A Draft Genome Sequence of the Burrowing Nematode Radopholus similis

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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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A Draft Genome Sequence of the Burrowing Nematode Radopholus similis

Reny Mathew / Mark Burke / Charles H. Opperman *

Keywords : Burrowing nematode, Genomics, Radopholus similis

Citation Information : Journal of Nematology. Volume 51, Pages 1-2, DOI: https://doi.org/10.21307/jofnem-2019-051

License : (CC-BY-4.0)

Published Online: 17-September-2019

ARTICLE

ABSTRACT

Radopholus similis also known as the burrowing nematode is a devastating pest of banana (Musa spp.) and many economically important crops and ornamentals. In this publication, we present the genome assembly of R. similis.

Plant-parasitic nematodes cause estimated crop losses of $100 billion worldwide (Coyne et al., 2018). In the United States alone, economic losses due to nematode induced damages have been estimated to be around $10 billion (Coyne et al., 2018). Recent advances in genome sequencing technologies combined with the suite of open source softwares have opened a new paradigm for molecular scientists and plant pathologists to examine the genomic variability that exists within pathogen populations. Starting from the free-living nematode C. elegans to the recently published genome of the root-knot nematode Meloidogyne graminicola (Somvanshi et al., 2018), nematode genomes and transcriptomes are being heavily explored to understand the underlying complexities that distinguishes a parasitic nematode from their free-living counterparts. The burrowing nematode Radopholus similis is a devastating pathogen of banana (Musa spp.), Citrus spp., anthurium, black pepper, and numerous other economically important crops and ornamentals (Jacob et al., 2008). Management strategies for R. similis are limited and expensive, emphasizing the need to understand the genomic and genetic makeup of this organism in order to seek better and specific tools to combat this parasite.

We sequenced the R. similis genome utilizing the Roche 454 platform and assembled it into 8,133 scaffolds with a 30X coverage using Newbler, resulting in an N50 of 13.4 Kb. At ~65 Mbp, the R. similis genome assembly size is smaller than the free-living nematode C. elegans (~100 Mbp) and multiple plant-parasitic nematodes in clade IV such as D. destructor (~112 Mbp) (Zheng et al., 2016), G. pallida (~124.6 Mbp) (Cotton et al., 2014), and B. xylophillus (~74.6 Mbp) (Kikuchi et al., 2011), although it is slightly larger than the root-knot nematode M. hapla (~53 Mbp) (Opperman et al., 2008). The GC content of the R. similis is ~51%, which is higher than most plant-parasitic nematodes in clade IV and in keeping with the observations noted by Jacob et al. (2008). NCBI platforms were utilized to pinpoint contaminations in the genome assembly and following this the resulting contaminated sequences were removed. The completeness of the genome assembly was assessed using Core Eukaryotic Gene Mapping Approach (CEGMA) (Parra et al., 2007) and Benchmarking Universal Single Copy Orthologs (BUSCO) (Simão et al., 2015). CEGMA analysis indicates approximately 221 (89.11%) complete and 230 (92.74%) partial genes (>75% amino acids) in the draft R. similis assembly. Utilizing the Eukaryota lineage to run BUSCO, we found 85.2% complete genes in the genome assembly and 4.6% fragmented genes. For gene predictions, MAKER v. 2.31.8 (Cantarel et al., 2008) platform was utilized. MAKER gene predictions were made by integrating predictions from evidence such as R. similis ESTs, Uniprot, and Swissprot databases, protein datasets of closely related nematode species as well as the ab initio tools SNAP and AUGUSTUS. MAKER predicted 18,564 protein-coding genes in R. similis. Furthermore, to assess completeness, we also performed a tblastx of the 7,382 R. similis expressed sequence tags (ESTs) extracted from NCBI EST database against the R. similis draft genome assembly. We found that 6,960 sequences (~94%) had hits in the R. similis draft genome assembly and only 422 sequences did not return hits. We hope that this genome assembly could provide valuable insight into the myriad mechanisms of parasitism utilized by this nematode to sustain as a parasite.

GenBank accession numbers:

The Whole genome shotgun (WGS) sequence has been deposited in NCBI Genbank under the accession number SJFO00000000.

Acknowledgments

The authors would like to thank Jorge Gonzalez and Miguel E. Munoz (Dole, Costa Rica) for providing the R. similis DNA. This project was supported by APC, Schneider Electric and North Carolina Agriculture Research Service.

References


  1. Cantarel, B. L., Korf, I., Robb, S. M., Parra, G., Ross, E., Moore, B., Holt, C., Alvarado, A. S. and Yandell, M.. 2008. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Research 18:188–196.
    [CROSSREF]
  2. Cotton, J. A., Lilley, C. J., Jones, L. M., Kikuchi, T., Reid, A. J., Thorpe, P., Tsai, I. J., Beasley, H., Blok, V. and Cock, P. J.. 2014. The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome Biology 15:R43.
    [PUBMED] [CROSSREF]
  3. Coyne, D. L., Cortada, L., Dalzell, J. J., Claudius-Cole, A. O., Haukeland, S., Luambano, N. and Talwana, H.. 2018. Plant-Parasitic Nematodes and Food Security in Sub-Saharan Africa. Annual Review of Phytopathology 56:381–403.
    [PUBMED] [CROSSREF]
  4. Jacob, J., Mitreva, M., Vanholme, B. and Gheysen, G.. 2008. Exploring the transcriptome of the burrowing nematode Radopholus similis. Molecular Genetics and Genomics 280:1–17.
    [PUBMED] [CROSSREF]
  5. Kikuchi, T., Cotton, J. A., Dalzell, J. J., Hasegawa, K., Kanzaki, N., McVeigh, P., Takanashi, T., Tsai, I. J., Assefa, S. A. and Cock, P. J.. 2011. Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. PLoS Pathogens 7(9): e1002219.
    [PUBMED] [CROSSREF]
  6. Opperman, C. H., Bird, D. M., Williamson, V. M., Rokhsar, D. S., Burke, M., Cohn, J., Cromer, J., Diener, S., Gajan, J. and Graham, S.. 2008. Sequence and genetic map of Meloidogyne hapla: a compact nematode genome for plant parasitism. Proceedings of the National Academy of Sciences. 105:14802–14807.
    [CROSSREF]
  7. Parra, G., Bradnam, K. and Korf, I.. 2007. CEGMA: A pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23:1061–1067.
    [PUBMED] [CROSSREF]
  8. Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. and Zdobnov, E. M.. 2015. BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31: 3210–3212.
    [PUBMED] [CROSSREF]
  9. Somvanshi, V. S., Tathode, M., Shukla, R. N.. and Rao, U. 2018. Nematode genome announcement: a draft genome for rice root-knot Nematode, Meloidogyne graminicola. Journal of Nematology 50:111–113.
    [PUBMED] [CROSSREF]
  10. Zheng, J., Peng, D., Chen, L., Liu, H., Chen, F., Xu, M., Ju, S., Ruan, L. and Sun, M.. 2016. The Ditylenchus destructor genome provides new insights into the evolution of plant parasitic nematodes. Proceedings of the Royal Society B 283:20160942.
    [PUBMED] [CROSSREF]
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REFERENCES

  1. Cantarel, B. L., Korf, I., Robb, S. M., Parra, G., Ross, E., Moore, B., Holt, C., Alvarado, A. S. and Yandell, M.. 2008. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Research 18:188–196.
    [CROSSREF]
  2. Cotton, J. A., Lilley, C. J., Jones, L. M., Kikuchi, T., Reid, A. J., Thorpe, P., Tsai, I. J., Beasley, H., Blok, V. and Cock, P. J.. 2014. The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome Biology 15:R43.
    [PUBMED] [CROSSREF]
  3. Coyne, D. L., Cortada, L., Dalzell, J. J., Claudius-Cole, A. O., Haukeland, S., Luambano, N. and Talwana, H.. 2018. Plant-Parasitic Nematodes and Food Security in Sub-Saharan Africa. Annual Review of Phytopathology 56:381–403.
    [PUBMED] [CROSSREF]
  4. Jacob, J., Mitreva, M., Vanholme, B. and Gheysen, G.. 2008. Exploring the transcriptome of the burrowing nematode Radopholus similis. Molecular Genetics and Genomics 280:1–17.
    [PUBMED] [CROSSREF]
  5. Kikuchi, T., Cotton, J. A., Dalzell, J. J., Hasegawa, K., Kanzaki, N., McVeigh, P., Takanashi, T., Tsai, I. J., Assefa, S. A. and Cock, P. J.. 2011. Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. PLoS Pathogens 7(9): e1002219.
    [PUBMED] [CROSSREF]
  6. Opperman, C. H., Bird, D. M., Williamson, V. M., Rokhsar, D. S., Burke, M., Cohn, J., Cromer, J., Diener, S., Gajan, J. and Graham, S.. 2008. Sequence and genetic map of Meloidogyne hapla: a compact nematode genome for plant parasitism. Proceedings of the National Academy of Sciences. 105:14802–14807.
    [CROSSREF]
  7. Parra, G., Bradnam, K. and Korf, I.. 2007. CEGMA: A pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23:1061–1067.
    [PUBMED] [CROSSREF]
  8. Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. and Zdobnov, E. M.. 2015. BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31: 3210–3212.
    [PUBMED] [CROSSREF]
  9. Somvanshi, V. S., Tathode, M., Shukla, R. N.. and Rao, U. 2018. Nematode genome announcement: a draft genome for rice root-knot Nematode, Meloidogyne graminicola. Journal of Nematology 50:111–113.
    [PUBMED] [CROSSREF]
  10. Zheng, J., Peng, D., Chen, L., Liu, H., Chen, F., Xu, M., Ju, S., Ruan, L. and Sun, M.. 2016. The Ditylenchus destructor genome provides new insights into the evolution of plant parasitic nematodes. Proceedings of the Royal Society B 283:20160942.
    [PUBMED] [CROSSREF]

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