Strong Purifying Selection Is Associated with Genome Streamlining in Epipelagic Marinimicrobia
Strong Purifying Selection Is Associated with Genome Streamlining in Epipelagic Marinimicrobia
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强净化选择与上层海洋微囊虫基因组精简有关
DOI：
10.1093/gbe/evz201
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发表时间：
2019-10-01
影响因子：
3.3
通讯作者：
Aylward, Frank O.
中科院分区：
文献类型：
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作者：
Martinez-Gutierrez, Carolina Alejandra;Aylward, Frank O.
生活在营养物枯竭水域的海洋微生物数量众多，分布广泛，在全球生物地球化学循环中发挥着重要作用。许多这些微生物具有相似的基因组特征，包括小基因组大小、低/0 G + C含量、短基因间区和编码氨基酸残基侧链（N-ARSC）中低氮含量，但这些特征的进化驱动因素尚不清楚。在这里，我们通过估计保守标记基因的非同义替换和同义替换（dN/dS）的比例，比较了海洋微生物的净化选择强度。海洋微生物是一个候选门，包含了广泛的具有不同基因组特征的系统发育群。我们的分析表明，与中远洋微生物相比，表现出与基因组流线型相一致的特征的上层海洋微生物的dN/dS值显着降低。我们还发现中位dN/dS值与% G + C含量、N-ARSC和种间区长度呈正相关。我们没有发现dN/dS比率和估计的基因组大小之间有显著的相关性，这表明选择的强度不是影响该群体基因组大小的主要因素。我们的研究结果与基因组流线型理论基本一致，该理论认为，丰富的上浮游细菌的许多基因组特征是适应少营养营养条件的结果。我们的研究结果也与之前的研究结果一致，即基因组流线型在上层海洋中很常见，这表明生活在海洋这一区域的微生物是在这种环境的强烈选择和普遍的营养限制下形成的。
Marine microorganisms inhabiting nutrient-depleted waters play critical roles in global biogeochemical cycles due to their abundance and broad distribution. Many of these microbes share similar genomic features including small genome size, low /0 G + C content, short intergenic regions, and low nitrogen content in encoded amino acid residue side chains (N-ARSC), but the evolutionary drivers of these characteristics are unclear. Here, we compared the strength of purifying selection across the Marinimicrobia, a candidate phylum which encompasses a broad range of phylogenetic groups with disparate genomic features, by estimating the ratio of nonsynonymous and synonymous substitutions (dN/dS) in conserved marker genes. Our analysis reveals that epipelagic Marinimicrobia that exhibit features consistent with genome streamlining have significantly lower dN/dS values when compared with their mesopelagic counterparts. We also found a significant positive correlation between median dN/dS values and % G + C content, N-ARSC, and intergenic region length. We did not identify a significant correlation between dN/dS ratios and estimated genome size, suggesting the strength of selection is not a primary factor shaping genome size in this group. Our findings are generally consistent with genome streamlining theory, which postulates that many genomic features of abundant epipelagic bacteria are the result of adaptation to oligotrophic nutrient conditions. Our results are also in agreement with previous findings that genome streamlining is common in epipelagic waters, suggesting that microbes inhabiting this region of the ocean have been shaped by strong selection together with prevalent nutritional constraints characteristic of this environment.