Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria.
Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria.
复制标题
DOI：
10.3389/fmicb.2020.567431
复制
发表时间：
2020
影响因子：
5.2
通讯作者：
Garczarek L
中科院分区：
文献类型：
--
作者：
Doré H;Farrant GK;Guyet U;Haguait J;Humily F;Ratin M;Pitt FD;Ostrowski M;Six C;Brillet-Guéguen L;Hoebeke M;Bisch A;Le Corguillé G;Corre E;Labadie K;Aury JM;Wincker P;Choi DH;Noh JH;Eveillard D;Scanlan DJ;Partensky F;Garczarek L
原绿球藻属和聚球藻属的海洋picocyanobacteria是地球上最丰富的光合生物，生态学上的成功被认为与不同生态型到特定生态位的差异分配有关。然而，控制这些微生物多样化的潜在过程以及与生态位相关的表型特征的出现才刚刚开始被阐明。在这里，通过比较81个基因组，包括34个新的聚球菌，我们探索了形成picocyanobacteria基因组多样性的进化过程。核心蛋白树的时间校准显示，不同谱系之间的基因增益/丢失率出乎意料地低，例如，主要聚珠球菌谱系（亚簇5.1）每百万年获得5.6个基因（My），其中只有0.71个/My长期固定。基因含量比较揭示了许多与营养适应有关的候选基因，其中很大一部分位于基因组岛中，这些基因组岛在近亲或远亲菌株之间共享，如使用原始网络构建方法所确定的那样。有趣的是，在缺磷水域中共同出现的代表不同生态型的菌株（枝聚球菌III、WPC1和亚簇5.3）对这一限制表现出不同的适应策略。相比之下，在比较冷热型时，我们发现很少有基因可能参与温度适应。事实上，核心蛋白序列的比较突出了冷热型特异性变异，特别是涉及类胡萝卜素生物合成和氧化应激反应的变异，揭示了对热生态位的长期适应依赖于氨基酸取代而不是基因含量变化。总之，本研究不仅揭示了基因获得/损失和序列变异的各自作用，而且揭示了许多可能涉及海洋浮游植物两种关键成员生态位分配的候选基因。
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.
登录
查看更多内容
影响因子：
12.3
作者：
Dufresne, Alexis;Ostrowski, Martin;Scanlan, David J.;Garczarek, Laurence;Mazard, Sophie;Palenik, Brian P.;Paulsen, Ian T.;de Marsac, Nicole Tandeau;Wincker, Patrick;Dossat, Carole;Ferriera, Steve;Johnson, Justin;Post, Anton F.;Hess, Wolfgang R.;Partensky, Frederic
通讯作者：
Partensky, Frederic
影响因子：
2.7
作者：
Delmont TO;Eren AM
通讯作者：
Eren AM
影响因子：
64.8
作者：
Edwards, M;Richardson, AJ
通讯作者：
Richardson, AJ
影响因子：
4.4
作者：
Chen, F;Wang, K;Wommack, KE
通讯作者：
Wommack, KE
DOI：
10.1073/pnas.1521093113
发表时间：
2016-05-17
影响因子：
11.1
作者：
Doblin, Martina A.;van Sebille, Erik
通讯作者：
van Sebille, Erik