{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T06:27:11Z","timestamp":1786602431666,"version":"build-2736575974"},"reference-count":76,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T00:00:00Z","timestamp":1786579200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"<jats:p>\n                    Urticaceae is an ecologically diverse family, yet comparative studies on plastome structure and codon usage remain limited. To investigate the structural evolution and codon usage patterns in Urticaceae, we sequenced the complete chloroplast genome of\n                    <jats:italic>Urtica cannabina<\/jats:italic>\n                    and performed comparative analyses of plastome structure, codon usage bias, simple sequence repeats (SSRs), selective pressure, and phylogenetic relationships using plastome sequences from 48 Urticaceae species. The\n                    <jats:italic>Urtica cannabina<\/jats:italic>\n                    plastome (147,958 bp) displays a canonical quadripartite architecture, encoding a total of 128 genes (83 protein-coding, 37 tRNAs, and 8 rRNAs). Comparative analysis revealed a pronounced A\/T bias (GC content: 36.56%), with a distinct decreasing GC gradient across codon positions (GC\n                    <jats:sub>1<\/jats:sub>\n                    &amp;gt; GC\n                    <jats:sub>2<\/jats:sub>\n                    &amp;gt; GC\n                    <jats:sub>3<\/jats:sub>\n                    ). Relative synonymous codon usage (RSCU) analysis indicated a preference for A\/U-ending codons, and the average effective number of codons (ENC) values ranged from 45.59 to 47.22, indicating generally weak codon bias. Parity rule 2 (PR2) analysis indicated a consistent preference for G and T at the third codon position in 48 Urticaceae chloroplast genomes, with highly conserved base usage across all species. Furthermore, a total of 3,552 SSRs were identified family-wide, with mononucleotide repeats (71.85%) predominating in intergenic regions. Ka\/Ks analysis indicated that 97.1% of protein-coding genes were under purifying selection (Ka\/Ks &amp;lt; 0.5). Phylogenetic analysis showed that\n                    <jats:italic>Hesperocnide tenella<\/jats:italic>\n                    is closely related to the genus\n                    <jats:italic>Urtica<\/jats:italic>\n                    . This study characterizes the structural features and codon usage patterns of chloroplast genomes in Urticaceae, providing new insights into their evolutionary dynamics and establishing a basis for investigating the interplay among genomic traits, codon bias, and adaptive evolution.\n                  <\/jats:p>","DOI":"10.3389\/fpls.2026.1846589","type":"journal-article","created":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T05:32:53Z","timestamp":1786599173000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Comparative chloroplast genomics reveals codon usage bias, simple sequence repeat dynamics, and phylogenomic relationships in Urticaceae"],"prefix":"10.3389","volume":"17","author":[{"given":"Fei","family":"Gao","sequence":"first","affiliation":[{"name":"School of Grassland Science, Beijing Forestry University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wendi","family":"Fan","sequence":"additional","affiliation":[{"name":"School of Grassland Science, Beijing Forestry University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zishuo","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Grassland Science, Beijing Forestry University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guy","family":"Smagghe","sequence":"additional","affiliation":[{"name":"Department of Biology, Vrije Universiteit Brussel (VUB)","place":["Brussels, Belgium"]},{"name":"Institute of Entomology, Guizhou University","place":["Guiyang, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aneela","family":"Riaz","sequence":"additional","affiliation":[{"name":"Institute of Pure and Applied Biology, Bahauddin Zakariya University","place":["Multan, Pakistan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Xue","sequence":"additional","affiliation":[{"name":"School of Grassland Science, Beijing Forestry University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dong","family":"Li","sequence":"additional","affiliation":[{"name":"School of Grassland Science, Beijing Forestry University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shushma","family":"Gosai","sequence":"additional","affiliation":[{"name":"College of Natural Resource Management, Agriculture and Forestry University","place":["Katari, Nepal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunpeng","family":"Gai","sequence":"additional","affiliation":[{"name":"School of Grassland Science, Beijing Forestry University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,8,13]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1007\/s00299-008-0507-z","article-title":"Advances in molecular marker techniques and their applications in plant sciences","volume":"27","author":"Agarwal","year":"2008","journal-title":"Plant Cell Rep."},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.3390\/genes14050976","article-title":"The first complete chloroplast genome of Cordia monoica: Structure and comparative analysis","volume":"14","author":"Alshegaihi","year":"2023","journal-title":"Genes"},{"key":"B3","doi-asserted-by":"publisher","first-page":"3030","DOI":"10.1093\/bioinformatics\/bty220","article-title":"IRscope: An online program to visualize the junction sites of chloroplast genomes","volume":"34","author":"Amiryousefi","year":"2018","journal-title":"Bioinformatics"},{"key":"B4","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1093\/sysbio\/syr041","article-title":"Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes","volume":"60","author":"Anisimova","year":"2011","journal-title":"Syst. 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