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.蓟马（Thrips）是一类隶属于缨翅目（Thysanoptera，六足总纲：有须类群Condylognatha）的小型昆虫，其中包含诸多吸汁性害虫，当前已在全球范围内对农作物造成日益加剧的危害。与它们的近缘类群半翅目（Hemiptera，Hexapoda: Condylognatha）——该类群包含大量吸汁性物种——相比，目前针对蓟马的基因组学研究资源仍较为匮乏。本研究以农业生产中的重大害虫瓜蓟马（Thrips palmi）为研究材料，利用PacBio长读长测序技术与Illumina短读长测序技术，首次组装获得了染色体级别的蓟马基因组。组装获得的基因组总长度为270.43 Mb，共包含4120个重叠群（contig），重叠群N50长度为426 kb。借助Hi-C技术，所有重叠群被挂载至16个连锁群中。本研究共预测得到16333个蛋白质编码基因，其中88.13%的基因获得了功能注释。在吸汁性昆虫中，多食性物种通常比寡食性物种拥有更多的解毒基因。截至目前已被表征的多食性蓟马基因组亦呈现出类似特征……为了修正不准确的功能注释，并直接从DNA序列中鉴定出此前未被发现的基因家族拷贝，本研究对7个基因家族进行了手动注释，其中包括细胞色素P450单加氧酶（cytochrome P450 monooxygenase, P450s）、谷胱甘肽S-转移酶（glutathione S-transferase, GSTs）、羧酸酯酶/胆碱酯酶（carboxyl/cholinesterases, CCEs）、UDP-糖基转移酶（UDP-glycosyltransferases, UGTs）、ATP结合盒转运蛋白（ATP-binding cassette transporter, ABCs）、热休克蛋白（heat shock proteins, HSPs）以及烟碱型乙酰胆碱受体（nicotinic acetylcholine receptors, nAChRs）。本研究借助隐马尔可夫模型（Hidden Markov Models, HMMs）以及来自近缘物种西花蓟马（Frankliniella occidentalis, F. occidentalis）和模式物种黑腹果蝇（Drosophila melanogaster, D. melanogaster）的直系同源基因进行基因鉴定；相关分析分别通过HMMER v3.3（Finn等，2011）与BLAST v2.2.31（Altschul等，1990）工具完成。隐马尔可夫模型下载自Pfam 32.0数据库（2018年9月，共17929条条目）（El-Gebali等，2018）。本研究采用生物信息学分析流程BITACORA（全模式）开展HMMER与BLAST分析（Vizueta等，2019）。分析得到的比对结果通过默认的E值阈值10^-……进行过滤。比较基因组学与功能基因组学。