{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,12]],"date-time":"2026-07-12T05:07:14Z","timestamp":1783832834925,"version":"3.55.0"},"reference-count":45,"publisher":"MDPI AG","issue":"14","license":[{"start":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T00:00:00Z","timestamp":1783641600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100010203","name":"Agriculture Research System of China","doi-asserted-by":"crossref","award":["CARS-49"],"award-info":[{"award-number":["CARS-49"]}],"id":[{"id":"10.13039\/501100010203","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biology"],"abstract":"<jats:p>In this study, we constructed a comparative genomic framework encompassing 57 genome sequences from four key taxonomic groups\u2014Bacillariophyta, Parmales, choanoflagellates, and Bacillus\u2014all of which possess either siliceous cell walls or silicon-transporting vesicle structures. By comparing these genomes with those of non-silicified species, including Chlorophyta, Streptophytes, Rhodophyta, and Dinoflagellates, we systematically analyzed the evolutionary distribution patterns of genes involved in silicon transport, silicification, and related processes across eukaryotes. Through orthogroup clustering and phylogenetic analysis, we identified 75 orthogroups universally conserved across all 57 species (including representing siliceous and non-siliceous groups), and an additional 105 orthogroups consistently present across the four silica-bearing lineages (Bacillariophyta, Parmales, choanoflagellates, and Bacillus), which were predominantly enriched in fundamental metabolic pathways. Furthermore, by integrating 120 known siliceous cell wall-related protein sequences, we identified three orthogroups broadly distributed across the four major lineages, suggesting an ancient evolutionary origin of certain silicon-related genetic components. Our findings provide genomic insights into the evolutionary trajectory of siliceous cell wall-associated genes and offer a valuable resource for future studies on biomineralization in eukaryotes.<\/jats:p>","DOI":"10.3390\/biology15141127","type":"journal-article","created":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T13:16:28Z","timestamp":1783689388000},"page":"1127","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Comparative Genomic Analysis Uncovers the Evolutionary Basis of Siliceous Cell Wall Formation Across Diverse Lineages"],"prefix":"10.3390","volume":"15","author":[{"given":"Limin","family":"Jia","sequence":"first","affiliation":[{"name":"College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China"},{"name":"BGI-Qingdao, Qingdao 266555, China"},{"name":"College of Fisheries, Henan Normal University, Xinxiang 453007, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liangwei","family":"Li","sequence":"additional","affiliation":[{"name":"BGI-Qingdao, Qingdao 266555, China"},{"name":"BGI-Shenzhen, Shenzhen 518083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaolei","family":"Zhang","sequence":"additional","affiliation":[{"name":"BGI-Qingdao, Qingdao 266555, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiahao","family":"Wang","sequence":"additional","affiliation":[{"name":"BGI-Qingdao, Qingdao 266555, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zengbao","family":"Yuan","sequence":"additional","affiliation":[{"name":"College of Fisheries, Southwest University, Chongqing 400715, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guangyi","family":"Fan","sequence":"additional","affiliation":[{"name":"BGI-Qingdao, Qingdao 266555, China"},{"name":"BGI-Shenzhen, Shenzhen 518083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chengcheng","family":"Shi","sequence":"additional","affiliation":[{"name":"BGI-Qingdao, Qingdao 266555, China"},{"name":"BGI-Shenzhen, Shenzhen 518083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Man","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Fisheries, Henan Normal University, Xinxiang 453007, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1126\/science.1101156","article-title":"The Genome of the Diatom Thalassiosira pseudonana: Ecology, Evolution, and Metabolism","volume":"306","author":"Armbrust","year":"2004","journal-title":"Science"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1038\/nature07410","article-title":"The Phaeodactylum genome reveals the evolutionary history of diatom genomes","volume":"456","author":"Bowler","year":"2008","journal-title":"Nature"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"R278","DOI":"10.1016\/j.cub.2018.01.085","article-title":"Assembly, Functions and Evolution of Archaella, Flagella and Cilia","volume":"28","author":"Khan","year":"2018","journal-title":"Curr. 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