{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T03:58:29Z","timestamp":1788494309273,"version":"build-2803163510"},"reference-count":55,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,1,29]],"date-time":"2026-01-29T00:00:00Z","timestamp":1769644800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"<jats:p>\n                    The chloroplast genome serves as a valuable tool for plant phylogenetic studies due to its conserved structure and slow evolutionary rate. Despite the economic importance of the genus\n                    <jats:italic>Citrus<\/jats:italic>\n                    , comprehensive comparative analyses of chloroplast genomes across multiple species remain limited. As one of the ancestors of\n                    <jats:italic>Citrus<\/jats:italic>\n                    ,\n                    <jats:italic>Citrus medica L<\/jats:italic>\n                    . serves as a key representative in studies of the origin and evolution of the genus. In this study, we conducted a comprehensive comparative analysis of chloroplast genomes from 35 Citrus species and their close relatives, with\n                    <jats:italic>C. medica<\/jats:italic>\n                    as a focal species, to investigate structural variation, codon usage patterns, and phylogenetic relationships. All genomes exhibited a typical quadripartite structure, ranging from 159 to 161 kb with GC contents of 38.41-38.49%. While genome synteny was highly conserved, expansions and contractions at IR boundaries provided species-specific variation. SSR analysis revealed abundant mononucleotide repeats with a strong AT bias, predominantly distributed in non-coding regions. Codon usage analysis indicated a preference for A\/U-ending codons, and ENC-GC3s, neutrality plot, and PR2 analyses suggested that natural selection was the main force shaping codon usage bias. Most protein-coding genes were under strong purifying selection, whereas\n                    <jats:italic>matK<\/jats:italic>\n                    and\n                    <jats:italic>rps16<\/jats:italic>\n                    exhibited elevated Ka\/Ks ratios, suggesting relaxed selective constraints or potential signals of positive selection. Phylogenomic analysis strongly supported the monophyly of\n                    <jats:italic>Citrus<\/jats:italic>\n                    and resolved intrageneric relationships, grouping species into distinct ancestral and cultivated clades. Overall, this study provides essential chloroplast genomic resources for molecular breeding, species identification, and understanding\n                    <jats:italic>Citrus<\/jats:italic>\n                    adaptation.\n                  <\/jats:p>","DOI":"10.3389\/fpls.2026.1769665","type":"journal-article","created":{"date-parts":[[2026,1,29]],"date-time":"2026-01-29T06:39:38Z","timestamp":1769668778000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["Integrative chloroplast omics in citrus: computational insights into genomic structural adaptation and phylogenetic relationships from 35 species"],"prefix":"10.3389","volume":"17","author":[{"given":"Su","family":"Lin","sequence":"first","affiliation":[{"name":"Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agricultural and Forestry (A&F) University","place":["Hangzhou, Zhejiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinfang","family":"Shu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agricultural and Forestry (A&F) University","place":["Hangzhou, Zhejiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chengnan","family":"Kang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agricultural and Forestry (A&F) University","place":["Hangzhou, Zhejiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenxin","family":"Fang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agricultural and Forestry (A&F) University","place":["Hangzhou, Zhejiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xingxing","family":"Liang","sequence":"additional","affiliation":[{"name":"School of Grassland Science, Beijing Forestry University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kai","family":"Xu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agricultural and Forestry (A&F) University","place":["Hangzhou, Zhejiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haijie","family":"Ma","sequence":"additional","affiliation":[{"name":"Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agricultural and Forestry (A&F) University","place":["Hangzhou, Zhejiang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,1,29]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1007\/BF01900449","article-title":"The photosynthetic energy conversion process in isolated chloroplasts","volume":"22","author":"Arnon","year":"1966","journal-title":"Experientia"},{"key":"B2","doi-asserted-by":"publisher","first-page":"e2691","DOI":"10.7717\/peerj.2691","article-title":"Factors influencing infection and transmission of Anopheles Gambiae densovirus (AgDNV) in mosquitoes","volume":"4","author":"Barik","year":"2016","journal-title":"PeerJ"},{"key":"B3","doi-asserted-by":"publisher","first-page":"1519","DOI":"10.1007\/s00122-006-0255-9","article-title":"Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs)","volume":"112","author":"Barkley","year":"2006","journal-title":"Theor. 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