Draft Genome of Toxocara canis, a Pathogen Responsible for Visceral Larva Migrans.
10.3347/kjp.2016.54.6.751
- Author:
Jinhwa KONG
1
;
Jungim WON
;
Jeehee YOON
;
UnJoo LEE
;
Jong Il KIM
;
Sun HUH
Author Information
1. Department of Computer Engineering, College of Engineering, Hallym University, Chuncheon 24252, Korea.
- Publication Type:Original Article
- Keywords:
Toxocara canis;
de novo synthesis;
genomics;
next generation sequencing
- MeSH:
Adult;
B-Lymphocytes;
Base Composition;
Classification;
DNA;
Female;
Genome*;
Genomics;
Humans;
Larva Migrans, Visceral*;
Metabolism;
Mucins;
Peptides;
Protein Structure, Tertiary;
Receptors, Antigen, T-Cell;
RNA;
Ryanodine Receptor Calcium Release Channel;
T-Lymphocytes;
Toxocara canis*;
Toxocara*;
Transcriptome;
Ubiquitin-Protein Ligases
- From:The Korean Journal of Parasitology
2016;54(6):751-758
- CountryRepublic of Korea
- Language:English
-
Abstract:
This study aimed at constructing a draft genome of the adult female worm Toxocara canis using 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 of T. 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 in T. 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 to T. canis, and the findings of this study are capable of serving as a basis for extending our biological understanding of T. canis.
