High quality genomic resources for stored product insects

Abstract

The expansion of genomic resources for stored product insects has largely been hampered by cost, time required for inbreeding, and technical issues that can arise during genome assembly from pooling multiple individuals together for DNA isolation and library preparation. However, newer library methods, such as 10X Chromium libraries, largely overcome these issues in that sufficient DNA can be recovered from a single individual for library prep and allelic variants are assembled as separate phase blocks, eliminating the need for inbreeding. Using 10X Chromium libraries coupled with 150 x 150 bp HiSeqX sequencing to a depth of at least 60X coverage, we are developing high quality draft genome assemblies for eight different stored product insect species, including Dermestidae (Trogoderma variabile, Trogoderma granarium, and Dermestes maculatus), Tenebrionidae (Tribolium confusum), Anobiidae (Lasioderma serricorne and Stegobium paniceum), Bostrichidae (Prostephanus truncatus), and Pyralidae (Plodia interpunctella). Overall, BUSCO (Benchmarking Using Single Copy Orthologs) scores exceeded 95% in all assemblies with few fragmented or duplicated genes, suggesting a high quality assembly of the gene space. Further, scaffold N50s exceeded 1 Mb in many cases and further improvements to these scaffolding metrics will be made using linkage maps and Hi-C libraries. Overall, this approach will yield high quality assemblies for eight different insects and could be used to quickly and efficiently generate draft assemblies of invasive or emerging stored product pests.