi-Yi","family":"Ye","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2024,4,16]]},"reference":[{"issue":"4","key":"pone.0302292.ref001","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1073\/pnas.1109047109","article-title":"Divergence 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