Comparative genomics in human parasite flatworms: Ehinococuccus granulosus s.s. (G1 genotype) and Echinococcus canadensis (G7 genotype)

LUCAS MALDONADO; JULIANA ASSIS; FLÁVIO GOMES ARAÚJO; NATALIA MACCHIAROLI; MARCELA CUCHER; MARA ROSENZVIT; GUILHERME OLIVEIRA; LAURA KAMENETZKY

Conferencia; V Argentinian Conference on Bioinformatics and Computational Biology; 2014

BACKGROUND: Echinococcus canadensis is a platyhelminth parasite which keeps close phylogenetic relationship with Echinococcus granulosus and Echinococcus multilocularis, members of the class Cestoda that are involved in hydatid infections of humans and animals. In South America three species of Echinococcus sensu lato have been reported E. granulosus sensu stricto (G1 and G2 genotypes), E. canadensis (G6 and G7 genotypes) and E. ortleppi (G5 genotype) (Kamenetzky and Cucher, 2014). Only limited genetic information of E. canadensis G7 was reported so far. In this work we have sequenced the genome of this species. METHODS:High quality genomic DNA has been extracted and two paired-end libraries have been sequenced by Illumina technology. Several pipelines of assembly have been evaluated. The genome has been de novo assembled with Velvet using different parameters until the best assembly was obtained. Also, reads have been mapped over E. multilocularis reference genome (Tsai et al., 2013) with BWA. Genes have been annotated by CEGMA and MAKER softwares with flatworm data for gene model training. RESULTS: Comparative studies have revealed high levels of nucleotidic identity of E. canadensis G7 with E. multilocularis as well as with E. granulosus s. s. G1. Almost all contigs have a correlation in E. multilocularis genome (Figure 1). Interestingly, the procedure for in silico annotation employed in this work allowed to identify 86% (387/450) of highly conserved genes (Table 1). Figure 1: Percentage of each E. multilocularis chromosome covered by E. canadensis contigs. Chromosome 10 is an already unassembled scaffolds of E. multilocularis Table 1: Number of predicted conserved genes in E. canadensis genome and chromosome localization using E. multilocularis as reference genome. A total of 385 out of 450 conserved genes were found. Localization in E. multilocularis # of genes Chromosome 1 95 Chromosome 2 56 Chromosome 3 59 Chromosome 4 60 Chromosome 5 41 Chromosome 6 16 Chromosome 7 24 Chromosome 8 24 Chromosome 9 7 Chromosome 10* 5 Chromosome 11* 0 Total 387 *already unasssembled scaffolds of E. multilocularis reference genome CONCLUSIONS: This is the first report of E. canadensis G7 genome. It was obtained by high throughput sequencing, allowing a broad genome view of this particular species that shows important biological and epidemiological features. The knowledge of this new genome would provide information for comparative genomics allowing adapting prevention and diagnosis tools to each epidemiological situation. REFERENCES: Kamenetzky Laura y Cucher Marcela, Hidatidosis: genotipos de Echinococcus granulosus presentes en Artgentina y el mundo. Capitulo 43, pags 411-421, Libro Temas de Zoonosis VI, 2014, 500 páginas totales, Editorial: Asociacion Argentina de Zoonosis, ISBN 978-987-97038-5-4 Tsai IJ et al. The genomes of four tapeworm species reveal adaptations to parasitism.Nature. 2013; 496(7443):57-63