Genome assembly and annotation of the mermithid nematodeMermis nigrescens

Abstract

Genetic studies of nematodes have been dominated by Caenorhabditis elegans as a model species. Lack of genomic resources has been a limiting factor for expansion of genetic research to other groups of nematodes. Here, we report a draft genome assembly of a mermithid nematode, Mermis nigrescens. Mermithidae are insect parasitic nematodes with hosts including a wide range of terrestrial arthropods. We sequenced, assembled, and annotated the whole genome of M. nigrescens using nanopore long-reads and 10X chromium link-reads. The assembly is 524 Mb in size consisting of 867 scaffolds. The N50 value is 2.42 Mb, and half of the assembly is in the 30 longest scaffolds. The assembly BUSCO score from the eukaryotic database (eukaryota_odb10) indicates that the genome is 86.7% complete and 5.1% partial. The genome has a high level of heterozygosity (6.6%) with a repeat content of 78.7%. mRNA-seq reads from different sized nematodes (≤2 cm, 3.5-7 cm, and >7 cm body length) representing different developmental stages were also generated and used for the genome annotation. Using ab initio and evidence-based gene model predictions, 12,313 protein-coding genes and 24,186 mRNAs were annotated. These genomic resources will help researchers investigate the various aspects of the biology and host-parasite interactions of mermithid nematodes.

First in family Rhabdiasidae: the reference-guided genome assembly of an invasive parasite, the cane toad lungworm (Rhabdias pseudosphaerocephala)

“…This is not completely surprising given the high genetic diversity amongst nematodes and the small proportion of them which have reference sequences available. Even the nematoda_odb10 database can be a poor reference for some species of nematodes that are dissimilar to those from reference databases, such as mermithid nematodes (75), and species from the family Panagrolaimidae (76, 77). CN spectra plots (Figure 4a) indicate a low level of duplicate genes were assembled as haplotigs; however, the length of the tail in Figure 4a indicate the presence of some false duplications present in the assembly.…”

“…This would help to address annotation issues caused by poorly assembled regions in this genome. In addition, it is clear from other research (81) that there is a larger issue of a lack of representation across diverse nematode species within publicly available databases, which can prevent certain analyses, such as accurate estimates of completeness (75)(76)(77). This emphasises the need for the generation of highly complete assemblies from underrepresented families such as the Rhabdiasidae.…”

Revisiting genomes of non-model species with long reads yields new insights into their biology and evolution

“…Enoplean research often revolves around Trichinella spiralis , given its significance as a mammalian parasite ( Mitreva et al 2011 ). Among mermithidae, only two genomes are currently publicly available ( Bhattarai et al 2022 ; Schiffer et al 2013 ). In contrast with the published assembly of the sexual R. culicivorax , the long-read genome assembly of the parthenogenetic Mermis nigrescens is more contiguous and contains approximately twice the repeat content and heterozygosity.…”

Revisiting genomes of non-model species with long reads yields new insights into their biology and evolution

“…Enoplean research often revolves around Trichinella spiralis , given its significance as a mammalian parasite [15]. Among mermithidae, only two genomes are currently publicly available [16, 17]. In contrast, the long-read genome assembly of the parthenogenetic Mermis nigrescens is more contiguous and contains approximately twice the repeat content and heterozygosity of the sexual R. culicivorax .…”