Species: Agriotes lineatus – Wireworm, Lined click beetle
Polyphaous, feeding on many agricultural crops, with a preference for root crops, especially potato. Found in most of Europe, Middle East, Asia, North and parts of South America, Haiti, and New Zealand.
This species prefers humid soil conditions along with relatively high temperatures. The adults appear in early spring, fly at night when temperatures are above 20ºC and are attracted to light. They place their eggs (100-300/female) in vegetation-covered humid soil. The emerging larvae, which are sensitive to dryness, initially feed on humus and then on under- and above-ground plant material. They may go through several (up to 12) instars. At maturity they pupate in the soil, to appear in the spring, sometimes dispersing by flying. Total development requires several years.
This polyphagous pest damages almost all agricultural crops, such as winter cereals, potato, beet, carrot, onion, alfalfa, clover, tomato, and fruit saplings. Most injury is due to feeding on germinating seeds and seedlings of winter crops, and penetrating into roots. Much injury is caused in fields that are periodically covered by standing or irrigation waters. Tomato seedlings, beet and carrot roots, and especially potatoes are heavily damaged. The larvae tunnel into potato tubers whereon they leave small, round holes on the surface and narrow tunnels that run into the flesh. About 20- 80% of the tubers may be affected, reducing their quality and rendering them unmarketable, even when damage is low. These holes also provides access for soil organisms, especially bacterial rots.
Adult stage: Collected June 2021 Syngenta research campus in Stein (collected in Switzerland/Aargau)
larval stage: Collected May 2021 i2L Research Ltd (collected in the UK).
Next Generation Sequencing
Adult stage sample used in PacBio HiFi sequencing.
i) Illumina Omni-C (Dovetail) sequencing 150 bp paired end data:
438,460,378 reads and ~20x coverage.
ii) Illumina RNA-seq stranded sequencing 150 bp paired end data, totalling 52,326,278 reads.
iii) PacBio HiFi data, of mean read length 12,963, total reads 4,549,23, read length N50 12,679, and total bases 58,971,308,893. DNA was extracted using the Qiagen Kit.
Dovetail pipeline - HiFiasm, purging and Omni-C. No Mt or bacteria assembled.
Rothamsted Pipeline - HiFiasm, purging. Mitochondria, Acinetobacter and Entomomonas assembled. Due to duplication present I had issues to get Hi-C step to work but using Juicer and 3d-dna should work well and if can scaffold and then remove duplication then should end up better than dovetail assembly, as the BUSCO is better.
Dovetail pipeline relies upon good coverage which we did not have.
Project ID: PRJEB47908
Largest scaffold: 263,587,734 (10 Chromosomes)
Number of scaffolds: 14,154
Number of gaps: 9,677
Number of N's: 844,561
Total size: 3,159,863,714 bp
Rothamsted Version (Further work needed to scaffold and merge duplication).
Largest scaffold: 1,407,197
Number of scaffolds: 25,481
Number of gaps: 0
Number of N's: 0
Total size: 4,250,135,493 bp
The coverage for this species is only x6 and the 2x smrt cells used should be 8x smrt cells but it was the end of the project and no time or funds to get additional data.