Phylogenomic analysis of chitinase
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Supplemental Information: Phylogenomic analysis of chitinase Picocyanobacterial sequences for genes involved in chitin degradation and peptidoglycan recycling pathways were found nested within branches of cyanobacterial genes, indicating vertical inheritance of peptidoglycan recycling. Picocyanobacterial sequences for chitinase (ChiA and ChiA-like) and N-acetylglucosamine kinase (NagK) were nested within non-cyanobacterial taxa, indicating Horizontal Gene Transfer (HGT) to picocyanobacteria after their divergence from other cyanobacteria. To contextualize the HGT of chitinase genes into ancestors of marine SynPro, we examined their phylogenetic relationships to similar sequences found within other bacteria. Picocyanobacterial chitinases contained two major chitin-binding domains that were homologous to different chitinase sequence variants found within other bacterial genomes. Gene sequence alignments suggest that the marine SynPro variant is likely the product of a fusion of two genes that were both acquired from Planctomycetes via Horizontal Gene Transfer (HGT). Methods Phylogenetic analysis Sequences were collected from the Genbank database for the following chitin degradation pathway proteins: The N-terminal region of ChiA/ChiA-like, the C-terminal region of ChiA/ChiA-like, UgpA, UgpE, NagZ, NagK, NagA, and NagB. Orthologs found within Prochlorococcus MIT1303 were used as protein search queries using BLASTP, with the top 500 or 250 hits recovered in each case. Each set of sequences were then aligned in MAFFT with the automatic algorithm selection option. Aligned sequences were then used for phylogenetic reconstruction using IQTree with automatic best-fitting model selection. All sequence alignment and phylogenetic data files are available in SI data (Data S1, SI Text 1 files), with alignment and tree filenames in each case describing the algorithms and parameters used for these reconstructions. Several BLAST hits for the ChiA and ChiA-like genes in SynPro overlapped, with some protein sequences containing multiple domains homologous to different chitinase orthologs in other bacteria. A phylogenomic analysis of our alignment data showed that the SynPro variant was likely the result of a fusion between genes from Planctomycetes, before or after horizontal gene transfer into SynPro (see SI Text 1 and SI Text 1 files for a detailed analysis of the protein fusion history).
补充信息：几丁质酶的系统发育基因组学分析 参与几丁质降解（chitin degradation）与肽聚糖（peptidoglycan）回收通路的微微型蓝细菌（Picocyanobacteria）基因序列，被鉴定为嵌套于蓝细菌基因的演化分支中，表明肽聚糖回收通路遵循垂直遗传模式。几丁质酶（chitinase，ChiA及ChiA同源蛋白）与N-乙酰葡糖胺激酶（N-acetylglucosamine kinase, NagK）的微微型蓝细菌基因序列，嵌套于非蓝细菌类群的演化分支中，这表明在微微型蓝细菌从其他蓝细菌分化之后，此类基因通过水平基因转移（Horizontal Gene Transfer, HGT）进入了微微型蓝细菌基因组。为阐明几丁质酶基因向海洋SynPro祖先的水平基因转移背景，我们分析了其与其他细菌中同源序列的系统发育关系。微微型蓝细菌的几丁质酶包含两个主要的几丁质结合结构域，其与其他细菌基因组中不同的几丁质酶序列变体具有同源性。基因序列比对结果显示，海洋SynPro的几丁质酶变体大概率是两个基因融合的产物，这两个基因均通过水平基因转移（HGT）从浮霉菌门（Planctomycetes）细菌中获取。 方法：系统发育分析 我们从GenBank数据库中获取了以下几丁质降解通路相关蛋白的序列：ChiA/ChiA同源蛋白的N端区域、ChiA/ChiA同源蛋白的C端区域、UgpA、UgpE、NagZ、NagK、NagA以及NagB。以原绿球藻MIT1303中的同源基因为蛋白搜索查询序列，使用BLASTP进行比对，每次检索均获取前500或250条匹配序列。随后，每组序列均使用MAFFT并启用自动算法选择选项进行多序列比对。比对完成的序列随后被用于IQTree进行系统发育重建，该工具会自动选择最优拟合模型。所有序列比对与系统发育数据文件均可在补充信息数据集（SI数据，包括Data S1、SI Text 1文件）中获取，比对文件与系统发育树文件的文件名均标注了本次重建所使用的算法与参数。SynPro中ChiA及ChiA同源基因的部分BLAST匹配结果存在重叠，部分蛋白序列包含多个与其他细菌中不同几丁质酶同源基因同源的结构域。对我们的比对数据进行的系统发育基因组学分析显示，SynPro的几丁质酶变体大概率是来自浮霉菌门的两个基因融合的产物，该融合事件可能发生在水平基因转移进入SynPro之前或之后（关于蛋白融合历史的详细分析，请参见SI Text 1与SI Text 1文件）。
