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. 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

Akker, Sebastian Eves-van den

Lord, Etienne

Masonbrink, Rick

Mimee, Benjamin

Véronneau, Pierre-Yves

Yu, Qing

English

Apollo (Cambridge)

© 2019 Authors. This is an Open Access article licensed under the Creative Commons CC BY 4.0 license, https://creativecommons.org/licenses/by/4.0/JOURNAL OF NEMATOLOGYArticle | DOI: 10.21307/jofnem-2019-027 e2019-27 | Vol. 511The draft genome of Ditylenchus dipsaciBenjamin Mimee1,*, Etienne Lord1, Pierre-Yves Véronneau1, Rick  Masonbrink2, Qing Yu3 and  Sebastian Eves-van den Akker41Agriculture and Agri-Food  Canada, St-Jean-sur-Richelieu Research and Development Centre, St-Jean-sur-Richelieu, J3B 3E6 QC, Canada.2Iowa State University, Ames, IA.3Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, K1A 0C6 Ottawa, ON, Canada.4Department of Plant Sciences, University of Cambridge, Cam-bridge.*E-mail: benjamin.mimee@canada.caThis paper was edited by Dee Denver.Received for publication November 27, 2018.AbstractDitylenchus 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.Key wordsCanu, Genome assembly, PacBio, Stem and bulb nematode.The stem and bulb nematode, Ditylenchus dipsaci, is a plant-parasitic nematode affecting over 500 plant species with major destruction oc-curring in onion, garlic, beet, strawberry, broad bean, potato, alfalfa, and oat (Sturhan and Brzeski, 1991). It is a quarantine pest in Europe (EPPO, 2004) and well known in garlic production where it can cause losses of up to 90% (Abawi and Moktan, 2010). The species exhibits a variety of host preferences for which biological groups were proposed (Sturhan and Brzeski, 1991). In this study, we report the first genome assembly of D. dipsaci, a resource that will improve our understanding of this impor-tant parasite.A population of D. dipsaci (E-105) was obtained from the Canadian National Collection of Insects, Arachnids, and Nematodes and originally isolated from garlic in Northern Ontario (Qiao et al., 2013). The nematodes were multiplied in vitro on pea sprout inoculated with only 15 mixed-stages individuals, as described in Poirier et al. (2019), to reduce heterozygosity. DNA was extracted from ~7,500 mixed-stage D. dipsaci, using the Qiagen DNeasy Blood & Tissue Kit (Valencia, CA). MUGQIC (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 assem-blies were generated using CANU v1.7 (Koren et al., 2017), one with de-fault parameters and one optimized for high heterogeneity (corMhapSen-sitvity = high, corMinCoverage = 0, and correctedErrorRate = 0.105). These pre-assemblies were merged using Quickmerge (Chakraborty et al., 2016) and decontaminated using Blobtools v1.0 (Laetsch and Blaxter, 2017). Before scaffolding, the assembly contained 3,559 contigs with a N50 of 152 kb. Contigs were then scaffolded using MeDuSa v1.6 (Bosi et al., 2015) with the genomes of Caenorhabditis elegans (GCA_000002985.3; The C. elegans Sequencing Consortium, 1998), D. destructor (GCA_001579705.1; Zheng et al., 2016), Globodera pallida (GCA_000724045.1; Cotton et al., 2014), G. rostochiensis (GCA_900079975.1; Eves-van den Akker et al., 2016), and Meloidogyne incognita (GCA_900182535.1; Abad et al., 2008). Scaffolding was further improved using Rascaf (Song et al., 2016) and 13,555,476 PE RNA-seq reads (Phred score > 20), obtained from mixed-stage D. dipsaci (Illumina HiSeq 2 × 100 bp, TruSeq Library Prep Kit). The draft genome of Ditylenchus dipsaci2Then, Purge Haplotigs (Roach et al., 2018) resolved highly polymorphic regions and reduced artifactual duplication.The D. dipsaci 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 D. destructor assembly (111.1 Mb). We used flow cytom-etry on D. dipsaci nuclei to investigate this discrepan-cy, 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 D. dipsaci assembly was 37.5% which is comparable to D. de-structor (36.8%), C. elegans (35.4%), G. rostochiensis (38.1%), and G. pallida (36.7%). A completeness as-sessment with BUSCO v 3.0.2 (Simão et al., 2015) using the Nematoda_odb9 database revealed 537 complete sequences (506 single-copy, 31 duplicat-ed), 133 fragmented, and 312 missing on a total of 982 BUSCO genes searched in D. dipsaci. The num-ber of complete genes was higher than G. pallida (431) but lower than D. destructor (749). Gene pre-diction was performed with Braker 2.1.0 (Hoff et al., 2015) on a genome masked with Repeatmodeler/Repeatmasker 4.0.7 (Chen, 2004), leaving simple re-peats unmasked. Transcript information was relayed to Braker via HISAT2 2.1.0 alignments of D. dipsaci RNA-seq and exonerate 2.4.0 aligned Ditylenchus destructor 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).GenBank accession numbers: The raw sequenc-es and genome assembly files are available under the NCBI BioProject PRJNA498219.AcknowledgmentsThe authors thank Sandra Poirier and Nathalie Dauph-inais for technical assistance with nematode rearing and DNA extraction. This work was funded by Agri-culture and Agri-Food Canada.ReferencesAbad, P., Gouzy, J., Aury, J. M., Castagnone-Sereno, P., Danchin, E. G., Deleury, E., Perfus-Barbeoch, L., Anthouard, V., Artiguenave, F., Blok, V. C., Cail-laud, M.-C., Coutinho, P. M., Dasilva, C., De Luca, F., Deau, F., Esquibet, M., Flutre, T., Goldstone, J. V., Hamamouch, N., Hewezi, T., Jaillon, O., Jubin, C., Leonetti, P., Magliano, M., Maier, T. R., Markov, G. 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The draft genome of Ditylenchus dipsaci.

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The draft genome of Ditylenchus dipsaci.

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