Abstract Cyanobacteria were the first oxygenic photosynthersizers, evolving ∼3.5 bya, they have since radiated into one of the most diverse and widely distributed phyla of bacteria. Cyanobacterial diversification occurs through ecological adaptation, facilitated by asexual reproduction, homologous recombination and horizontal gene transfer, and selection pressures on ecotypes leading to speciation. Delimiting cyanobacterial species is, thus, fraught with difficulties and a clear taxonomy has not yet been universally accepted. This review discusses diversity and description of cyanobacteria: covering traditional and new methods to define species boundaries and concluding with a focus on the advances made through genomics. Examples from the genera Raphidiopsis, Microcystis, and Prochlorococcus are used throughout. Genome plasticity allows cyanobacteria to rapidly adapt and be resilient to environmental changes, illustrating the means of their persistence, and is an important aspect of their biology. Genomics has revealed generalist and specialist genome strategies, intraspecific diversity, and genome evolution in response to environmental stimuli. New taxonomic definitions will need to account for intraspecific genetic variation, with a species classification that is relevant to a species concept and scientific endeavors. Capturing intraspecific diversity with comparative genomics may provide a new path to species classification. This is demonstrated with two case studies; comparison of available genomes shows differing species delineation of Raphidiopsis and Microcystis. In both genera, species boundaries occur at ∼96% average nucleotide identity (ANI), where homologous recombination is constrained, but speciation of Raphidiopsis raciborskii, R. brookii, and R. curvata has occurred through geographic isolation, whereas available data on Microcystis contain at least 15 species, reflecting, to differing extents, different ecotypes, which may co-exist. Both case studies question the relative importance of species-specific versus habitat specific gene pools as drivers of inter- and intraspecific diversity.

中文翻译：

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定义蓝藻物种：通过基因组学的多样性和描述

摘要 蓝藻是第一个含氧光合作用者，进化了约 3.5 bya，从那时起，它们已经辐射到最多样化和分布最广泛的细菌门之一。蓝藻多样化是通过生态适应发生的，通过无性繁殖、同源重组和水平基因转移以及导致物种形成的生态型选择压力来促进。因此，界定蓝藻物种充满困难，明确的分类尚未被普遍接受。这篇综述讨论了蓝藻的多样性和描述：涵盖了定义物种边界的传统和新方法，并以通过基因组学取得的进步作为结论。来自 Raphidiopsis、Microcystis 和 Prochlorococcus 属的例子贯穿始终。基因组可塑性使蓝藻能够快速适应并适应环境变化，说明了它们的持久性，并且是它们生物学的一个重要方面。基因组学揭示了通才和专业基因组策略、种内多样性以及响应环境刺激的基因组进化。新的分类学定义需要考虑种内遗传变异，以及与物种概念和科学努力相关的物种分类。用比较基因组学捕获种内多样性可能为物种分类提供一条新途径。两个案例研究证明了这一点；可用基因组的比较显示 Raphidiopsis 和 Microcystis 的不同物种描述。在这两个属中，物种边界都出现在约 96% 的平均核苷酸同一性 (ANI) 处，在同源重组受到限制的情况下，Raphidiopsis raciborskii、R. brookii 和 R. curvata 的物种形成是通过地理隔离发生的，而微囊藻的可用数据至少包含 15 个物种，在不同程度上反映了不同的生态型，它们可能共同存在。这两个案例研究都质疑了物种特异性与栖息地特异性基因库作为种间和种内多样性驱动因素的相对重要性。