Draft Genome Assembly and Comparative Genomic Analysis of the Plant-Parasitic Nematode Rotylenchulus reniformis

The plant-parasitic nematode, Rotylenchulus reniformis, can infect a large number of agriculturally important crop species, and accounts for an estimated $130,000,000 USD annual loss in cotton production. Very little molecular characterization of R. reniformis has been conducted previously, and prior literature suggests that only 37 Mb (19.5%) of the estimated 190 Mb genome has been analyzed. We have generated a draft genome assembly for R. reniformis assembled from Illumina sequence reads from both pooled populations of recently colonized R. reniformis and whole genome amplification (WGA) of a single R. reniformis egg. Obtaining contiguity and completeness for the R. reniformis genome assembly comparable to that of the genome assemblies of model organisms is difficult due to the heterozygosity present in recently colonized species, and this is a known issue when working with pooled populations of plant-parasitic nematodes. Both the pooled population sequence reads and the WGA sequence reads were assembled independently with ABySS, and both assemblies were then merged into a unified set of sequences. Finishing of the assembly was performed using GapFiller and SSPACE. Here we present our R. reniformis draft genome assembly, initial genome annotations, and comparative analysis of our assembly to the assemblies of other plant-parasitic nematode species.