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<italic>Ditylenchus dipsaci</italic> is a devastating pest to many crops worldwide. We present the first genome sequence for this species, produced with PacBio sequencing and assembled with CANU.
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Ditylenchus dipsaci is a devastating pest to many crops worldwide. We present the first genome sequence for this species, produced with PacBio sequencing and assembled with CANU.

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The stem and bulb nematode, <italic>Ditylenchus dipsaci</italic>, is a plant-parasitic nematode affecting over 500 plant species with major destruction occurring in onion, garlic, beet, strawberry, broad bean, potato, alfalfa, and oat (<a ref-type="bibr" href="#j_jofnem-2019-027_ref_017">Sturhan and Brzeski, 1991</a>). It is a quarantine pest in Europe (<a ref-type="bibr" href="#j_jofnem-2019-027_ref_007">EPPO, 2004</a>) and well known in garlic production where it can cause losses of up to 90% (<a ref-type="bibr" href="#j_jofnem-2019-027_ref_002">Abawi and Moktan, 2010</a>). The species exhibits a variety of host preferences for which biological groups were proposed (<a ref-type="bibr" href="#j_jofnem-2019-027_ref_017">Sturhan and Brzeski, 1991</a>). In this study, we report the first genome assembly of <italic>D. dipsaci</italic>, a resource that will improve our understanding of this important parasite.
A population of <italic>D. dipsaci</italic> (E-105) was obtained from the <italic>Canadian National Collection of Insects, Arachnids, and Nematodes</italic> and originally isolated from garlic in Northern Ontario (<a ref-type="bibr" href="#j_jofnem-2019-027_ref_013">Qiao et al., 2013</a>). The nematodes were multiplied <italic>in vitro</italic> on pea sprout inoculated with only 15 mixed-stages individuals, as described in <a ref-type="bibr" href="#j_jofnem-2019-027_ref_012">Poirier et al. (2019)</a>, to reduce heterozygosity. DNA was extracted from ~7,500 mixed-stage <italic>D. dipsaci,</italic> using the Qiagen DNeasy Blood &amp; Tissue Kit (Valencia, CA). <italic>MUGQIC</italic> (Montréal, Canada) performed the library preparation (sheared large insert) and sequencing on a PacBio RSII instrument using 12 SMRT cells yielding 941,946 long reads at a mean size of 10,207 bp for an estimated coverage of 42×. Two assemblies were generated using CANU v1.7 (<a ref-type="bibr" href="#j_jofnem-2019-027_ref_010">Koren et al., 2017</a>), one with default parameters and one optimized for high heterogeneity (corMhapSensitvity = high, corMinCoverage = 0, and correctedErrorRate = 0.105). These pre-assemblies were merged using Quickmerge (<a ref-type="bibr" href="#j_jofnem-2019-027_ref_004">Chakraborty et al., 2016</a>) and decontaminated using Blobtools v1.0 (<a ref-type="bibr" href="#j_jofnem-2019-027_ref_011">Laetsch and Blaxter, 2017</a>). Before scaffolding, the assembly contained 3,559 contigs with a N50 of 152 kb. Contigs were then scaffolded using MeDuSa v1.6 (<a ref-type="bibr" href="#j_jofnem-2019-027_ref_003">Bosi et al., 2015</a>) with the genomes of <italic>Caenorhabditis elegans</italic> (GCA_000002985.3; <a ref-type="bibr" href="#j_jofnem-2019-027_ref_018">The C. elegans Sequencing Consortium, 1998</a>), <italic>D. destructor</italic> (GCA_001579705.1; <a ref-type="bibr" href="#j_jofnem-2019-027_ref_019">Zheng et al., 2016</a>), <italic>Globodera pallida</italic> (GCA_000724045.1; <a ref-type="bibr" href="#j_jofnem-2019-027_ref_006">Cotton et al., 2014</a>), <italic>G. rostochiensis</italic> (GCA_900079975.1; <a ref-type="bibr" href="#j_jofnem-2019-027_ref_008">Eves-van den Akker et al., 2016</a>), and <italic>Meloidogyne incognita</italic> (GCA_900182535.1; <a ref-type="bibr" href="#j_jofnem-2019-027_ref_001">Abad et al., 2008</a>). Scaffolding was further improved using Rascaf (<a ref-type="bibr" href="#j_jofnem-2019-027_ref_016">Song et al., 2016</a>) and 13,555,476 PE RNA-seq reads (Phred score > 20), obtained from mixed-stage <italic>D. dipsaci</italic> (Illumina HiSeq 2 × 100 bp, TruSeq Library Prep Kit). Then, Purge Haplotigs (<a ref-type="bibr" href="#j_jofnem-2019-027_ref_014">Roach et al., 2018</a>) resolved highly polymorphic regions and reduced artifactual duplication.
The <italic>D. dipsaci</italic> genome assembly is comprised of 1,394 scaffolds, a largest scaffold of ~3.6 Mb, 22 scaffolds >1 Mb, and a N50 of 287 kb. The assembly is 227,234,012 bp (227.2 Mb), double the size of the <italic>D. destructor</italic> assembly (111.1 Mb). We used flow cytometry on <italic>D. dipsaci</italic> nuclei to investigate this discrepancy, revealing a haploid genome size of 160 to 170 Mb. Thus, obtaining 227 Mb with heterozygous material is not surprising. The GC content of the <italic>D. dipsaci</italic> assembly was 37.5% which is comparable to <italic>D. destructor</italic> (36.8%), <italic>C. elegans</italic> (35.4%), <italic>G. rostochiensis</italic> (38.1%), and <italic>G. pallida</italic> (36.7%). A completeness assessment with BUSCO v 3.0.2 (<a ref-type="bibr" href="#j_jofnem-2019-027_ref_015">Simão et al., 2015</a>) using the Nematoda_odb9 database revealed 537 complete sequences (506 single-copy, 31 duplicated), 133 fragmented, and 312 missing on a total of 982 BUSCO genes searched in <italic>D. dipsaci.</italic> The number of complete genes was higher than <italic>G. pallida</italic> (431) but lower than <italic>D. destructor</italic> (749). Gene prediction was performed with Braker 2.1.0 (<a ref-type="bibr" href="#j_jofnem-2019-027_ref_009">Hoff et al., 2015</a>) on a genome masked with Repeatmodeler/Repeatmasker 4.0.7 (<a ref-type="bibr" href="#j_jofnem-2019-027_ref_005">Chen, 2004</a>), leaving simple repeats unmasked. Transcript information was relayed to Braker via HISAT2 2.1.0 alignments of <italic>D. dipsaci</italic> RNA-seq and exonerate 2.4.0 aligned <italic>Ditylenchus destructor</italic> proteins to produce a gene annotation of 26,428 putative genes. On average, these genes contained seven exons (max = 114) with a mean length of 120 bp (from 2 to 9,194 bp) and six introns (max = 113) with a mean length of 515 bp (from 36 to 27,260 bp).

<italic>GenBank accession numbers</italic>: The raw sequences and genome assembly files are available under the NCBI BioProject PRJNA498219.
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The draft genome of <italic>Ditylenchus dipsaci</italic>

Journal of Nematology

This work is licensed under the Creative Commons Attribution 4.0 International License.

running-head

Ditylenchus dipsaci is a devastating pest to many crops worldwide. We present the first genome sequence for this species, produced with PacBio sequencing and...

The draft genome of Ditylenchus dipsaci

Article Category: Arts & Humanities

Published Online: May 27, 2019

Page range: 1 - 3

Received: Nov 27, 2018

DOI: https://doi.org/10.21307/jofnem-2019-027

© 2019 Benjamin Mimee et al., published by Sciendo

This work is licensed under the Creative Commons Attribution 4.0 International License.