The Draft Genome of Deladenus siricidicola

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Journal of Nematology

Society of Nematologists

Subject: Life Sciences

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ISSN: 0022-300X
eISSN: 2640-396X

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The Draft Genome of Deladenus siricidicola

Alisa Postma / X. Osmond Mlonyeni / Frederick Clasen / Fourie Joubert / Bernard Slippers *

Keywords : Biological control, Deladenus siricidicola, Entomoparasitic nematode, Genome, Sirex noctilio

Citation Information : Journal of Nematology. Volume 51, Pages 1-4, DOI: https://doi.org/10.21307/jofnem-2019-036

License : (CC-BY-4.0)

Received Date : 16-February-2019 / Published Online: 29-July-2019

ARTICLE

ABSTRACT

The nematode Deladenus siricidicola is used as biological control agent against the invasive woodwasp Sirex noctilio, a serious invasive pest of Pinus plantations globally. The draft genome of this ecologically and economically important entomoparasitic nematode was determined.

Graphical ABSTRACT

The number of invasive insect pests affecting forestry and agriculture globally is rapidly increasing (Ramsfield et al., 2016). The Sirex woodwasp, Sirex noctilio (Hymenoptera: Siricidae), along with its symbiotic fungus, Amylostereum areolatum (Russulales: Amylostereaceae), are amongst the most important invasive pests of Pinus trees globally and has caused billions of dollars’ worth of losses since its first detection in New Zealand in the early 1900s (Slippers et al., 2012). The most effective control of S. noctilio is via the biological control agent, Deladenus siricidicola (Tylenchida: Neotylenchidae). This nematode has a bicyclic life-cycle, where in the free-living phase it reproduces in wood whilst feeding on A. areolatum, while in the parasitic phase it infects S. noctilio larvae and results in sterilized females. The parasitized adult female S. noctilio becomes the natural vector that disperses D. siricidicola into new trees.

In this study, the genome of D. siricidicola was sequenced and assembled. These data will be useful to understand the evolution and biology underlying the unique symbiotic relationships within this multipartite symbiotic system, including the genomic features linked to the adaptation to the bicyclic lifestyle of this nematode.

A D. siricidicola strain known as the “Kamona strain,” that is widely used in biological control of S. noctilio in the Southern Hemisphere, was used for genomic DNA extraction using the phenol-chloroform method (Mlonyeni et al., 2011). Two single-end shotgun libraries were sequenced using Roche 454 technology at Inqaba, South Africa. Three paired end and two mate pair (~2 and ~5 kb inserts) libraries were sequenced using Illumina HiSeq and MiSeq platforms at Inqaba, South Africa and Fasteris SA, Switzerland. All DNA samples qualified based on quality criteria set by the sequencing facilities, with DNA concentrations measured above 4 μg and sample volumes above 50 μl (Table A1). The data obtained produced a genome coverage of ~90× the estimated genome size.

The quality of all raw data was analysed using FastQC (www.bioinformatics.bbsrc.ac.uk/projects/fastqc) and quality trimming and filtering were performed on Illumina data using Trimmomatic (Bolger et al., 2014) with customised parameters relevant for each library (Table A2). Roche 454 reads were assembled using Newbler/GS De Novo Assembler with default parameters and the resulting long contigs were incorporated into a first draft assembly together with the Illumina paired-end reads using VelvetOptimiser with a kmer-size of 77 and a coverage cutoff of 2× (Zerbino and Birney, 2008). The resulting paired-end assembly was scaffolded with available mate pair data using SSPACE (Boetzer et al., 2011). This produced a draft assembly ~100.56 Mb in size, containing 3,169 contigs with an N50 of 124 kb. The CEGMA program (Parra et al., 2007) was used to confirm genome completeness by searching for the presence of 248 core eukaryotic genes. The completeness of the D. siricidicola genome assembly was estimated at 92%. The assembly and genome completeness statistics are comparable to other nematodes in the Tylenchida order, such as Meloidogyne incognita (size: 122 Mb, 83% complete) and Meloidogyne arenaria (size: 163 Mb, 91% complete) (Szitenberg et al., 2017).

These data provide a valuable resource to study the evolution and biology of this nematode, specifically considering the adaptations necessary to sustain its unique symbiotic relationship with S. noctilio and A. areolatum.

GenBank accession numbers: the raw DNA sequence data and genome assembly were deposited at GenBank under BioSample No. SAMN10502236.

Acknowledgments

The authors acknowledge Dr Charles Hefer for his assistance with bioinformatics analyses as well as Katrin Fitza and Dr Chongxing Zhang for technical assistance with DNA extractions. The Tree Protection Cooperative Programme and the Genomics Research Institute at the University of Pretoria, South Africa supported this study.

Appendices

Appendix

Table A1.

DNA samples and concentrations.

10.21307_jofnem-2019-036-t001.jpg

Table A2.

Illumina library information.

10.21307_jofnem-2019-036-t002.jpg

References


  1. Boetzer, M., Henkel, C. V., Jansen, H. J., Butler, D. and Pirovano, W. 2011. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27(4):578–9, doi: 10.1093/bioinformatics/btq683.
    [PUBMED] [CROSSREF]
  2. Bolger, A. M., Lohse, M. and Usadel, B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–20, doi: 10.1093/bioinformatics/btu170.
    [PUBMED] [CROSSREF]
  3. Mlonyeni, X., Wingfield, B., Wingfield, M., Ahumada, R., Klasmer, P., Leal, I., de Groot, P. and Slippers, B. 2011. Extreme homozygosity in Southern Hemisphere populations of Deladenus siricidicola, a biological control agent of Sirex noctilio. Biological Control 59:348–53, doi:10.1016/j.biocontrol.2011.09.009.
    [CROSSREF]
  4. Parra, G., Bradnam, K. and Korf, I. 2007. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23(9):1061–7, doi: 10.1093/bioinformatics/btm071.
    [PUBMED] [CROSSREF]
  5. Ramsfield, T. D., Bentz, B. J., Faccoli, M., Jactel, H. and Brockerhoff, E. G. 2016. Forest health in a changing world: effects of globalization and climate change on forest insect and pathogen impacts. Forestry: An International Journal of Forest Research 89(3):245–52, doi: 10.1093/forestry/cpw018.
    [CROSSREF]
  6. Slippers, B., de Groot, P. and Wingfield, M. 2012. The Sirex Woodwasp and its Fungal Symbiont: Research and Management of a Worldwide Invasive Pest. 1st ed., Springer, Dordrecht, Netherlands. doi: 10.1007/978-94-007-1960-6.
    [CROSSREF]
  7. Szitenberg, A., Salazar-Jaramillo, L., Blok, V. C., Laetsch, D. R., Joseph, S., Williamson, V. M., Blaxter, M. L. and Lunt, D. H. 2017. Comparative genomics of apomictic root-knot nematodes: hybridization, ploidy, and dynamic genome change. Genome Biology and Evolution 9(10):2844–61, doi: 10.1093/gbe/evx201.
    [PUBMED] [CROSSREF]
  8. Zerbino, D. R. and Birney, E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18(5):821–9, doi: 10.1101/gr.074492.107.
    [PUBMED] [CROSSREF]
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REFERENCES

  1. Boetzer, M., Henkel, C. V., Jansen, H. J., Butler, D. and Pirovano, W. 2011. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27(4):578–9, doi: 10.1093/bioinformatics/btq683.
    [PUBMED] [CROSSREF]
  2. Bolger, A. M., Lohse, M. and Usadel, B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–20, doi: 10.1093/bioinformatics/btu170.
    [PUBMED] [CROSSREF]
  3. Mlonyeni, X., Wingfield, B., Wingfield, M., Ahumada, R., Klasmer, P., Leal, I., de Groot, P. and Slippers, B. 2011. Extreme homozygosity in Southern Hemisphere populations of Deladenus siricidicola, a biological control agent of Sirex noctilio. Biological Control 59:348–53, doi:10.1016/j.biocontrol.2011.09.009.
    [CROSSREF]
  4. Parra, G., Bradnam, K. and Korf, I. 2007. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23(9):1061–7, doi: 10.1093/bioinformatics/btm071.
    [PUBMED] [CROSSREF]
  5. Ramsfield, T. D., Bentz, B. J., Faccoli, M., Jactel, H. and Brockerhoff, E. G. 2016. Forest health in a changing world: effects of globalization and climate change on forest insect and pathogen impacts. Forestry: An International Journal of Forest Research 89(3):245–52, doi: 10.1093/forestry/cpw018.
    [CROSSREF]
  6. Slippers, B., de Groot, P. and Wingfield, M. 2012. The Sirex Woodwasp and its Fungal Symbiont: Research and Management of a Worldwide Invasive Pest. 1st ed., Springer, Dordrecht, Netherlands. doi: 10.1007/978-94-007-1960-6.
    [CROSSREF]
  7. Szitenberg, A., Salazar-Jaramillo, L., Blok, V. C., Laetsch, D. R., Joseph, S., Williamson, V. M., Blaxter, M. L. and Lunt, D. H. 2017. Comparative genomics of apomictic root-knot nematodes: hybridization, ploidy, and dynamic genome change. Genome Biology and Evolution 9(10):2844–61, doi: 10.1093/gbe/evx201.
    [PUBMED] [CROSSREF]
  8. Zerbino, D. R. and Birney, E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18(5):821–9, doi: 10.1101/gr.074492.107.
    [PUBMED] [CROSSREF]

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