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. 2023 Jul 15;16(9):1745–1754. doi: 10.1111/1751-7915.14320

FIGURE 1.

FIGURE 1

Phylogenomic analysis of Lactococcus species. Unrooted supertree of the Lactococcus genus. Phylogenomic analysis was performed based on nucleotide alignments of 478 single‐copy orthologues identified between Lactococcus‐type strains and the outgroup Bacillus subtilis (green). Orthologous and single‐copy genes were obtained using OrthoFinder (Emms & Kelly, 2019) and the amino acid sequence of the strain of interest obtained from the NCBI RefSeq database. Multiple sequence alignment of protein sequences in each single‐copy orthogroup was conducted using MUSCLE v.3.8.31 (Edgar, 2004), followed by alignment refinement using Gblocks (Talavera & Castresana, 2007) and the construction of a maximum likelihood phylogenetic tree using PhyML v3.0 (Guindon et al., 2010), followed by concatenation of the tree. A final consensus tree was computed using the Consense module from Phylip package v3.69 (http://evolution.genetics.washington.edu/phylip.html) using the majority rule method. The webserver iTOL was used for tree visualisation (https://itol.embl.de/). A list of computed single‐copy orthologues is provided in Table S1.