Chromosome-level assembly of the brown planthopper genome with a characterized Y chromosome
Chromosome-level assembly of the brown planthopper genome with a characterized Y chromosome
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具有特征性 Y 染色体的褐飞虱基因组的染色体水平组装
DOI：
10.1111/1755-0998.13328
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发表时间：
2021
影响因子：
7.7
通讯作者：
Zhang Chuan-Xi
中科院分区：
文献类型：
--
作者：
Ye Yu-Xuan;Zhang Hou-Hong;Li Dan-Ting;Zhuo Ji-Chong;Shen Yan;Hu Qing-Ling;Zhang Chuan-Xi
已经报道了数百种昆虫基因组序列;然而，大多数测序项目尚未确定性染色体，迄今为止还没有鉴定和表征异代谢昆虫的Y染色体。褐飞虱（Nilaparvata lugensStål）是水稻上危害最大的害虫，也是水稻生态学和功能基因组学的理想研究对象。我们之前主要使用第二代测序技术组装了一个女性基因组草图，由于N. lugens基因组中的大尺寸和过度重复区域，重叠群N50仅为24 kb。在这里，我们利用第三代测序技术和Hi-C数据来生成高质量的雄性N. lugens组装体，其重叠群N50为1.01 Mb，支架N50为69.96 Mb，超过95.6%的组装碱基位于16条染色体上。鉴定出14条常染色体和2条性染色体（X + Y），填补了异代谢昆虫Y染色体的差距。利用全长cDNA测序数据预测了总共18，021个蛋白质编码基因和6423个长非编码RNA。所有315个Y染色体基因（Y基因）都来自常染色体和X染色体复制。针对N.lugensY基因进行了大规模RNA干扰（RNAi）实验，证明7个Y基因对正常BPH发育或雄性器官发育至关重要，表明Y基因的重要性。首次在异代谢昆虫中发现Y染色体，将有助于深入了解性别决定、生育力和染色体进化。
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 lugensStål) 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 theN.lugensgenome. Here, we utilize third‐generation sequencing technologies and Hi‐C data to generate a high‐quality maleN.lugensassembly 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 theN.lugensY‐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.