Chromosome-level genome of the melon thrips yields insights into evolution of a sap-sucking lifestyle and pesticide resistance

Thrips are tiny insects from the order Thysanoptera (Hexapoda: Condylognatha), including many sap-sucking pests that are causing increasing damage to crops worldwide. In contrast to their closest relatives of Hemiptera (Hexapoda: Condylognatha) including numerous sap-sucking species, there are few genomic resources available for thrips. In this study, we assembled the first thrips genome at the chromosome level from the melon thrips, Thrips palmi, a notorious pest in agriculture, using PacBio long-read and Illumina short-read sequences. The assembled genome was 270.43 Mb in size with 4,120 contigs and a contig N50 of 426 kb. All contigs were assembled into 16 linkage groups assisted by the Hi-C technique. In total, 16,333 protein-coding genes were predicted, of which 88.13% were functionally annotated. Among sap-sucking insects, polyphagous species usually possess more detoxification genes than oligophagous species. The polyphagous thrips genomes characterized so far have relatively mor..., To facilitate both the curation of inaccurate annotations and the identification of previously undetected gene family copies directly from DNA sequences, we manually annotated seven gene families, including detoxification genes of cytochrome P450 monooxygenase (P450s), glutathione S-transferase (GSTs), carboxyl/cholinesterases (CCEs), UDP-glycosyltransferases (UGTs) and ATP-binding cassette (ABC) transporter, heat shock proteins (HSPs), and nicotinic acetylcholine receptors (nAChRs). Hidden Markov models (HMMs) and orthologs from related species of F. occidentalis and model species of D. melanogaster provided evidence for gene identification, run with HMMER v3.3 (Finn et al. 2011) and BLAST v2.2.31 (Altschul et al. 1990). The HMMs were downloaded from Pfam 32.0 (September 2018, 17929 entries) (El-Gebali et al. 2018). We used the bioinformatic pipeline BITACORA (full mode) to conduct HMMER and BLAST analyses (Vizueta et al. 2019). Hits were filtered with a default cut-off E-value of 10e-..., Comparative and functional genomics.