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Long-read sequencing improves assembly of Trichinella genomes 10-fold, revealing substantial synteny between lineages diverged over 7 million years

Published online by Cambridge University Press:  06 June 2017

PETER C. THOMPSON Open the ORCID record for PETER C. THOMPSON [Opens in a new window] ,
DANTE S. ZARLENGA ,
MING-YUAN LIU  and
BENJAMIN M. ROSENTHAL
PETER C. THOMPSON*
Affiliation:
USDA, Agricultural Research Service, Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
DANTE S. ZARLENGA
Affiliation:
USDA, Agricultural Research Service, Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
MING-YUAN LIU
Affiliation:
Key Laboratory for Zoonosis Research, Ministry of Education, First Hospital/Institute of Zoonoses, Jiangsu Co-innovation Centre for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jilin University, 5333 Xian Road, 130062 Changchun, People's Republic of China
BENJAMIN M. ROSENTHAL
Affiliation:
USDA, Agricultural Research Service, Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
*
*Corresponding author: USDA, Agricultural Research Service, Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, BARC-East Bldg. 1180 Rm. 104, 10300 Baltimore Avenue, Beltsville, MD 20705, USA. E-mail: pete.c.thompson@gmail.com
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Summary

Genome assemblies can form the basis of comparative analyses fostering insight into the evolutionary genetics of a parasite's pathogenicity, host–pathogen interactions, environmental constraints and invasion biology; however, the length and complexity of many parasite genomes has hampered the development of well-resolved assemblies. In order to improve Trichinella genome assemblies, the genome of the sylvatic encapsulated species Trichinella murrelli was sequenced using third-generation, long-read technology and, using syntenic comparisons, scaffolded to a reference genome assembly of Trichinella spiralis, markedly improving both. A high-quality draft assembly for T. murrelli was achieved that totalled 63·2 Mbp, half of which was condensed into 26 contigs each longer than 571 000 bp. When compared with previous assemblies for parasites in the genus, ours required 10-fold fewer contigs, which were five times longer, on average. Better assembly across repetitive regions also enabled resolution of 8 Mbp of previously indeterminate sequence. Furthermore, syntenic comparisons identified widespread scaffold misassemblies in the T. spiralis reference genome. The two new assemblies, organized for the first time into three chromosomal scaffolds, will be valuable resources for future studies linking phenotypic traits within each species to their underlying genetic bases.

Keywords

Genomicslong-read assemblysyntenyscaffoldingrepetitive DNATrichinellachromosomenematode
Type
Research Article
Information
Parasitology , Volume 144 , Issue 10 , September 2017 , pp. 1302 - 1315
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Copyright
Copyright © Cambridge University Press 2017 

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