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The brown planthopper (<jats:italic>Nilaparvata lugens<\/jats:italic> St\u00e5l) is the most economically damaging pest to rice and is also an ideal research subject for paddy ecology and functional genomics. We previously assembled a draft female genome mainly using second\u2010generation sequencing technologies, with a contig N50 of only 24\u00a0kb, due to the large size and excessive repetitive regions in the <jats:italic>N<\/jats:italic>.<jats:italic>\u00a0lugens<\/jats:italic> genome. Here, we utilize third\u2010generation sequencing technologies and Hi\u2010C data to generate a high\u2010quality male <jats:italic>N<\/jats:italic>.<jats:italic>\u00a0lugens<\/jats:italic> assembly with a contig N50 of 1.01\u00a0Mb, a scaffold N50 of 69.96\u00a0Mb and more than 95.6% of the assembled bases located on 16 chromosomes. Fourteen autosomes and two sex chromosomes (X\u00a0+\u00a0Y) were identified, filling in the gap related to the Y chromosome in heterometabolous insects. A total of 18,021 protein\u2010coding genes and 6423 long\u2010noncoding RNAs were predicted with full\u2010length cDNA sequencing data. All 315 of the Y chromosome genes (Y\u2010genes) were derived from autosomal and X\u2010chromosome duplications. Large\u2010scale RNA interference (RNAi) experiments were conducted against the <jats:italic>N<\/jats:italic>.<jats:italic>\u00a0lugens<\/jats:italic> Y\u2010genes, demonstrating that 7 Y\u2010genes were essential for normal BPH development or male organ development, suggesting the importance of Y\u2010genes. The first identified Y chromosome in heterometabolous insects will help gain more insight into sex determination, fertility and chromosome evolution.<\/jats:p>","DOI":"10.1111\/1755-0998.13328","type":"journal-article","created":{"date-parts":[[2021,1,18]],"date-time":"2021-01-18T21:59:56Z","timestamp":1611007196000},"page":"1287-1298","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":45,"title":["Chromosome\u2010level assembly of the brown planthopper genome with a characterized Y chromosome"],"prefix":"10.1111","volume":"21","author":[{"given":"Yu\u2010Xuan","family":"Ye","sequence":"first","affiliation":[{"name":"State Key Laboratory of Rice Biology Institute of Insect Science Zhejiang University Hangzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hou\u2010Hong","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Rice Biology Institute of Insect Science Zhejiang University Hangzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dan\u2010Ting","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Rice Biology Institute of Insect Science Zhejiang University Hangzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ji\u2010Chong","family":"Zhuo","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro\u2010products, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province Institute of Plant Virology Ningbo University Ningbo China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Shen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Rice Biology Institute of Insect Science Zhejiang University Hangzhou 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China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2021,2,16]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13100-015-0041-9"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx198"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.1865504"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cois.2014.12.003"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.2727"},{"key":"e_1_2_8_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giz100"},{"key":"e_1_2_8_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0959-437X(02)00356-8"},{"key":"e_1_2_8_9_1","doi-asserted-by":"publisher","DOI":"10.1104\/pp.18.00848"},{"issue":"6333","key":"e_1_2_8_10_1","first-page":"92","article-title":"De novo assembly of the Aedes aegypti genome using Hi\u2010C yields chromosome\u2010length 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