Cyanobacteria form harmful algal blooms and are highly adapted to a range of habitats, in part due to their phenotype plasticity. This plasticity is partially the result of co-existence of multiple strains within a single population. The toxic cyanobacterium Cylindrospermopsis raciborskii has remarkable phenotypic plasticity, strain variation and environmental adaptation resulting in an expansion of its global range. To understand the genetic basis of the high level of plasticity within a C. raciborskii population, the genomes of nine co-occurring strains were compared. The strains differed in morphology, toxin cell quotas and physiology, despite being obtained from a single water sample. Comparative genomics showed that three coiled strains were 3.9 Mbp in size, with 3544 ± 11 genes, while straight strains were 3.8 Mbp in size, with 3485 ± 20 genes. The core proteome comprised 86% of the genome and consisted of 2891 orthologous groups (OGs), whereas the variable genome comprised ∼14% (847 OGs), and the strain specific genome only ∼1% (433 OGs).There was a high proportion of variable strain-specific genes for the very closely related strains, which may underpin strain differentiation. The variable genes were associated with environmental responses and adaptation, particularly phage defence, DNA repair, membrane transport, and stress, illustrative of the adaptability of the strains in response to environmental and biological stressors. This study shows that high genomic variability exists between co-occurring strains and may be the basis of strain phenotypic differences and plasticity of populations. Therefore management and prediction of blooms of this harmful species requires different approaches to capture this strain variability.

蓝细菌形成有害的藻华，并高度适应各种生境，部分是由于它们具有表型可塑性。这种可塑性部分是单个种群内多种菌株共存的结果。有毒的蓝藻cylindrospermopsis raciborskii具有显着的表型可塑性，菌株变异和环境适应性，从而扩大了其全球范围。了解雷氏梭菌中高水平可塑性的遗传基础人口，比较了九个同时出现的菌株的基因组。尽管它们是从单个水样中获得的，但它们在形态，毒素细胞配额和生理上却有所不同。比较基因组学表明，三个卷曲菌株的大小为3.9 Mbp，具有3544±11个基因，而直链菌株的大小为3.8 Mbp，具有3485±20个基因。核心蛋白质组占基因组的86％，由2891个直系同源基团（OGs）组成，而可变基因组约占14％（847 OGs），而菌株特异性基因组仅约1％（433 OGs）。密切相关的菌株的可变菌株特异性基因的比例，这可能是菌株分化的基础。可变基因与环境响应和适应有关，特别是噬菌体防御，DNA修复，膜转运和应激，说明了菌株对环境和生物胁迫的适应性。这项研究表明，同时存在的菌株之间存在高度的基因组变异性，这可能是菌株表型差异和种群可塑性的基础。因此，管理和预测这种有害物种的花期需要不同的方法来捕获这种菌株的变异性。