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Fig. 2 | Standards in Genomic Sciences

Fig. 2

From: Genome sequence of the model plant pathogen Pectobacterium carotovorum SCC1

Fig. 2

Maximum likelihood tree of Pectobacterium carotovorum SCC1 and other closely related Pectobacterium strains. The phylogenetic tree was constructed from the seven housekeeping genes (dnaN, fusA, gyrB, recA, rplB, rpoS and gyrA). The concatenated sequences were aligned using MAFFT multiple sequence alignment program (version 7) with default parameters [42]. The phylogenetic tree was built in RAxML (Randomized Axelerated Maximum Likelihood) program with Maximum likelihood (ML) inference [43]. 88 different nucleotide substitution models were tested with jModelTest 2.0 and the best model was selected using Akaike information criterion (AIC) [44]. Bootstrap values from 1000 replicates are shown in each branch. Dickeya solani IPO2222 was used as the outgroup. Type strains are marked with T after the strain name. GenBank accession numbers are presented in the parentheses. The scale bar indicates 0.04 substitutions per nucleotide position

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