DOI: 10.5061/dryad.1rn8pk0qb
title: Data from: Chromosome-level genome of the melon thrips yields insights into evolution of a sap-sucking lifestyle and pesticide resistance

description: 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 more detoxification genes in the GST and CCE families than
 polyphagous aphids, but they have fewer UGTs. HSP genes, especially from
 the Hsp70s group, have expanded in thrips compared to other hemipteran
 insects. These differences point to different genetic mechanisms
 associated with detoxification and stress responses in these two groups of
 sap-sucking insects. The expansion of these gene families may contribute
 to the rapid development of pesticide resistance in thrips, as supported
 by a transcriptome comparison of resistant and sensitive populations of T.
 palmi. The high-quality genome developed here provides an invaluable
 resource for understanding the ecology, genetics and evolution of thrips
 as well as their relatives more generally.
description: 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 <i>F. occidentalis</i> and model species of
 <i>D. melanogaster</i> provided evidence for gene
 identification, run with
 HMMER v3.3 <i>(</i><i>Finn et al.
 2011</i><i>)</i> and BLAST v2.2.31 <i>(</i><i>Altschul et
 al. 1990</i><i>)</i>. The HMMs were downloaded from Pfam 32.0
 (September 2018, 17929 entries) <i>(</i><i>El-Gebali et al.
 2018</i><i>)</i>. We used the bioinformatic pipeline BITACORA
 (full
 mode) to conduct HMMER and
 BLAST analyses <i>(</i><i>Vizueta et al.
 2019</i><i>)</i>. Hits were filtered with a default cut-off
 E-value of 10e-5. The
 annotated genes were further filtered manually based on gene length and
 the presence of conserved domains. We removed genes with a length shorter
 than 80% of the average gene length. Orthologs were aligned with the
 G-INS-I algorithm implemented in MAFFT v7.450
 <i>(</i><i>Katoh& Standley
 2013</i><i>)</i>. A neighbor-joining tree was constructed for each
 gene family using MEGA7 <i>(</i><i>Kumar et al.
 2016</i><i>)</i> with 500 bootstrap
 replicates.
description: Comparative and functional genomics.