Data_Sheet_1_Insights Into the Evolution of Picocyanobacteria and Phycoerythrin Genes (mpeBA and cpeBA).docx

Marine picocyanobacteria, Prochlorococcus and Synechococcus, substantially contribute to marine primary production and have been the subject of extensive ecological and genomic studies. Little is known about their close relatives from freshwater and non-marine environments. Phylogenomic analyses (using 136 proteins) provide strong support for the monophyly of a clade of non-marine picocyanobacteria consisting of Cyanobium, Synechococcus and marine Sub-cluster 5.2; this clade itself is sister to marine Synechococcus and Prochlorococcus. The most basal lineage within the Syn/Pro clade, Sub-Cluster 5.3, includes marine and freshwater strains. Relaxed molecular clock (SSU, LSU) analyses show that while ancestors of the Syn/Pro clade date as far back as the end of the Pre-Cambrian, modern crown groups evolved during the Carboniferous and Triassic. Comparative genomic analyses reveal novel gene cluster arrangements involved in phycobilisome (PBS) metabolism in freshwater strains. Whilst PBS genes in marine Synechococcus are mostly found in one type of phycoerythrin (PE) rich gene cluster (Type III), strains from non-marine habitats, so far, appear to be more diverse both in terms of pigment content and gene arrangement, likely reflecting a wider range of habitats. Our phylogenetic analyses show that the PE genes (mpeBA) evolved via a duplication of the cpeBA genes in an ancestor of the marine and non-marine picocyanobacteria and of the symbiotic strains Synechococcus spongiarum. A ‘primitive’ Type III-like ancestor containing cpeBA and mpeBA had thus evolved prior to the divergence of the Syn/Pro clade and S. spongiarum. During the diversification of Synechococcus lineages, losses of mpeBA genes may explain the emergence of pigment cluster Types I, II, IIB, and III in both marine and non-marine habitats, with few lateral gene transfer events in specific taxa.

海洋超微蓝细菌（marine picocyanobacteria）原绿球藻（Prochlorococcus）与聚球藻（Synechococcus）对海洋初级生产力贡献卓著，同时也是生态学与基因组学领域被广泛研究的对象。目前学界对其淡水及非海洋生境下的近缘类群却了解甚少。基于136种蛋白的系统基因组学分析（phylogenomic analyses），为包含蓝细菌属（Cyanobium）、聚球藻以及海洋亚簇5.2（Sub-cluster 5.2）的非海洋超微蓝细菌演化支（clade）的单系性（monophyly）提供了强有力的支持；该演化支本身与海洋聚球藻和原绿球藻构成姊妹演化支。聚球藻-原绿球藻演化支（Syn/Pro clade）内最基部的谱系为亚簇5.3（Sub-Cluster 5.3），其涵盖了海洋与淡水菌株。基于小亚基核糖体RNA（SSU）与大亚基核糖体RNA（LSU）的松弛分子钟（relaxed molecular clock）分析显示，尽管聚球藻-原绿球藻演化支的祖先可追溯至前寒武纪（Pre-Cambrian）末期，但现代冠群类群是在石炭纪（Carboniferous）与三叠纪（Triassic）时期演化而来的。比较基因组分析揭示了淡水菌株中参与藻胆体（phycobilisome, PBS）代谢的新型基因簇排布模式。海洋聚球藻中的藻胆体基因多存在于单一的富藻红蛋白（phycoerythrin, PE）基因簇（类型III）中，而非海洋生境的菌株目前来看在色素组成与基因排布上均更为多样，这或许反映了其更广泛的生境适应性。本研究的系统发育分析表明，藻红蛋白基因（mpeBA）是通过在海洋与非海洋超微蓝细菌以及共生菌株海绵共生聚球藻（Synechococcus spongiarum）的祖先体内复制cpeBA基因演化而来的。由此可见，携带cpeBA与mpeBA的“原始”类III型祖先，早在聚球藻-原绿球藻演化支与海绵共生聚球藻发生分化之前就已经出现。在聚球藻谱系的多样化过程中，mpeBA基因的丢失或许可以解释海洋与非海洋生境中色素簇类型I、II、IIB以及III的出现，仅在特定类群中存在少量水平基因转移（lateral gene transfer）事件。