Improving helminth genome resources in the post-genomic era

Abstract

Genomics resources for helminth parasites are growing rapidly; however, it is still difficult to fully assemble a genome so most genome resources vary significantly in completeness and contiguity.Genome annotations rely heavily on computational prediction and shared orthology between closely (and sometimes not so closely) related species, which can result in incomplete and incorrect annotations and may bias against some genes, such as those that are species-specific or phylogenetically restricted.New approaches are required to generate, improve, and extend these valuable resources.Community-based efforts could build on and exploit different areas of specific expertise, from single genes to whole gene families, to provide iterative improvement of centralised resources.Coordinated annotation will provide new opportunities for interaction and collaboration among the parasitology community. Rapid advancement in high-throughput sequencing and analytical approaches has seen a steady increase in the generation of genomic resources for helminth parasites. Now, helminth genomes and their annotations are a cornerstone of numerous efforts to compare genetic and transcriptomic variation, from single cells to populations of globally distributed parasites, to genome modifications to understand gene function. Our understanding of helminths is increasingly reliant on these genomic resources, which are primarily static once published and vary widely in quality and completeness between species. This article seeks to highlight the cause and effect of this variation and argues for the continued improvement of these genomic resources – even after their publication – which is necessary to provide a more accurate and complete understanding of the biology of these important pathogens. Rapid advancement in high-throughput sequencing and analytical approaches has seen a steady increase in the generation of genomic resources for helminth parasites. Now, helminth genomes and their annotations are a cornerstone of numerous efforts to compare genetic and transcriptomic variation, from single cells to populations of globally distributed parasites, to genome modifications to understand gene function. Our understanding of helminths is increasingly reliant on these genomic resources, which are primarily static once published and vary widely in quality and completeness between species. This article seeks to highlight the cause and effect of this variation and argues for the continued improvement of these genomic resources – even after their publication – which is necessary to provide a more accurate and complete understanding of the biology of these important pathogens. In 2022, the first gapless human genome assembly was published [1.Nurk S. et al.The complete sequence of a human genome.Science. 2022; 376: 44-53Crossref PubMed Scopus (168) Google Scholar], a little more than 20 years after the landmark completion of the draft assembly was announced [2.International Human Genome Sequencing Consortium Finishing the euchromatic sequence of the human genome.Nature. 2004; 431: 931-945Crossref PubMed Scopus (3472) Google Scholar]. This publicly available resource – the result of multinational collaborative efforts – is arguably one of our most important scientific achievements. The impact of this project extends far beyond the genome sequence itself; technological and analytical advancement made during and after the Human Genome Project has driven the ever-increasing accessibility of ‘genomics’ – the study of the structure, composition, function, and evolution of genomes – to other, nonhuman species. Such advances now allow genome-sequencing projects to be undertaken all over the world on potentially any organism with accessible DNA, from routine experiments found in any modest molecular biology laboratory to sequencing in extreme environments [3.Castro-Wallace S.L. et al.Nanopore DNA sequencing and genome assembly on the International Space Station.Sci. Rep. 2017; 7: 18022Crossref PubMed Scopus (177) Google Scholar] or in response to disease [4.Volz E. et al.Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England.Nature. 2021; 593: 266-269Crossref PubMed Scopus (463) Google Scholar], to cataloguing the genomes of all life on Earth [5.Lewin H.A. et al.Earth BioGenome Project: Sequencing life for the future of life.Proc. Natl. Acad. Sci. U. S. A. 2018; 115: 4325-4333Crossref PubMed Scopus (352) Google Scholar]. The study of parasitic worms, collectively termed helminths, has benefited significantly from this genomic revolution. Often considered ‘neglected’ parasites, helminths affect over a billion people living in some of the lowest-resource countries worldwide and significantly impact global livestock and agriculture industries. Despite this neglect, several sustained efforts have been made to generate genomic resources for helminths, with broad aims including the understanding of parasite biology and life-history traits [6.International Helminth Genomes Consortium Comparative genomics of the major parasitic worms.Nat. Genet. 2019; 51: 163-174Crossref PubMed Scopus (216) Google Scholar], mining new drug targets [7.Cotton J.A. et al.The genome of Onchocerca volvulus, agent of river blindness.Nat. Microbiol. 2016; 2: 16216Crossref PubMed Scopus (62) Google Scholar], and characterising genetic traits such as drug resistance [8.Doyle S.R. Cotton J.A. Genome-wide approaches to investigate anthelmintic resistance.Trends Parasitol. 2019; 35: 289-301Abstract Full Text Full Text PDF PubMed Scopus (37) Google Scholar]. The principal repository for these data, WormBase ParaSite [9.Howe K.L. et al.WormBase ParaSite − a comprehensive resource for helminth genomics.Mol. Biochem. Parasitol. 2017; 215: 2-10Crossref PubMed Scopus (277) Google Scholar], now contains 210 genomes and annotations (see Glossary) from 169 species of nematodes and flatworms (WormBase ParaSite release 17), representing some of the most pathogenic helminth species of humans, animals, and plants as well as closely related species for comparison. These genome resources are the starting point of many molecular and computational experiments and form the scaffold upon which many ‘omic experiments and analyses rely. Although intentionally provocative and somewhat oversimplified, there is some truth to this statement; a genome assembly and its annotation are a hypothesis of the structure and content of the genomic DNA within an organism from which they are derived but, despite best efforts, rarely resemble the complete product. For example, biologically, a genome is defined as all of the DNA within a cell and is found assembled into discrete chromosomes but, more often than not, genomes are represented informatically by contigs and scaffolds that number in the thousands or more and vary significantly in their ‘completeness’ (see Figure 1 for a comparison of helminth genome assemblies and BUSCO [10.Manni M. et al.BUSCO Update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes.Mol. Biol. Evol. 2021; 38: 4647-4654Crossref PubMed Scopus (283) Google Scholar] completeness available from WormBase ParaSite release 17; 80.9% of genome assemblies are in 1000 or more contigs/scaffolds). Despite recent technological and analytical advancements that make it cheaper, easier, and more likely to produce highly contiguous and even chromosome-scale assemblies, it is still challenging to generate finished genomes for eukaryotic species such as helminths. A key challenge is that there is not one molecular/sequencing/analytical approach optimised for all organisms. Although helminth genomes are not considered to be large or particularly complex for a eukaryotic organism (the median genome assembly size is 122.18 Mb, and range from 38.18 Mb for Meloidogyne graminicola to 1.25 Gb for Spirometra erinaceieuropaei), helminth-focused genome projects are further challenged by a range of factors. These challenges include: (i) vast differences in morphology and tissue composition, both within species (i.e., between life stages) and between species, may require different approaches to DNA extraction and lead to differences in extraction efficiencies [11.Ayana M. et al.Comparison of four DNA extraction and for the molecular and of helminths in 2019; S.R. et of DNA extraction on helminth and for Genet. 2019; PubMed Scopus Google the of parasite DNA, for example, life with more DNA are likely to be in parasitic for some species, accessible such as and are and may be further DNA extraction further to DNA on parasite and for example, despite over a billion people of helminths can be difficult to particularly in they are most found S.R. et genomics of and 2021; PubMed Scopus Google Scholar], and even it can be difficult to or to a laboratory or is and the of genetic among of many helminth species of is required to generate DNA for can lead to assembly S.R. et and transcriptomic variation the chromosome-scale assembly of a Biol. 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