The migratory endoparasite, Radopholus similis, is a pest to over 250 plant species, including economically important crops such as banana and citrus (Haegeman et al., 2010). Damage caused by R. similis feeding on roots can lead to secondary infections by fungi and bacteria, eventually leading to root collapse and in some instances, as with banana, plant toppling (Haegeman et al., 2010). With a wide geographical distribution including North and South America, the Caribbean, Africa, and Asia, there have been efforts to better understand the mechanisms behind this nematode’s ability to infect its hosts. These efforts include characterizing cell-wall degrading enzymes (Haegeman et al., 2008; Haegeman et al., 2009), sequencing of the mitochondrial genome (Jacob et al., 2009), and generating multi-stage transcriptomes (Jacob et al., 2008; Huang et al., 2019). The addition of genomes from multiple populations would be beneficial to the community characterizing this nematode.
Radopholus similis samples were collected from two different locations and hosts in Costa Rica. Nematodes were collected from plantain roots in La Virgen, Sarapiquí (Rv) and from bananas in Río Frío, Horquetas, Sarapiquí (Rd). After samples were collected, adult R. similis were randomly hand-picked from each sample. QIAmp DNA Micro Kit (Qiagen, Hilden, Germany) was used to extract DNA from 560 and 1,000 adults from the Rd and Rv populations, respectively. From these DNA extractions, genomic libraries were made using NEBNext Ultra II DNA Library Prep Kit for Illumina (San Diego, CA). Whole genome sequencing was performed on the Illumina HiSeq 3000 at the Center for Genome Research and Biocomputing at Oregon State University (Corvallis, OR). Raw reads were screened for sequencing adapters, trimmed and filtered for quality (Q = 20) using BBDuk (https://github.com/BioInfoTools/BBMap) and resulted in 5,376,812 and 14,006,275 paired-end 150 reads for Rd and Rv, respectively. Quality-filtered reads were assembled de novo using metaSPAdes (Nurk et al., 2017) and putative taxonomic origins of the resulting contigs were investigated using the Blob Tools workflow (Kumar et al., 2013). Briefly, individual contigs were assigned a phylum based on BLAST similarity (E-value < 10e−25) to sequences found in the NCBI “nt” database and visualized based on average read coverage and GC content (Kumar et al., 2013). To remove fungal and bacterial contamination, reads that were identified as belonging to contigs assigned to the phylum Nematoda or had no identity were then used to assemble the R. similis genome in the de novo assembler SPAdes Version 3.12 (Bankevich et al., 2012). Contigs in the assembly that were less than 500 bp were removed and QUAST was used to calculate genome assembly statistics (Gurevich et al., 2013).
The resulting genome assemblies for R. similis populations Rv and Rd were 50,532,728 and 50,089,881 bp in size, respectively (Table 1). The Rv assembly had approximately 1,000 contigs fewer than the Rd assembly, which had 6,195 contigs in total. The N50 for the two assemblies were similar in size; the Rv assembly had a N50 of 27,798 bp while the Rd assembly N50 was 20,071 bp. The largest contig in the Rd assembly was over 170,000 bp, while the largest contig in the Rv assembly was ~160,000 bp. Both assemblies had a GC% content of 47%, consistent with the GC content of the R. similis transcriptome, found to be 49% (Jacob et al., 2008).
Table 1.
Comparison of the genome assemblies of Radopholus similis population collected from Costa Rica.
| Assembly Statistic | Population (Rv)a | Population (Rd)b | ASM476467v1c |
|---|---|---|---|
| Size (bp) | 50,555,211 | 50,089,881 | 65,195,707 |
| Number of Scaffolds | 5,194 | 6,195 | 8,133 |
| Largest Scaffold (bp) | 159,742 | 174,442 | 502,931 |
| GC Content (%) | 47.06 | 47.11 | 51.64 |
| N50 Value (bp) | 27,798 | 20,071 | 13,529 |
| No. Contigs > 5,000 bp | 2,081 | 2,476 | 3,451 |
| No. Contigs > 10,000 bp | 1,468 | 1,587 | 1,726 |
| No. Contigs > 25,000 bp | 618 | 499 | 419 |
| No. Contigs > 50,000 bp | 167 | 95 | 83 |
| Complete BUSCOs | 588 (59.9%) | 593 (60.4%) | 585 (59.5%) |
| Complete and single-copy BUSCOs | 573 (58.4%) | 577 (58.8%) | 564 (57.4%) |
| Complete and duplicated BUSCOs | 15 (1.5%) | 16 (1.6%) | 21 (2.1%) |
| Fragmented BUSCOs | 93 (9.5%) | 95 (9.7%) | 85 (8.7%) |
| Missing BUSCOs | 301 (30.6%) | 294 (29.2%) | 312 (31.8%) |