Genomic/Transcriptomic Analysis of Toxocara Cati, The Most Common Parasitic Nematode of Cats
Principal Investigator: Dwight Bowman
DESCRIPTION (provided by applicant):
Toxocara cati is one of the most common nematode parasites (and perhaps the most common internal parasite of cats) in the United States and around the world. Many cats are infected by the ingestion of paratenic hosts, such as rodents, that contain the larvae of this parasite. Once in their hosts, these larvae can survive within the tissues of the host for years, and commonly the life of an experimentally infected mouse. Drug treatments for larval T. cati do not exist, and also, there exists no T. cati vaccine. We propose to decipher T. cati infection and identify possible new treatments by characterizing the T. cati genome and transcriptome. First, in collaboration with New England Biolabs, Inc. (NEB), we will sequence a third-generation (long-read) genome assembly for T. cati. We will sequence T. cati genomic DNA with both Oxford Nanopore (long-read) and Illumina (short-read) technology, and then assemble a genome sequence that we expect will have high accuracy (1 error in ≥104 nt) and high contiguity (contig N50 [size-weighted median length] of ≥1 Mb). Second, with NEB, we will sequence T. cati transcriptomes (RNA-seq) from whole worms and secreted extracellular vesicles; this will be performed on both protein-coding mRNA (oligo-T selected) and small non-coding RNAs (size-selected; e.g., miRNA). If we cannot assemble a T. cati genome, we will use RNA-seq reads to assemble a transcriptome instead. Third, we will predict both protein-coding and ncRNA genes in our T. cati genome assembly, guided by RNA-seq. If genome assembly fails, we will instead assemble and annotate a transcriptome from RNA-seq data; conversely, if RNA-seq fails we will use purely in silico methods to predict T. cati genes. Importantly, we will computationally identify possible mammalian targets of T. cati miRNAs. We will make our T. cati genome and transcriptome and their annotations publicly available in both GenBank and WormBase ParaSite (https://parasite.wormbase.org), while also permanently archiving them at Cornell (https://biohpc.cornell.edu/lab/lab.aspx). We expect this work will take one year from inception, that it will provide researchers potential intervention targets for T. cati control, and that it will enable several long-term goals in feline biomedicine.