{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T10:31:34Z","timestamp":1785407494562,"version":"3.56.0"},"reference-count":24,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2026,6,22]],"date-time":"2026-06-22T00:00:00Z","timestamp":1782086400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002383","name":"King Saud University","doi-asserted-by":"publisher","award":["ORF-2026-2043"],"award-info":[{"award-number":["ORF-2026-2043"]}],"id":[{"id":"10.13039\/501100002383","id-type":"DOI","asserted-by":"publisher"}]},{"award":["ORF-2026-2043"],"award-info":[{"award-number":["ORF-2026-2043"]}],"id":[{"id":"https:\/\/ror.org\/02f81g417","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Huanglongbing, a destructive citrus disease of global importance that is also present in Saudi Arabia, is associated with Candidatus Liberibacter asiaticus (CLas) and remains a major threat to citrus production. Although previous studies have documented sequence variation and prophage polymorphism in CLas, broader comparisons of prophage-associated gene content remain limited. In particular, comparative orthogroup analysis of prophage gene-content conservation across geographically structured CLas populations has rarely been explored. In this study, we analyzed 42 CLas prophage genomes from Saudi Arabia and other geographic regions using a comparative orthogroup framework. OrthoFinder assigned 99.1% of predicted proteins (1825 of 1841) to 64 orthogroups, with only 16 genes remaining unassigned. A small number of rare orthogroups restricted to only a few genomes were identified, and no orthogroup was detected in all genomes. Presence\u2013absence analyses supported a predominantly conserved prophage gene repertoire together with a small accessory component, while also indicating that apparent absences should be interpreted in light of mixed assembly status and prophage-region completeness. Saudi Arabian genomes were distributed within the broader global framework and exhibited generally similar gene-content profiles rather than a deeply separated lineage. Functional interpretation of representative orthogroups identified conserved prophage-associated genes related to replication, helicase activity, and phage packaging, whereas variable orthogroups were primarily associated with hypothetical or accessory prophage-related functions. Overall, these results are consistent with a model in which CLas prophage diversification is associated more with sequence-level variation and localized structural differences than with extensive gain or loss of prophage genes. These findings further refine current understanding of CLas genome evolution and highlight conserved prophage-associated targets that may support molecular diagnostics and epidemiological surveillance.<\/jats:p>","DOI":"10.3390\/ijms27125638","type":"journal-article","created":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T03:09:17Z","timestamp":1782270557000},"page":"5638","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Orthogroup-Based Comparative Analysis of Prophage Gene Content in Candidatus Liberibacter Asiaticus Supports a Predominantly Conserved Global Repertoire with Limited Accessory Variation"],"prefix":"10.3390","volume":"27","author":[{"given":"Abdullah F.","family":"Alhashel","sequence":"first","affiliation":[{"name":"Department of Plant Protection, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-3990-5380","authenticated-orcid":false,"given":"Ali A.","family":"Almasrahi","sequence":"additional","affiliation":[{"name":"Department of Plant Protection, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammed A.","family":"Alsaleh","sequence":"additional","affiliation":[{"name":"Department of Plant Protection, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2208-3794","authenticated-orcid":false,"given":"Arya","family":"Widyawan","sequence":"additional","affiliation":[{"name":"Department of Plant Protection, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2814-1537","authenticated-orcid":false,"given":"Mahmoud H.","family":"El-Komy","sequence":"additional","affiliation":[{"name":"Department of Plant Protection, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7184-7418","authenticated-orcid":false,"given":"Yasser E.","family":"Ibrahim","sequence":"additional","affiliation":[{"name":"Department of Plant Protection, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,22]]},"reference":[{"key":"ref_1","first-page":"7","article-title":"Huanglongbing: A destructive, newly emerging, century-old disease of citrus","volume":"88","year":"2006","journal-title":"J. Plant Pathol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1146\/annurev.py.29.090191.000545","article-title":"Citrus greening disease","volume":"29","year":"1991","journal-title":"Annu. Rev. 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