Sarah, D.; Nelson, D. R.; Fu, W.; Jaiswal, A.; Dohai, B.; Alzahmi, A. S.; Koussa, J.; Huang, X.; Shen, Y.; Twizere, J.-C.; Salehi-Ashtiani, K. Adaptive Evolution Signatures in Prochlorococcus: ORFeome Resources and Insights from Comparative Genomics. Preprints2024, 2024051202. https://doi.org/10.20944/preprints202405.1202.v1
APA Style
Sarah, D., Nelson, D. R., Fu, W., Jaiswal, A., Dohai, B., Alzahmi, A. S., Koussa, J., Huang, X., Shen, Y., Twizere, J. C., & Salehi-Ashtiani, K. (2024). Adaptive Evolution Signatures in Prochlorococcus: ORFeome Resources and Insights from Comparative Genomics. Preprints. https://doi.org/10.20944/preprints202405.1202.v1
Chicago/Turabian Style
Sarah, D., Jean-Claude Twizere and Kourosh Salehi-Ashtiani. 2024 "Adaptive Evolution Signatures in Prochlorococcus: ORFeome Resources and Insights from Comparative Genomics" Preprints. https://doi.org/10.20944/preprints202405.1202.v1
Abstract
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 HL and LL strains. HL strains harbor genes (ABC-2 transporters) related to stress resistance, such as DNA repair and RNA processing, while LL strains exhibit unique chlorophyll adaptations (ion transport proteins, HEAT repeats). We report variable, depth-dependent endogenous viral elements in the 40 strains. We constructed the ORFeomes of MED4 and NATL1A covering 99 % of the annotated protein-coding sequences of the two species, totaling 3976 cloned, sequence-verified ORFs. These comparative genomics analyses, paired with MED4 and NATL1A ORFeomes, will facilitate future genotype-to-phenotype mappings and systems biology exploration of Prochlorococcus ecology.
Keywords
Prochlorococcus; comparative genomics; deep learning; artificial neural networks; ORFeomes
Subject
Biology and Life Sciences, Ecology, Evolution, Behavior and Systematics
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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