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Additional file 4: Table S3. Synthetic nucleic acid sequences used in this work.

Additional file 3: Figure S1. Detailed presentation of the cladogram shown in Figure 1. Information of the accession number, domain architecture and origin of each sequence is provided, as explained for Fig. 1.

Additional file 5: Figure S2. Chromatographic analysis of compounds used as standards: xylose (peak 1) and xylooligosaccharides, xylobiose to xylohexaose (peaks 2 to 6).

In this work we report a detailed analysis of the topology and phylogenetics of family 2 glycoside hydrolases (GH2). We distinguish five topologies or domain architectures based on the presence and distribution of protein domains defined in Pfam and Interpro databases. All of them share a central TIM barrel (catalytic module) with two β-sandwich domains (non-catalytic) at the N-terminal end, but differ in the occurrence and nature of additional non-catalytic modules at the C-terminal region. Phylogenetic analysis was based on the sequence of the Pfam Glyco_hydro_2_C catalytic module present in most GH2 proteins. Our results led us to propose a model in which evolutionary diversity of GH2 enzymes is driven by the addition of different non-catalytic domains at the C-terminal region. This model accounts for the divergence of β-galactosidases from β-glucuronidases, the diversification of β-galactosidases with different transglycosylation specificities, and the emergence of bicistronic β-galactosidases. This study also allows the identification of groups of functionally uncharacterized protein sequences with potential biotechnological interest.

Additional file 2: Table S2. Phylogenetic analysis of the GH11 domain. The figure was generated as described for Figure 1 but including tags for each sequence that shown the accession number and the domain architecture. Sequences tagged with “E” or “A” at the end of the domain architecture correspond to xylanases from eukaryotic organisms or archaea organisms respectively. The meaning of Ct1, Ct2 and Ct3 tags is detailed is the manuscript.

Additional file 2: Table S2. Phylogenetic analysis of the GH11 domain. The figure was generated as described for Figure 1 but including tags for each sequence that shown the accession number and the domain architecture. Sequences tagged with “E” or “A” at the end of the domain architecture correspond to xylanases from eukaryotic organisms or archaea organisms respectively. The meaning of Ct1, Ct2 and Ct3 tags is detailed is the manuscript.