Journal: Frontiers in Cellular and Infection Microbiology
Article Title: Comparative Genomics of the Zoonotic Pathogen Ehrlichia chaffeensis Reveals Candidate Type IV Effectors and Putative Host Cell Targets
doi: 10.3389/fcimb.2016.00204
Figure Lengend Snippet: Comparative genomics of 8 Ehrlichia chaffeensis strains. (A) Phylogenetic tree of 8 E. chaffeensis strains. FastTree based on the Mauve alignment of the whole genomes of 8 E. chaffeensis strains. The node values indicate the local support values of the Shimodaira-Hasegawa test. The number outside the tree shows the genetic group of each strain, the West Paces strain was assigned to genetic group II due to the high level of conservation with the Heartland strain. (B) Alignments of 8 E. chaffeensis genomes generated using Mauve software (Darling et al., ) ( http://gel.ahabs.wisc.edu/mauve/ ). Locally collinear blocks (LCBs), shown as rounded rectangles, represent regions with no rearrangement of homologous sequences across genomes. The forward or reverse orientation of the LCBs is indicated by their position, respectively above or below the line. Lines between the genomes trace orthologous LCBs. Using default parameters resulting in a minimum LCB weight of 70, there are 7 LCBs across all the genomes. The LCB weight defines the minimum number of matching nucleotides in a collinear region for it to be considered homologous across genomes and not the result of a spurious match. Regions outside LCBs were too divergent in at least one genome to be aligned successfully. Inside each LCB, vertical bars represent the similarity profile of the genome sequence. The height of each bar corresponds to the average level of conservation in that region of the genome sequence. (C) Shared and specific gene content between 8 E. chaffeensis strains. Each colored petal represents a different E. chaffeensis genome. The number in the center of the diagram represents the number of orthologous genes shared by all the genomes, thus defining the E. chaffeensis core genome. The number inside each individual petal corresponds to the number of genes that are absent from the core genome, and the numbers in brackets correspond to the number of genes specific to this strain. The number outside each petal shows the genetic group of each strain.
Article Snippet: Complete genome sequences of E. chaffeensis strains were obtained from the National Center for Biotechnology Information (NCBI) database ( ftp://ftp.ncbi.nih.gov/genomes/Bacteria/ ).
Techniques: Generated, Software, Sequencing
