PuSH - Publikationsserver des Helmholtz Zentrums München

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)
Verlagsversion DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
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.
Altmetric
Weitere Metriken?
[➜Einloggen]
Zusatzinfos bearbeiten [➜Einloggen]
Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Korrespondenzautor
Schlagwörter 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
Zeitschrift Microorganisms
Quellenangaben Band: 12, Heft: 8, Seiten: , Artikelnummer: 1720 Supplement: ,
Verlag MDPI
Verlagsort Basel
Nichtpatentliteratur Publikationen
Begutachtungsstatus Peer reviewed
Institut(e) Institute of Network Biology (INET)
Förderungen 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