Phyllotreta striolata

Profile

Species: Phyllotreta striolata (Fabricius) – Striped flea beetle/Cabbage flea beetle

Order: Coleoptera

Family: Chrysomelidae

Subfamily: Galerucinae

Tribe: Alticini

Genus: Phyllotreta

P. striolata is Eurasian in origin but now occurs throughout Europe, Asia, Africa and the US.

It is a pest of cabbage and other brassicas. It overwinters among debris in and around fields. Emerging early in spring, they attack seedlings and young plants. Eggs are deposited in tiny crevices gnawed out of the base of host plant stems. About ten days later, the grubs hatch from the eggs and move into the soil to attack roots.

The primary damage is caused by adult beetles feeding on the foliage. With their chewing mouthparts, beetles make small round pits in the cotyledons and leaves of young plants. As the plants grow, the remaining thin layers of tissue eventually dry up and fall away, leaving small "shot holes" in the foliage. This type of injury is capable of killing young plants. The seedlings may be killed if severe damage occurs. In addition, beetles may act as vectors of plant disease.

Source: https://en.wikipedia.org/wiki/Striped_flea_beetle

Sample collection

Single individual, of unknown sex. A mixed sample was taken with Phyllotreta cruciferae 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 10,255, total reads 241,153, read length N50 11,043, and total bases 2,473,243,844. Summarized in figures below. DNA was extracted using MagAttract kit at the University of Delaware (150ng gDNA).

Methods

Non-sexed single-individual was 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.

RNA-seq data was taken from PRJNA299458 (male and female antenna and terminal abdomen), PRJNA679396 (No meta data) and assembled into a transcriptome (BUSCO: C:98.2%[S:96.2%,D:2.0%],F:0.1%,M:1.7%). This was 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, ABC and IRAC gene models were found and curated using mapped RNA-seq and a Maker gene annotation.

An endosymbiont Wolbachia (1,546,488 bp) was assembled.

Genome files

Genome fasta file

Annotation gff file

Other files

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

Genomic PFAM annotation track

Non-coding RNA annotation track

Repeat annotation track

Repeat library