Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria

Frontiers in Microbiology

Jae Hoon Noh¹  Damien Eveillard²  Laurence Garczarek²  Antoine Bisch³  Erwan Corre³  Mark Hoebeke³  Gildas Le Corguillé³  Karine Labadie⁴  Jean-Marc Aury⁴  Patrick Wincker⁵  Julie Haguait⁶  Dong Han Choi⁸  David J. Scanlan⁹  Martin Ostrowski⁹  Frances D. Pitt⁹  Florian Humily^1,10  Frédéric Partensky^1,10  Gregory K. Farrant^1,10  Morgane Ratin^1,10  Hugo Doré^1,10  Ulysse Guyet^1,10  Christophe Six^1,10  Loraine Brillet-Guéguen^1,11 

[1] 0Department of Marine Biology, Korea University of Science and Technology, Daejeon, South Korea;1Research Federation (FR2022) Tara Océans GO-SEE, Paris, France;CNRS, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), Roscoff, France;Genoscope, Institut de Biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Évry, France;Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université d’Evry, Université Paris-Saclay, Évry, France;LS2N, UMR CNRS 6004, IMT Atlantique, ECN, Université de Nantes, Nantes, France;Marine Ecosystem Research Center, Korea Institute of Ocean Science and Technology, Busan, South Korea;Ocean Science and Technology School, Korea Maritime and Ocean University, Busan, South Korea;School of Life Sciences, University of Warwick, Coventry, United Kingdom;Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France;Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France;

关键词: marine cyanobacteria;    Prochlorococcus;    Synechococcus;    comparative genomics;    niche adaptation;    amino-acid substitutions;   

DOI  :  10.3389/fmicb.2020.567431

来源: DOAJ

【 摘 要 】

Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus are the most abundant photosynthetic organisms on Earth, an ecological success thought to be linked to the differential partitioning of distinct ecotypes into specific ecological niches. However, the underlying processes that governed the diversification of these microorganisms and the appearance of niche-related phenotypic traits are just starting to be elucidated. Here, by comparing 81 genomes, including 34 new Synechococcus, we explored the evolutionary processes that shaped the genomic diversity of picocyanobacteria. Time-calibration of a core-protein tree showed that gene gain/loss occurred at an unexpectedly low rate between the different lineages, with for instance 5.6 genes gained per million years (My) for the major Synechococcus lineage (sub-cluster 5.1), among which only 0.71/My have been fixed in the long term. Gene content comparisons revealed a number of candidates involved in nutrient adaptation, a large proportion of which are located in genomic islands shared between either closely or more distantly related strains, as identified using an original network construction approach. Interestingly, strains representative of the different ecotypes co-occurring in phosphorus-depleted waters (Synechococcus clades III, WPC1, and sub-cluster 5.3) were shown to display different adaptation strategies to this limitation. In contrast, we found few genes potentially involved in adaptation to temperature when comparing cold and warm thermotypes. Indeed, comparison of core protein sequences highlighted variants specific to cold thermotypes, notably involved in carotenoid biosynthesis and the oxidative stress response, revealing that long-term adaptation to thermal niches relies on amino acid substitutions rather than on gene content variation. Altogether, this study not only deciphers the respective roles of gene gains/losses and sequence variation but also uncovers numerous gene candidates likely involved in niche partitioning of two key members of the marine phytoplankton.

【 授权许可】

Unknown