{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T14:17:25Z","timestamp":1783520245955,"version":"3.55.0"},"reference-count":94,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T00:00:00Z","timestamp":1783468800000},"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:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>\n                      <jats:italic>Rhodiola juparensis<\/jats:italic>\n                      , a cushion plant, plays a critical role in sustaining the fragile ecological environment of the Qinghai\u2011Tibet Plateau. Understanding its adaptive evolution is essential, yet the organelle genomic architecture and evolutionary dynamics of this species remain poorly characterized.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      We sequenced and assembled the chloroplast (plastome) and mitochondrial (mitogenome) genomes of\n                      <jats:italic>R. juparensis<\/jats:italic>\n                      . Comprehensive comparative analyses were performed on organellar genome structure, RNA editing events, and positively selected genes. Divergence time estimation and genome\u2011wide positive selection scans were conducted using phylogenetic and bioinformatic approaches.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>The plastome exhibited a more conserved structure but a faster nucleotide substitution rate, whereas the mitogenome showed greater structural complexity but a slower substitution rate. Divergence time estimation suggested that rapid differentiation of Crassulaceae species occurred around 7.15 Mya, likely linked to decreasing atmospheric CO\u2082 levels and the dramatic uplift of the Qinghai\u2011Tibet Plateau during the Late Miocene. Positive selection analysis identified three candidate genes (matR, ccmFc, and ATP8) under positive selection. Additionally, numerous pentatricopeptide repeat (PPR) proteins were detected in the nuclear genome.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>\n                      The contrasting evolutionary patterns between the two organellar genomes highlight distinct selective constraints and mutation rates. The identified positively selected genes may contribute to mitochondrial function and stress adaptation. The abundance of nuclear\u2011encoded PPR proteins suggests a potential repair mechanism via RNA editing that could mitigate UV\u2011induced DNA damage, offering an adaptive advantage in the high\u2011altitude environment. Collectively, these findings provide valuable insights into the adaptive evolution of\n                      <jats:italic>R. juparensis<\/jats:italic>\n                      and the evolutionary history of Crassulaceae on the Qinghai\u2011Tibet Plateau.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fpls.2026.1881546","type":"journal-article","created":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T13:25:43Z","timestamp":1783517143000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Structural divergence and molecular adaptation of Rhodiola juparensis organelle genomes"],"prefix":"10.3389","volume":"17","author":[{"given":"Guocui","family":"Deng","sequence":"first","affiliation":[{"name":"College of Life Science and Technology, Xinjiang University, and Xinjiang Key Laboratory of Biological Resources and Genetic Engineering","place":["\u00dcr\u00fcmqi, China"]},{"name":"State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University","place":["Wuhan, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yebing","family":"Yin","sequence":"additional","affiliation":[{"name":"School of Ecology and Environment, Tibet University","place":["Lhasa, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaili","family":"Duan","sequence":"additional","affiliation":[{"name":"College of Life Science and Technology, Xinjiang University, and Xinjiang Key Laboratory of Biological Resources and Genetic Engineering","place":["\u00dcr\u00fcmqi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junze","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Ecology and Environment, Tibet University","place":["Lhasa, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Niyang","family":"Xiang","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Regional Development and Environmental Response, School of Resources and Environmental Science, Hubei University","place":["Wuhan, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Yuan","sequence":"additional","affiliation":[{"name":"College of Life Science and Technology, Xinjiang University, and Xinjiang Key Laboratory of Biological Resources and Genetic Engineering","place":["\u00dcr\u00fcmqi, China"]},{"name":"State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University","place":["Wuhan, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,7,8]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"2289","DOI":"10.1093\/oxfordjournals.molbev.a003775","article-title":"Mitochondrial gene transfer in pieces: fission of the ribosomal protein gene rpl2 and partial or complete gene transfer to the nucleus","volume":"18","author":"Adams","year":"2001","journal-title":"Mol. 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