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The reniform nematode (<italic>Rotylenchulus reniformis</italic>) is a sedentary semi-endoparasitic species that is pathogenic on many row crops, fruits, and vegetables. Here, the authors present a draft genome assembly of <italic>R</italic>. <italic>reniformis</italic> using small- and large-insert libraries sequenced on the Illumina GAIIx and MiSeq platforms.
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The reniform nematode (Rotylenchulus reniformis) is a sedentary semi-endoparasitic species that is pathogenic on many row crops, fruits, and vegetables. Here, the authors present a draft genome assembly of R. reniformis using small- and large-insert libraries sequenced on the Illumina GAIIx and MiSeq platforms.

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The reniform nematode (<italic>Rotylenchulus reniformis</italic> Linford &amp; Oliveira) is a sedentary semi-endoparasitic species that infects 77 plant families, including cotton and soybean, and other high-value crops such as sweet potato and pineapple (<a ref-type="bibr" href="#j_jofnem-2019-013_ref_012">Robinson et al., 1997</a>). Here, we report the genome sequencing and assembly of <italic>R. reniformis.</italic>

Biological material for sequencing was a <italic>R. reniformis</italic> stock culture maintained on cotton. Eggs of <italic>R. reniformis</italic> were collected from infected cotton roots (<a ref-type="bibr" href="#j_jofnem-2019-013_ref_006">Hussey and Barker, 1973</a>), purified (<a ref-type="bibr" href="#j_jofnem-2019-013_ref_007">Jenkins, 1964</a>), surface-sterilized (<a ref-type="bibr" href="#j_jofnem-2019-013_ref_001">Baum et al., 2000</a>), pelleted by centrifugation, flash-frozen with liquid nitrogen, and stored at −80°C until DNA extraction. Genomic DNA extraction was performed as described by <a ref-type="bibr" href="#j_jofnem-2019-013_ref_002">Blin and Stafford (1976)</a>.
Three short-read small-insert libraries (250, 350, and 550 bp) and four large-insert Nextera mate-pair libraries (2-3.5-, 4-6-, 8-10-, and 2-10-kb) were constructed from a pooled population of <italic>R. reniformis</italic> eggs using standard protocols provided by Illumina (San Diego, CA). Additionally, a single <italic>R. reniformis</italic> egg was isolated, its DNA was amplified by whole genome amplification (WGA) using the Qiagen Repli-G single cell kit (Valencia, CA) and short-read small-insert libraries (400- and 600-bp) were constructed and sequenced using standard protocols provided by Illumina (San Diego, CA). Paired-end sequencing was conducted on Illumina GAIIx and Illumina MiSeq systems. We obtained 19.17 Gb and 29.85 Gb from the pooled population short- and long-read libraries, respectively, and 22.29 Gb from the WGA libraries. Pooled population and WGA sequence data was combined for genome assembly.
Mate-pair reads were processed with NextClip (v1.3; <a ref-type="bibr" href="#j_jofnem-2019-013_ref_011">Richard et al., 2014</a>) with default parameters to identify fragments containing linker sequence indicating proper circulation and removal of duplicate reads. All libraries were trimmed for adapters and low-quality base calls with Trimmomatic (v0.32; <a ref-type="bibr" href="#j_jofnem-2019-013_ref_004">Bolger et al., 2014</a>) and then assembled with ABySS (v1.5.2; <a ref-type="bibr" href="#j_jofnem-2019-013_ref_013">Simpson et al., 2009</a>) with a <italic>k</italic>-mer value of 175. The mate-pair libraries were used for scaffolding the assembly with SSPACE (v3.0; <a ref-type="bibr" href="#j_jofnem-2019-013_ref_003">Boetzer et al., 2011</a>) followed by gap filling of all libraries with GapFiller (v1.10; <a ref-type="bibr" href="#j_jofnem-2019-013_ref_009">Nadalin et al., 2012</a>).
The resultant <italic>R</italic>. <italic>reniformis</italic> genome assembly (RREN1.0, GCA_001026735.1) contained 314 Mb distributed among 100,525 scaffolds with scaffold and contig N50s of 22,705 bp and 5,991 bp, respectively. The genome assembly contained 86.29% of the core eukaryotic proteins utilized by CEGMA (v2.5; <a ref-type="bibr" href="#j_jofnem-2019-013_ref_010">Parra et al., 2007</a>). Flow cytometry of propidium iodide stained <italic>R. reniformis</italic> nuclei indicated a genome size of ~190 Mb. The larger genome size (310 Mb) represented by the assembly is likely the result of unresolved haplotypes stemming from heterogeneity within the <italic>R. reniformis</italic> population used for DNA extraction. Repeat prediction with RepeatModeler (<a ref-type="bibr" href="#j_jofnem-2019-013_ref_014">Smit and Hubley, 2015</a>) and repeat quantification with RepeatMasker (<a ref-type="bibr" href="#j_jofnem-2019-013_ref_015">Smit et al., 2015</a>) identified 245 repeat families within 35.1 Mb of the assembled genome; most elements were DNA transposons or LTR retroelements (20.6 Mb and 11.3 Mb, respectively), while low complexity repeats accounted for 7 Mb. Homologs of known plant-parasitic nematode effector molecules were identified via tBLASTn and included beta-1–4 endogluconase, chitinase, CLE, CEP, chorismate mutase, invertase, ubiquitin extension protein, and venom allergen-like protein as well as cyst nematode pioneers 4D06, GLAND1, GLAND11, GLAND14, GLAND15, 10C02, 20E03, 33A09, 4G05, 7E05, and 10A06 (reviewed by <a ref-type="bibr" href="#j_jofnem-2019-013_ref_008">Mitchum et al., 2013</a>). A variant of the DOG (DOrsal Gland) box DNA motif, an enhancer element associated with dorsal gland effectors (<a ref-type="bibr" href="#j_jofnem-2019-013_ref_005">Eves-van den Akker et al., 2016</a>), was identified in the assembly.
GenBank accession numbers: The raw DNA sequence data and genome assembly were deposited at GenBank under BioProject No. PRJNA214681.
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A genomic resource for the sedentary semi-endoparasitic reniform nematode, <italic>Rotylenchulus reniformis</italic> Linford &amp; Oliveira

Journal of Nematology

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

A genomic resource for the sedentary semi-endoparasitic reniform nematode,  Linford & Oliveira

running-head

The reniform nematode (Rotylenchulus reniformis) is a sedentary semi-endoparasitic species that is pathogenic on many row crops, fruits, and vegetables. Here,...

A genomic resource for the sedentary semi-endoparasitic reniform nematode, Rotylenchulus reniformis Linford & Oliveira

Article Category: Arts & Humanities

Publié en ligne: 23 avr. 2019

Pages: 1 - 2

Reçu: 17 août 2018

DOI: https://doi.org/10.21307/jofnem-2019-013

© 2019 Kurt C. Showmaker et al., published by Sciendo

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