Species: Meligethes aeneus (previously Brassicogethes aeneus) – rape beetle
M. aeneus is a common and widespread species throughout most of the Holarctic Region. Audisio (1993) gave its distribution as the whole of Europe, North Africa, eastwards through Central Asia to the Russian Far East and Mongolia, and in the western states of North America as far south as the north of Mexico. The Asian and North American populations have been regarded as separate subspecies.
The major hosts for M. aeneus in Europe are various Brassica and Sinapis species. It is as a pest of rape that the species is best known. Host plant quality affects egg size. However, at times of the year when its breeding hosts are not in flower, it will feed from the flowers of an enormous range of plant species, especially in early spring and late summer, and has been reported as a pest of strawberry.
The most obvious sign of attack is the presence of shiny black beetles crawling around the flowers of the host plant. Holes in the buds indicate where adults have fed on or laid their eggs in the buds. Severe damage to buds can cause the buds to drop leaving podless stalks. Feeding in the flowers is restricted to the pollen-bearing stamens and few visible symptoms are apparent.
Source: Centre for Agriculture and Bioscience International https://www.cabi.org/isc/datasheet/33259
Adult beetles collected from oilseed rape on the Rothamsted farm in April 2019 (GPS 51.8093°, -0.3548°).
Next Generation Sequencing
i) Illumina Hi-C sequencing 150 bp paired end data:
709,616,444 reads and 182x coverage.
ii) PacBio HiFi data, of mean read length 15,048, total reads 1,046,296, read length N50 16,775, and total bases 15,745,006,744. DNA was extracted using the MagAttract kit (3000ng gDNA).
Non-sexed single-individual 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 and 3d-dna and Hi-C data used 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 and using only homozygous mutations.
RNA-seq transcriptome (BUSCO: C:98.8%[S:47.6%,D:51.2%],F:0.7%,M:0.5%), PRJNA223353 (adult), and PRJEB1765 (larval stages as well as untreated and immunized beetles (injected with different bacteria and yeast)), which were used in the Maker2 annotation pipeline with trained Augustus and Genemark gene predictors. PASA was used to update the gene models to add UTR, correct existing models and add isoforms. Non-coding RNA was annotated using infernal v1.1.4.
A Pfam genomic track was created by converting to six reading frames and utilizing hmmer to identify loci of interest i.e. P450 pfam domains on the genome. Using this information, loci of interest including UDP, P450, and ABC gene models were found and curated using mapped RNA-seq and a Maker gene annotation.
A complete annotated 11 chromosome assembly deposited at NCBI under accession PRJEB48953 (incl. raw data).
BUSCO (Insecta odb10): C:98.6%,F:0.6%,M:0.8%
13,381 gene models - BUSCO C:95.8%[S:85.6%,D:10.2%],F:0.5%,M:3.6%
Scaffold No.(incl Mt): 12
N bases (bp): 40,500
Total size (bp) (chr no.): 585,278,342 (11)
Curated: 127x P450, 91x ABC transporter, 53x UGT, and the 0/130 defined IRAC gene models.
These are files that were not submitted to NCBI but might be useful.
Non-coding RNA annotation track