Chromosome‐level assembly of the brown planthopper genome with a characterized Y chromosome

Abstract Hundreds of insect genome sequences have been reported; however, most sequencing projects have not determined the sex chromosomes, and no Y chromosomes from a heterometabolous insect have been identified and characterized to date. The brown planthopper ( Nilaparvata lugens Stål) 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‐generation sequencing technologies, with a contig N50 of only 24 kb, due to the large size and excessive repetitive regions in the N . lugens genome. Here, we utilize third‐generation sequencing technologies and Hi‐C data to generate a high‐quality male N . lugens assembly with a contig N50 of 1.01 Mb, a scaffold N50 of 69.96 Mb and more than 95.6% of the assembled bases located on 16 chromosomes. Fourteen autosomes and two sex chromosomes (X + Y) were identified, filling in the gap related to the Y chromosome in heterometabolous insects. A total of 18,021 protein‐coding genes and 6423 long‐noncoding RNAs were predicted with full‐length cDNA sequencing data. All 315 of the Y chromosome genes (Y‐genes) were derived from autosomal and X‐chromosome duplications. Large‐scale RNA interference (RNAi) experiments were conducted against the N . lugens Y‐genes, demonstrating that 7 Y‐genes were essential for normal BPH development or male organ development, suggesting the importance of Y‐genes. The first identified Y chromosome in heterometabolous insects will help gain more insight into sex determination, fertility and chromosome evolution.