About this Research Topic
Helminth Genomics initiated at the dawn of the millennium with promised to provide novel tools to decipher the biology of several parasitic worms that are agents of some of the most prevalent neglected diseases. Today more than a hundred helminth genomes are available but the unraveling of targets for diagnosis, prevention and control is still challenging. One of the main contributors to this challenge is the draft nature of these genome assemblies, resulting in compromised genome annotation. In addition, a high fraction of the predicted genes in each species corresponds to conserved hypothetical genes and proteins that appear devoid of function.
Comparative genomics are highlighting the common presence of helminth exclusive conserved hypothetical proteins, challenging researchers to invent innovative ways to unravel their function and relevance. Multi-omics approaches are needed to fully understand the complexity of parasitic helminths at a molecular level. Genomes on their own cannot explain the life cycles of roundworms (nematodes) or flatworms (trematodes and cestodes). Transcriptomic and epigenetic-based studies of diverse developmental stages and tissues started to provide new insights into parasite developmental gene expression and the molecular mechanisms underlying host-parasite interactions and immune evasion.
Reference genome availability allowed for variome studies, such as genome-wide analysis based on variable markers associated with different pathologies or drug resistance. Seminal studies in this direction are emerging for the major parasitic worms and they emphasize the relevance of genetic variability and defining population structures, expanding the area of parasite population genetics.
Putative targets found by predictive, comparative or genetic methods need validation and consequently a whole area of helminth functional genomics have emerged, with RNAi-mediated gene silencing as the main tool but also attempting to develop stable transgenesis methods. The advent of site-specific mutagenesis with CRISPR-Cas9 systems boosted hopes for rapid and simple tools to analyze helminth genomes, and the first few successful efforts have recently been reported.
We propose this Research Topic as an open forum to present and discuss these innovative genetic and genomic-based approaches that are helping to develop tools and leading the community towards solutions to understand many of the challenging aspects of helminth biology. We will be welcoming Original Research and Short Review submissions regarding:
- Improving genomics resources for helminths: including third-generation sequencing technologies for improving genome assembly and annotation, novel algorithms and packages, and new bioinformatic tools.
- Evolutionary genomics of helminths: including comparative genomics to unveil helminth genomic evolution and the emergence of parasitism, identification of genes, gene families and/or pathways that are taxonomically restricted and conserved among helminths and might be relevant to host adaptation and pathogenicity
- Genome wide and population studies: inclusive of genomic variation associated with drug resistance and other relevant phenotypes, or relevant to identifying biomarkers and/or unravelling differences relevant to adaptation and pathogenicity.
- Integrated omics approaches to comprehensively study helminths at a molecular level: including efforts towards the development of a toolkit to unravel gene function, such as transgenesis, RNAi and CrispR-Cas9, and furthering our understanding of transcriptional regulation in helminths with special emphasis in particularities like transplicing, gene editing, post-transcriptional regulation and/or the role of non-coding RNA and epigenetic mechanisms.
Keywords: Helminths, Comparative and evolutionary genomics, Genome, Transcriptome, Regulome
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