Fig. 7
From: Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes
Phylogenetic analysis and characterization of vertically transmitted rice seed endophytes. a Maximum likelihood phylogeny of 21 isolates of Pantoea with 20 type strains based on the concatenated multiple alignment of the 1258 single-copy orthologous genes. Shimodaira-Hasegawa test support values (percentage of 1000 replications) greater than 75% were indicated at branching nodes. Selected biosynthetic, secretion system-related and catabolic genes or gene clusters were predicted using the genome sequences of the Pantoea isolates. b Maximum likelihood phylogeny of 27 isolates of Xanthomonas with 22 type strains based on the concatenated multiple alignment of the 892 single-copy orthologous genes. Selected biosynthetic, secretion system-related, and catabolic genes or gene clusters were predicted using the genome sequences of the Xanthomonas isolates. SM, secondary metabolites; PSS, protein secretion systems; ENZ, digestive enzymes. Dark green and brown boxes represent the presence and absence of a gene or gene cluster within a genome, respectively. The bootstrap values greater than 80 are not displayed