Additional file 10: of The Echinococcus canadensis (G7) genome: a key knowledge of parasitic platyhelminth human diseases
Creators: name: Maldonado, Lucas
name: Assis, Juliana
name: Araújo, Flávio
name: Salim, Anna
name: Macchiaroli, Natalia
name: Cucher, Marcela
name: Camicia, Federico
name: Fox, Adolfo
name: Rosenzvit, Mara
name: Oliveira, Guilherme
name: Kamenetzky, Laura
Publisher: name: Figshare
Year: 2017
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Global phylogeny of Echinococcus and model species. (A) Phylogeny reconstruction from complete Echinococcus mitochondrial genomes. Nucleotide sequences of 12 protein-coding genes were aligned according to Nakao et al. [53]. Phylogenetic analysis was performed using the Maximum Likelihood method based on the JTT matrix-based model. Bootstrap consensus tree was inferred from 100 replicates. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. Mitochondrial genomes used for Echinococcus species phylogeny reconstruction: E. oligarthrus, NC_009461, Nakao et al., [108]; E. vogeli, NC_009462, Nakao et al., [108]; E. equinus, AB786665, Nakao et al., [53]; E. granulosus, AB786664, Nakao et al., [53]; E. felidis, AB732958, Nakao et al., [53]; E. multilocularis, NC_000928, Nakao et al., [109]; E. shiquicus, NC_009460, Nakao et al., [108]; E. ortleppi, NC_011122, Nakao et al., [108]; E. canadensis (G6), NC_011121, Nakao et al., [108]; E. canadensis (G7), AB235847, Nakao et al., [108]; E. canadensis (G7), PRJEB8992, this work; E. canadensis (G8), AB235848, Nakao et al., [108]; E. canadensis (G10), AB745463, Nakao et al., [53]. (B) Proteins encoded by single-copygenes were analysed using the Maximum Likelihood method based on the JTT matrix-based model. The analysis involved 14 amino acid sequences from 29 single-copy genes. There were a total of 7001 positions in the final dataset. (C) Single-copy coding DNA sequences (CDS). The analysis involved 14 nucleotide sequences from 29 single-copy genes using the Maximum Likelihood method based on the Tamura-Nei model. There were a total of 14,364 positions in the final dataset. All of the positions with less than 60% site coverage were eliminated. Evolutionary analyses were conducted in MEGA5. Hsap: Homo sapiens; Mmus: Mus musculus; Drer: Danio rerio; Bflo: Branchiostoma floridae; Dmel: Drosophila melanogaster; Cele: Caenorhabditis elegans; ECANG7: Echinococcus canadensis; Egra: Echinococcus granulosus; Emul: Echinococcus multilocularis; Gsal: Gyrodactylus salaris; Hmic: Hymenolepis microstoma; Sman: Schistosoma mansoni; Smed: Schimdtea mediterranea; TsM1: Taenia solium. (D) Venn diagram of shared loci between the different Echinococcus species. (i) The number of total SNPs in each species using E. canadensis (G7) genome as reference. (ii) The number of total SNPs in each species using E. multilocularis genome as reference. (iii) The number of total SNPs in each species using E. granulosus (G1) genome as reference. The numbers under each species name indicate the number of SNPs in the species against the corresponding reference genome. The numbers in the overlap region indicate the number of SNPs with the same polymorphism at the same locus between the species. (PDF 530 kb)