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However, limited organellar genomic data for the Ishigeales, presently confined to\n                    <jats:italic>Ishige okamurae<\/jats:italic>\n                    , have hindered a comprehensive understanding of organelle genome dynamics in that order. To address this, we de novo assembled the complete plastomes and mitogenomes of the four Ishigeales species:\n                    <jats:italic>Pilinia rimosa<\/jats:italic>\n                    ,\n                    <jats:italic>Petroderma maculiforme<\/jats:italic>\n                    ,\n                    <jats:italic>I.\u00a0okamurae<\/jats:italic>\n                    , and\n                    <jats:italic>I. foliacea<\/jats:italic>\n                    . Phylogenetic analyses based on plastome and mitogenome datasets using both concatenation and coalescent\u2010based approaches supported the divergence order from the less complex filamentous morphology of\n                    <jats:italic>Pi. rimosa<\/jats:italic>\n                    to the more morphologically complex terete and foliose\n                    <jats:italic>Ishige<\/jats:italic>\n                    species, yet it also revealed a phylogenetic conflict at the branching point of\n                    <jats:italic>Pe. maculiforme<\/jats:italic>\n                    , suggesting an intricate evolutionary history in filamentous species. Both plastomes and mitogenomes exhibited extensive genomic rearrangement. Notably, mitochondrial genome expansion was observed in\n                    <jats:italic>Pi. rimosa<\/jats:italic>\n                    and\n                    <jats:italic>Pe. maculiforme<\/jats:italic>\n                    , and massive\n                    <jats:italic>cox<\/jats:italic>\n                    2 gene duplication was found in\n                    <jats:italic>Pi. rimosa<\/jats:italic>\n                    . These expansions were likely driven by the proliferation of tandem repeats, and most copies are likely under relaxed purifying selection. Analysis of synonymous substitution rate to the nonsynonymous substitution rate revealed the rapid divergence in several plastid genes between\n                    <jats:italic>I. okamurae<\/jats:italic>\n                    and\n                    <jats:italic>I. foliacea<\/jats:italic>\n                    . In particular, the DPOR gene family exhibited a signal of relaxed purifying selection, potentially linked to their distinct morphological changes in\n                    <jats:italic>Ishige<\/jats:italic>\n                    species. Overall, our findings reveal that Ishigeales underwent lineage\u2010specific differentiation and dynamic evolutionary patterns in the organelle genomes along with morphological variation.\n                  <\/jats:p>","DOI":"10.1111\/jpy.70180","type":"journal-article","created":{"date-parts":[[2026,5,26]],"date-time":"2026-05-26T12:58:03Z","timestamp":1779800283000},"page":"1090-1107","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Organelle genome evolution in the early\u2010diverging brown algal lineage, Ishigeales"],"prefix":"10.1111","volume":"62","author":[{"given":"Hayeon","family":"Hwang","sequence":"first","affiliation":[{"name":"Department of Biological Sciences Sungkyunkwan University  Suwon Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hocheol","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences Sungkyunkwan University  Suwon Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seok\u2010Wan","family":"Choi","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences Sungkyunkwan University  Suwon Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hiroshi","family":"Kawai","sequence":"additional","affiliation":[{"name":"Kobe University Research Center for Inland Seas  Kobe Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9507-0105","authenticated-orcid":false,"given":"Hwan Su","family":"Yoon","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences Sungkyunkwan University  Suwon 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