Fig. 3: Phylogenetic tree of the 4,4′-diapophytoene desaturase (crtN) gene detected in Lactobacillaceae, which shows clustering into two clades. | Communications Biology

Fig. 3: Phylogenetic tree of the 4,4′-diapophytoene desaturase (crtN) gene detected in Lactobacillaceae, which shows clustering into two clades.

From: Distribution of C30 carotenoid biosynthesis genes suggests habitat adaptation function in insect-adapted and nomadic Lactobacillaceae

Fig. 3

The tree was inferred with IQtree via the LG + F + G4 method. To reduce the number of branches, sequences were first clustered with cd-hit with a 95% similarity threshold. When a cluster contained multiple species, the species were clustered into multi-species horizontal gene transfer (HGT) groups, as shown in a table for clarity. The numbers indicate the number of strains that collapsed for each cluster. For each tip, the biosynthetic cluster is also shown as predicted by Bigscape using one representative.

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