title: Draft Genome ofToxocara canis, a Pathogen Responsible for Visceral Larva Migrans.
abstract: This study aimed at constructing a draft genome of the adult female wormToxocara canisusing next-generation sequencing (NGS) and de novo assembly, as well as to find new genes after annotation using functional genomics tools. Using an NGS machine, we produced DNA read data ofT. canis. The de novo assembly of the read data was performed using SOAPdenovo. RNA read data were assembled using Trinity. Structural annotation, homology search, functional annotation, classification of protein domains, and KEGG pathway analysis were carried out. Besides them, recently developed tools such as MAKER, PASA, Evidence Modeler, and Blast2GO were used. The scaffold DNA was obtained, the N50 was 108,950 bp, and the overall length was 341,776,187 bp. The N50 of the transcriptome was 940 bp, and its length was 53,046,952 bp. The GC content of the entire genome was 39.3%. The total number of genes was 20,178, and the total number of protein sequences was 22,358. Of the 22,358 protein sequences, 4,992 were newly observed inT. canis. Following proteins previously unknown were found: E3 ubiquitin-protein ligase cbl-b and antigen T-cell receptor, zeta chain for T-cell and B-cell regulation; endoprotease bli-4 for cuticle metabolism; mucin 12Ea and polymorphic mucin variant C6/1/40r2.1 for mucin production; tropomodulin-family protein and ryanodine receptor calcium release channels for muscle movement. We were able to find new hypothetical polypeptides sequences unique toT. canis, and the findings of this study are capable of serving as a basis for extending our biological understanding ofT. canis.
authors.affiliation: Department of Computer Engineering, College of Engineering, Hallym University, Chuncheon 24252, Korea.|Smart Computing Lab., Hallym University, Chuncheon 24252, Korea.
authors.forename: Jinhwa
authors.initials: J
authors.lastname: Kong
authors.affiliation: Smart Computing Lab., Hallym University, Chuncheon 24252, Korea.
authors.forename: Jungim
authors.initials: J
authors.lastname: Won
authors.affiliation: Department of Computer Engineering, College of Engineering, Hallym University, Chuncheon 24252, Korea.
authors.forename: Jeehee
authors.initials: J
authors.lastname: Yoon
authors.affiliation: Department of Electronic Engineering, College of Engineering, Hallym University, Chuncheon 24252, Korea.
authors.forename: UnJoo
authors.initials: U
authors.lastname: Lee
authors.affiliation: Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea.
authors.forename: Jong-Il
authors.initials: JI
authors.lastname: Kim
authors.affiliation: Department of Parasitology and Institute of Medical Education, College of Medicine, Hallym University, Chuncheon 24253, Korea.
authors.forename: Sun
authors.initials: S
authors.lastname: Huh
mesh_terms: D000818:Animals; D001482:Base Composition; D019295:Computational Biology; D018509:DNA, Helminth / Q000737:chemistry / Q000235:genetics; D005260:Female; D017238:Genes, Helminth; D049751:Genome, Helminth; D015801:Helminth Proteins / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D017422:Sequence Analysis, DNA; D017166:Toxocara canis / Q000235:genetics* / Q000302:isolation & purification
chemical_list: D018509:DNA, Helminth; D015801:Helminth Proteins
keywords: Toxocara canis; de novo synthesis; genomics; next generation sequencing