Genomes Of Two Sap-sucking Rice Insect Pests And Population Genetics Of The Rice Brown Planthopper

As the staple food of more than half of the world’s population,rice suffers from many pests in production.To better study the molecular outbreak mechanisms of these rice pests and for better pests control and management,it is essential to obtain their genomic sequences.At present,the genomic information of most species is still unknown.Moreover,the quality of the genomes that have been reported is also uneven.In addition,how to make good use of these genomes to unravel more genetic mechanisms associated with biological traits still need further efforts.In this study,high-throughput sequencing technologies were used to carry out researches on the genomes of three sap-sucking rice pests.The main conclusions obtained are as follows:1)We generated a chromosome-level genome of three rice planthoppers(brown planthopper,white-backed planthopper and small brown planthopper)using Oxford Nanopore Technologies(ONT)and high-throughput chromatin conformation capture(Hi-C)technology,and here we report genome of SBPH.We also sequenced RNA-seq data from SBPH 16 tissue samples to annotate the genome and analyze gene dosage compensation.We finally obtained a 510.2 megabases(Mb)genome with 99.12% of the scaffolds anchored on 15 chromosomes(14 autosomes and 1 X-chromosome)and annotated 16160 protein-coding genes based on full-length c DNA sequencing data.Furthermore,we found complete dosage compensation in all L.striatellus somatic tissues,but lack of dosage compensation in gonad tissue testis.We also found that female-biased genes were significantly enriched on the X-chromosome in all tissues,whereas male-biased genes in gonad tissues were enriched on autosomes.2)By combining multiple sequencing technologies,including Pac Bio,Illumina short-reads,and Hi-C technology,we de nova assembled the chromosome-level genome of Stenchaetothrips biformis,an oligophagous rice pest.A 338.86 Mb genome was obtained,with a scaffold N50 size of 18.21 Mb.Thereafter,17,167 protein-coding genes and 36.25% repetitive elements were annotated.By comparative genomic analyses with another two polyphagous thrips,we found that in S.biformis,the chemosensory-related genes GRs,ORs and IRs were contracted,reflecting its lower host range,whereas genes in response to stress and diary/detoxification sublineages of carboxyl/cholinesterase were expanded,which might be involved in rice adaptation.In polyphagous thrips,Frankliniella occidentalis and Thrips palmi,expansion gene families were enriched in the metabolism of aromatic and anthocyanin-containing compounds,and immunity to viruses and bacteria.3)By globally sampling and sequencing 358 genomes of the brown planthopper(BPH),the most destructive rice pest,we genetically uncover the landscape of the worldwide migration and dispersal in this tiny migratory pest.We characterize the sources of global BPHs as three migratory and three localized groups,showing the strong role of migration in shaping population structures.Furthermore,we find that only East Asia populations migrate within a complete loop between Indochina and the Far East,which differs from Southeast Asia and South Asia migrants who are one-way imported to Indochina from respectively distal ends.More surprisingly,the uniquely evolved regions of these more active migrants are limited to a chromosome that is simultaneously highly diverged between BPH and related species.We also find that the insecticide-resistance alleles are more likely to be derived upon the selection relaxation,and that their evolution is more related to the application of insecticides than migration.This study not only provides a high-quality genome assembly of L.striatellus and T.palmi,but also lays a foundation for a better understanding of the sexual regulatory network in hemipteran insects and for further studies on thrips evolution and pest management.Specifically,this study enhances our understanding of how seasonal migration drives the speciation and evolution in tiny insects,and yields valuable genomic resources for the early warning and management of N.lugens.