The Lesser Grain Borer, Rhyzopertha dominica, Genome Sequencing Project

The order Coleoptera contains more than 350,000 species and includes some of the most problematic agricultural pests, but there are only two fully sequenced beetle genome assemblies to date, although several are in the pipeline at i5k.  The lesser grain borer, Rhyzopertha dominica, is an economically important pest of grains and stored products, and the immature stages develop within a wheat kernel and are difficult to control.  Phosphine fumigation is the most effective control method for R. dominica infestations, but efficacy has decreased because of worldwide development of resistant insects.  We need genomic data to identify new control strategies and to analyze phosphine-resistant and -susceptible colonies of R. dominica.  Therefore, we selected a highly inbred strain (more than 30 generations of single-pair matings) for genomic sequencing.  We acquired both short and long read data, including long read data (P6 chemistry) from mixed sex pupae of the inbred R. dominica strain estimated at 56x coverage.  We developed a pipeline for error correction and assembly of long-read data using Mhap/CA on a public compute cluster.  We compared Mhap assemblies using different parameters to another using Falcon.  We also performed quality assessments with BUSCO and CEGMA that indicate coverage of reference sequences is approximately 88–98%, but some of the reference gene sequences are fragmented.  We discuss genes found in the dataset related to grain borer biology and phosphine resistance.  We also make recommendations regarding future insect genome sequencing.  The genome database will be useful to develop new insect control products for R. dominica, and also will provide valuable information for cross-genome comparisons of beetles.  Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.  USDA is an equal opportunity employer.