Phylogenomic analysis of chitinase

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).