Advances in molecular tools for parasitic nematodes of animals – From genetic markers to metabarcoding and genomics

Abstract

Parasitic nematodes are globally important pathogens of animals, humans and plants. The accurate identification and characterisation of these nematodes are essential for diagnostics, systematics and epidemiological surveillance. Over the past decades, molecular technologies have progressed from targeted PCR-based assays using nuclear ribosomal markers – particularly the first and second internal transcribed spacers (ITS-1 and ITS-2) – to high-throughput metabarcoding and genome-enabled approaches. These advances have transformed species discovery, facilitated the detection of cryptic taxa and supported the development of sensitive diagnostic tools for parasitic nematodes of veterinary, medical and agricultural importance. This review traces the progression of molecular technologies used to study parasitic nematodes, with emphasis on the definition and validation of ribosomal and mitochondrial DNA markers, metabarcoding frameworks, such as the “nemabiome”, and the expanding availability of genomic resources. Particular attention is given to the emergence of workflows and bioinformatic pipelines supporting primer evaluation, variant detection, taxonomic assignment and analyses of genetic diversity. The integration of curated reference databases, multi-marker strategies and advanced informatics has allowed for scalable, reproducible and high-resolution investigations of nematode diversity. Recent innovations in long-read sequencing and CRISPR-based enrichment, which may enable amplification-free, multi-locus profiling of nematode communities, are also highlighted. Collectively, these advances in molecular and genomic technologies – underpinned by reproducible informatic frameworks – are transforming the systematics, diagnostics and epidemiological surveillance of parasitic nematodes of animals.