Phyllotreta cruciferae

Profile

Species: Phyllotreta cruciferae (Goeze) - Crucifer flea beetle

Order: Coleoptera

Family: Chrysomelidae

Tribe: Alticini

Genus: Phyllotreta

P. Cruciferae is widespread in the northern hemisphere, where it is a limiting factor in the production of oilseed rape on the Canadian prairies and midwestern USA. It feeds on a variety of Brassicas and other crucifers. It also a chronic pest in Europe and Russia.

Seedlings are most vulnerable with adults feeding on hypocotyls and meristems of emerging plants, as well as on cotyledons, leaves and stems. Larvae are root feeders. On maturing crops, adults will feed on green pods and heads. Later in the season, feeding by adults can cause brown flecks on curds of cauliflower or florets of broccoli, making the heads unmarketable. Severe de-barking by adult beetles of seed pod epidermal tissue can result in premature pod drying, shriveled seeds and pod shattering, and may encourage fungal growth within the pods in damp weather.

Plant phytochemistry plays an important part in host selection by the crucifer flea beetle. Crucifer species and varieties within species have been shown to vary in damage to crucifer flea beetles. Brassica oleracea, B. napus and B. rapa are generally susceptible, B. juncea is partially resistant, and B. carinata, Sinapis alba and Crambe abyssinica are generally resistant to flea beetle feeding.

Source: CABI PlantWIse Knowledge Bank https://www.plantwise.org/knowledgebank

Sample collection

Single individual, of unknown sex. A mixed sample was taken with Phyllotreta striolata from Canada in September 2020.

Next Generation Sequencing

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

852,080,958 reads and 478x coverage.

ii) PacBio HiFi data, of mean read length 10,707, total reads 392,759, read length N50 11,416, and total bases 4,205,341,306. DNA was extracted using MagAttract kit at the University of Delaware (200ng 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.

Two endosymbiont, Wolbachia (1,795,892 bp) and Spiroplasma (736,059 bp) were assembled.


Final Results

A complete annotated 17 chromosome assembly deposited at NCBI under accession PRJEB47901 (incl. raw data).

BUSCO (Insecta odb10): C:99.3%,F:0.1%,M:0.6%

Scaffold No. (incl Mt): 18

N50: 7,733,062

N bases (bp) 44,500

Repeat: N/A

Total size (bp) (chr no.): 135,120,912 (17)

An annotation was not performed due to a lack of RNA-seq data.

Two endosymbiont Wolbachia (1,795,892 bp) and Spiroplasma (736,059 bp) were assembled.

An annotation request at NCBI will be placed upon public release.


Other files

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

Non-coding RNA annotation track