Genomics of the Parasitic Nematode Ascaris and Its Relatives

Abstract

Nematodes of the genus Ascaris are important parasites of humans and swine, and the phylogenetically related genera (Parascaris, Toxocara, and Baylisascaris) infect mammals of veterinary interest. Over the last decade, considerable genomic resources have been established for Ascaris, including complete germline and somatic genomes, comprehensive mRNA and small RNA transcriptomes, as well as genome-wide histone and chromatin data. These datasets provide a major resource for studies on the basic biology of these parasites and the host-parasite relationship. Ascaris and its relatives undergo programmed DNA elimination, a highly regulated process where chromosomes are fragmented and portions of the genome are lost in embryonic cells destined to adopt a somatic fate, whereas the genome remains intact in germ cells. Unlike many model organisms, Ascaris transcription drives early development beginning prior to pronuclear fusion. Studies on Ascaris demonstrated a complex small RNA network even in the absence of a piRNA pathway. Comparative genomics of these ascarids has provided perspectives on nematode sex chromosome evolution, programmed DNA elimination, and host-parasite coevolution. The genomic resources enable comparison of proteins across diverse species, revealing many new potential drug targets that could be used to control these parasitic nematodes.

Keywords: Ascaris; chromatin; chromosome; comparative genomics; evolution; genome; histone modification; parasitic nematode; small RNA; transcriptome.

Figure 1

Ascaris genome, programmed DNA elimination, and chromosome evolution. Germline chromosomes are illustrated with the length of the chromosome in Mb on the right. Chromosome regions that are eliminated are colored in red. The retained regions, which will become somatic chromosomes after DNA elimination, are colored based on their corresponding C. elegans chromosomes (see legends). CENP-A deposition (data from 12 developmental stages [37]) are illustrated by green dots underneath the chromosomes, illustrating possible centromeric regions for the holocentric chromosomes; shown are the top 2000 (out of 3342) CENP-A enriched sites.

Figure 2

Ascaris genome data illustration. Genome browser tracks with gene models, RNA expression, small RNAs, histone marks, and other datasets are illustrated. For the gene models, RNA transcribed on the plus strand is in red and minus strand is in blue. The data for tracks on nascent transcripts, histone marks, and chromatin accessibility are derived from 32–64-cell (5-day) embryos. The genome browser can be accessed at http://genome.ucsc.edu/s/jianbinwang/Ascaris_genome_browser_genes_review, access on 24 March 2021.