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Adaptive evolution signatures in Prochlorococcus: Open reading frame (ORF)eome resources and insights from comparative genomics.
Microorganisms 12:1720 (2024)
Prochlorococcus, a cyanobacteria genus of the smallest and most abundant oceanic phototrophs, encompasses ecotype strains adapted to high-light (HL) and low-light (LL) niches. To elucidate the adaptive evolution of this genus, we analyzed 40 Prochlorococcus marinus ORFeomes, including two cornerstone strains, MED4 and NATL1A. Employing deep learning with robust statistical methods, we detected new protein family distributions in the strains and identified key genes differentiating the HL and LL strains. The HL strains harbor genes (ABC-2 transporters) related to stress resistance, such as DNA repair and RNA processing, while the LL strains exhibit unique chlorophyll adaptations (ion transport proteins, HEAT repeats). Additionally, we report the finding of variable, depth-dependent endogenous viral elements in the 40 strains. To generate biological resources to experimentally study the HL and LL adaptations, we constructed the ORFeomes of two representative strains, MED4 and NATL1A synthetically, covering 99% of the annotated protein-coding sequences of the two species, totaling 3976 cloned, sequence-verified open reading frames (ORFs). These comparative genomic analyses, paired with MED4 and NATL1A ORFeomes, will facilitate future genotype-to-phenotype mappings and the systems biology exploration of Prochlorococcus ecology.
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Publication type
Article: Journal article
Document type
Scientific Article
Keywords
Med4 ; Nalt1a ; Prochlorococcus ; Comparative Genomics ; Deep Learning ; Endogenous Viral Elements ; Light Adaptations; Climate-change; Lipoic Acid; Protein; Light; Gene; Synechococcus; Sequence; Family; Growth; Virus
ISSN (print) / ISBN
2076-2607
e-ISSN
2076-2607
Journal
Microorganisms
Quellenangaben
Volume: 12,
Issue: 8,
Article Number: 1720
Publisher
MDPI
Publishing Place
Basel
Non-patent literature
Publications
Reviewing status
Peer reviewed
Institute(s)
Institute of Network Biology (INET)
Grants
The "Maitre de Recherche" of the Fonds National de la recherche Scientifique (FRS-FNRS, Belgium)
NYUAD Center for Genomics and Systems Biology
NYUAD Faculty Research Funds
NYUAD Center for Genomics and Systems Biology
NYUAD Faculty Research Funds