Diabrotica virgifera

Profile

Species: Diabrotica virgifera virgifera (western corn rootworm)

Order: Coleoptera

Family: Chrysomelidae

Genus: Diabrotica

D. virgifera virgifera is thought to originate from Central America. In the twentieth century, Diabrotica virgifera virgifera became a major pest of maize in North America as maize growing areas increased. The practice of continuous maize growing was largely responsible for the expanding range of D. virgifera virgifera. It is wide-spread in central Europe.

The larvae damage maize roots, which reduces the ability of the plant to absorb water and nutrients from the soil and causes harvesting difficulties due to plant lodging. Adult feeding on silks interferes with pollination. The quantification of yield loss varies according to cultivation practices and location of the field. Generally, yield losses have been estimated at around 15% for every node (i.e. circle of roots) damaged from larval feeding

Source: Centre for Agriculture and Bioscience International https://www.cabi.org/

Sample collection

Collected in Minnesota, USA in 1998. It is susceptible to all known resistant corn and common rootworm insecticides and is accepted as a standard susceptible control by all the major rootworm researchers including University researchers. Genetic studies show that for all practical purposes it is the same as the Brookings WCR population.

Next Generation Sequencing

i) Illumina Hi-C sequencing 150 bp paired end data:

828,362,098 reads and 49x coverage.

ii) PacBio HiFi data (4 smrt cells), of mean read length 11,821, total reads 5,470,381, read length N50 12,719, and total bases 64,666,931,417. Summarized in figures below. DNA was extracted using MagAttract kit at Delaware University (4000ng gDNA).

Methods

Non-sexed single-individual DNA (used for PacBio HiFi (University of Delaware, USA) and multi-individual for Hi-C Illumina sequencing (Arima Genomics USA). Hifiasm was used to assemble the PacBio HiFi, with Juicer then 3d-dna using Hi-C data for chromosome level assembly. Haplotigs were removed (purge_haplotigs). Manual curation was done to bring the genome together and check for miss-assemblies. Unmapped reads were mapped back to the original assembly to check for missing sequence and incorporated into the final assembly. Error correction was done with Hi-C data using freebayes.

BUSCO scores of transcriptome assemblies and public genome annotations:

i) PGI transcriptome Assembly: C:93.1%[S:78.8%,D:14.3%],F:1.2%,M:5.7%

ii) Isoseq mRNA: C:65.1%[S:43.3%,D:21.8%],F:3.9%,M:31.0%

iii) Public genome annotated proteins: C:93.2%[S:73.7%,D:19.5%],F:4.4%,M:2.4%

Other files

These are files that were not submitted to NCBI but might be useful.

Genome PFAM annotation track

Non-coding RNA annotation track