Location: Animal Parasitic Diseases Laboratory
Project Number: 8042-32000-105-08-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Sep 15, 2016
End Date: Sep 15, 2018
1) Sequence the genome of the cattle/sheep gastrointestinal nematode Trichostrongylus coulibriformis to 60X coverage (samples to be provided by USDA, ARS, Animal Parasitic Diseases Lab); 2) Evaluate the ability of nutritional supplements and pathogen-associated molecules in modulating the immune response, and 3) Annotate the protein encoding genes identified in the sequence.
Parasite samples will be isolated by ARS scientists. Nucleic acids will be purified and submitted for genome sequencing of 1 genome an estimated size of 400 Mb to the McDonnell Genome Institute using either PacBio sequencing methodology or Luminex technology. For PacBio sequencing, the genome will be sequenced to 60X coverage. Six 20Kb libraries will be constructed and loaded across 32 SMRT cells. For de Novo Illumina sequencing, reactions will be performed on one lane of an Illumina HiSeq4000 machine with the coverage achieving coverage of 100X as follows: short inserts – 45-50X coverage; 3kb inserts – 45-50X coverage.