First Draft Genome Assembly of Root-Lesion Nematode Pratylenchus scribneri Generated Using Long-Read Sequencing

Abstract

Root-lesion nematodes (genus Pratylenchus) belong to a diverse group of plant-parasitic nematodes (PPN) with a worldwide distribution. Despite being an economically important PPN group of more than 100 species, genome information related to Pratylenchus genus is scarcely available. Here, we report the draft genome assembly of Pratylenchus scribneri generated on the PacBio Sequel IIe System using the ultra-low DNA input HiFi sequencing workflow. The final assembly created using 500 nematodes consisted of 276 decontaminated contigs, with an average contig N50 of 1.72 Mb and an assembled draft genome size of 227.24 Mb consisting of 51,146 predicted protein sequences. The benchmarking universal single-copy ortholog (BUSCO) analysis with 3131 nematode BUSCO groups indicated that 65.4% of the BUSCOs were complete, whereas 24.0%, 41.4%, and 1.8% were single-copy, duplicated, and fragmented, respectively, and 32.8% were missing. The outputs from GenomeScope2 and Smudgeplots converged towards a diploid genome for P. scribneri. The data provided here will facilitate future studies on host plant-nematode interactions and crop protection at the molecular level.

Keywords: BUSCO; contigs; diploid; genome; root-lesion nematode; sequencing; ultra-low DNA input.

Figure 1

Blobplot contaminant analysis of Pratylenchus scribneri assembly obtained using two DNA extraction methods, before removing contaminants. The contig length is represented by circles proportionally scaled and colored by taxonomic annotation based on BLAST similarity search results. Nematode genome contigs are represented by red circles for: (a) Method 1 (library prepared from 8000 to 10,000 mixed-stage P. scribneri in nematode suspension obtained from carrot culture); (b) Method 2 (library prepared from 500 hand-picked P. scribneri juveniles and adults). Contigs are placed based on the GC proportion (X-axis) and the coverage of reads (Y-axis). The legend box on the top right of each Blobplot provides a color-coded description of the different taxonomic groups identified.

Figure 2

Genome ploidy estimation of Pratylenchus scribneri genome assembly: (a) Smudgeplots showing the coverage and distribution of k-mer pairs that fit to diploid genome model; (b) GenomeScope k-mer (k = 21) profile plot of the P. scribneri showing the fit of the GenomeScope model (black) to the observed k-mer frequencies (blue) with two major peaks.