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Here, we present a comprehensive comparative genomic analysis of 53 reference genomes to elucidate the dynamics, functional diversity, and biosynthetic potential of this genus. Reference genomes representing each deposited species were selected in order to avoid bias associated with unequal numbers of genomes per species. Pangenome reconstruction revealed an open structure comprising a small core genome (1,350 gene families) and a large proportion of accessory and strain-specific genes, reflecting extensive genomic plasticity. Functional annotation indicated that accessory regions are enriched for genes involved in secondary metabolism, stress adaptation, and environmental resilience. Notably, biosynthetic gene cluster (BGC) mining uncovered a rich repertoire of potentially novel RiPPs and other secondary metabolite clusters, underscoring\n                    <jats:italic>Pseudoalteromonas<\/jats:italic>\n                    as a promising source of unexplored bioactive compounds. Statistical analyses revealed that pigmented strains harbor significantly higher numbers of BGCs compared to non-pigmented strains, while only a weak and non-significant correlation was observed between BGC abundance and carbohydrate-active enzyme (CAZyme) content. No significant effect of the isolation source was detected on either BGC or CAZyme distributions. Together, these findings provide new insights into the genomic basis of ecological adaptation and metabolic diversification in\n                    <jats:italic>Pseudoalteromonas<\/jats:italic>\n                    , supporting the role of pigmentation as a proxy for enhanced biosynthetic potential, while carbohydrate utilization capabilities evolve more independently and offering a framework for targeted bioprospecting of marine-derived metabolites with industrial and environmental applications.\n                  <\/jats:p>","DOI":"10.1007\/s10126-026-10674-7","type":"journal-article","created":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T08:22:21Z","timestamp":1784535741000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Pangenome Dynamics and Functional Diversification in the Marine Genus Pseudoalteromonas: Association to Colony Pigmentation"],"prefix":"10.1007","volume":"28","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-5184-2382","authenticated-orcid":false,"given":"J\u00e9ssica","family":"Scherer","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-0883-7230","authenticated-orcid":false,"given":"Renato Kulakowski","family":"Cor\u00e1","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8679-2448","authenticated-orcid":false,"given":"Diego","family":"Bonatto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8951-4029","authenticated-orcid":false,"given":"Alexandre Jos\u00e9","family":"Macedo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,20]]},"reference":[{"issue":"10","key":"10674_CR1","doi-asserted-by":"publisher","first-page":"2039","DOI":"10.1099\/mic.0.000147","volume":"161","author":"MA Ay\u00e9","year":"2015","unstructured":"Ay\u00e9 MA, Bonnin-Jusserand M, Brian-Jaisson F, Ortalo-Magn\u00e9 A, Culioli G, Koffi Nevry R, Rabah N, Blache Y, Molmeret M (2015) Modulation of violacein production and phenotypes associated with biofilm by exogenous quorum sensing N-acylhomoserine lactones in the marine bacterium Pseudoalteromonas ulvae TC14. 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