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Evolutionary mechanisms of long-term genome diversification associated with niche partitioning in marine picocyanobacteria
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(2020) Evolutionary mechanisms of long-term genome diversification associated with niche partitioning in marine picocyanobacteria. Frontiers in Microbiology, 11 . 567431. doi:10.3389/fmicb.2020.567431 ISSN 1664-302X.
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Official URL: https://doi.org/10.3389/fmicb.2020.567431
Abstract
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.
| Item Type: | Journal Article | |||||||||||||||
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| Subjects: | Q Science > QH Natural history > QH301 Biology Q Science > QH Natural history > QH426 Genetics Q Science > QR Microbiology |
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| Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | |||||||||||||||
| SWORD Depositor: | Library Publications Router | |||||||||||||||
| Library of Congress Subject Headings (LCSH): | Cyanobacteria -- Evolution, Comparative genomics, Adaptation (Physiology) | |||||||||||||||
| Journal or Publication Title: | Frontiers in Microbiology | |||||||||||||||
| Publisher: | Frontiers Media S.A. | |||||||||||||||
| ISSN: | 1664-302X | |||||||||||||||
| Official Date: | 15 September 2020 | |||||||||||||||
| Dates: |
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| Volume: | 11 | |||||||||||||||
| Article Number: | 567431 | |||||||||||||||
| DOI: | 10.3389/fmicb.2020.567431 | |||||||||||||||
| Status: | Peer Reviewed | |||||||||||||||
| Publication Status: | Published | |||||||||||||||
| Reuse Statement (publisher, data, author rights): | ** From Frontiers via Jisc Publications Router ** History: collection 2020; received 29-05-2020; accepted 12-08-2020; epub 15-09-2020. ** Licence for this article: http://creativecommons.org/licenses/by/4.0/ | |||||||||||||||
| Access rights to Published version: | Open Access (Creative Commons) | |||||||||||||||
| Date of first compliant deposit: | 2 October 2020 | |||||||||||||||
| Date of first compliant Open Access: | 6 October 2020 | |||||||||||||||
| RIOXX Funder/Project Grant: |
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