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Daakour, S.* ; Nelson, D.R.* ; Fu, W.* ; Jaiswal, A.* ; Dohai, B.S.M. ; Alzahmi, A.S.* ; Koussa, J.* ; Huang, X.* ; Shen, Y.* ; Twizere, J.C.* ; Salehi-Ashtiani, K.*

Adaptive evolution signatures in Prochlorococcus: Open reading frame (ORF)eome resources and insights from comparative genomics.

Microorganisms 12:1720 (2024)
Publ. Version/Full Text DOI PMC
Open Access Gold
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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
Language english
Publication Year 2024
HGF-reported in Year 2024
ISSN (print) / ISBN 2076-2607
e-ISSN 2076-2607
Journal Microorganisms
Quellenangaben Volume: 12, Issue: 8, Pages: , Article Number: 1720 Supplement: ,
Publisher MDPI
Publishing Place Basel
Reviewing status Peer reviewed
Institute(s) Institute of Network Biology (INET)
POF-Topic(s) 30203 - Molecular Targets and Therapies
Research field(s) Environmental Sciences
PSP Element(s) G-506400-001
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
DOI 10.3390/microorganisms12081720
WOS ID 001306875300001
Scopus ID 85202620130
PubMed ID 39203562
Erfassungsdatum 2024-10-14
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