Data_Sheet_2_Toxic/Bioactive Peptide Synthesis Genes Rearranged by Insertion Sequence Elements Among the Bloom-Forming Cyanobacteria Planktothrix.docx

It has been generally hypothesized that mobile elements can induce genomic rearrangements and influence the distribution and functionality of toxic/bioactive peptide synthesis pathways in microbes. In this study, we performed in depth genomic analysis by completing the genomes of 13 phylogenetically diverse strains of the bloom-forming freshwater cyanobacteria Planktothrix spp. to investigate the role of insertion sequence (IS) elements in seven pathways. Chromosome size varied from 4.7–4.8 Mbp (phylogenetic Lineage 1 of P. agardhii/P. rubescens thriving in shallow waterbodies) to 5.4–5.6 Mbp (Lineage 2 of P. agardhii/P. rubescens thriving in deeper physically stratified lakes and reservoirs) and 6.3–6.6 Mbp (Lineage 3, P. pseudagardhii/P. tepida including planktic and benthic ecotypes). Although the variation in chromosome size was positively related to the proportion of IS elements (1.1–3.7% on chromosome), quantitatively, IS elements and other paralogs only had a minor share in chromosome size variation. Thus, the major part of genomic variation must have resulted from gene loss processes (ancestor of Lineages 1 and 2) and horizontal gene transfer (HGT). Six of seven peptide synthesis gene clusters were found located on the chromosome and occurred already in the ancestor of P. agardhii/P. rubescens, and became partly lost during evolution of Lineage 1. In general, no increased IS element frequency in the vicinity of peptide synthesis gene clusters was observed. We found a higher proportion of IS elements in ten breaking regions related to chromosomal rearrangements and a tendency for colocalization of toxic/bioactive peptide synthesis gene clusters on the chromosome.

学界普遍提出假说：可移动遗传元件（mobile elements）可诱发基因组重排，并影响微生物中毒性/生物活性肽合成通路的分布与功能。本研究针对13株系统发育多样的水华形成型淡水蓝细菌浮丝藻属（Planktothrix spp.）菌株完成基因组组装，开展深度基因组分析，以探究插入序列（insertion sequence, IS）在7条通路中的作用。该属菌株的染色体长度介于4.7~4.8 Mbp（对应栖息于浅水环境的水华浮丝藻/微红浮丝藻谱系1）、5.4~5.6 Mbp（对应栖息于深度物理分层湖泊与水库的水华浮丝藻/微红浮丝藻谱系2）以及6.3~6.6 Mbp（对应包含浮游与底栖生态型的假水华浮丝藻（P. pseudagardhii）/ tepida浮丝藻谱系3）。尽管染色体长度变异与插入序列占比（染色体上的1.1%~3.7%）呈正相关，但定量分析显示，插入序列与其他旁系同源基因仅对染色体长度变异贡献较小。因此，基因组变异的主要来源应为基因丢失事件（谱系1与谱系2的共同祖先）与水平基因转移（horizontal gene transfer, HGT）。7个肽合成基因簇中有6个定位于染色体上，且已存在于水华浮丝藻/微红浮丝藻的祖先基因组中，并在谱系1的演化过程中部分丢失。总体而言，未观察到肽合成基因簇附近存在插入序列频率升高的现象。本研究发现，在与染色体重排相关的10个断裂区域中，插入序列占比更高，且毒性/生物活性肽合成基因簇在染色体上存在共定位趋势。