The brown planthopper Nilaparvata lugens, white‐backed planthopper Sogatella furcifera, and small brown planthopper Laodelphax striatellus are three major insect pests of rice. They are genetically close; however, they differ in several ecological traits such as host range, migration capacity, and in their sex chromosomes. Though the draft genome of these three planthoppers have been previously released, the quality of genome assemblies need to be improved. The absence of chromosome‐level genome resources has hindered in‐depth research of these three species. Here, we performed a de novo genome assembly for N. lugens to increase its genome assembly quality with PacBio and Illumina platforms, increasing the contig N50 to 589.46 Kb. Then, with the new N. lugens genome and previously reported S. furcifera and L. striatellus genome assemblies, we generated chromosome‐level scaffold assemblies of these three planthopper species using HiC scaffolding technique. The scaffold N50s significantly increased to 77.63 Mb, 43.36 Mb and 29.24 Mb for N. lugens, S. furcifera and L. striatellus, respectively. To identify sex chromosomes of these three planthopper species, we carried out genome re‐sequencing of males and females and successfully determined the X and Y chromosomes for N. lugens, and X chromosome for S. furcifera and L. striatellus. The gene content of the sex chromosomes showed high diversity among these three planthoppers suggesting the rapid evolution of sex‐linked genes, and all chromosomes showed high synteny. The chromosome‐level genome assemblies of three planthoppers would provide a valuable resource for a broad range of future research in molecular ecology, and subsequently benefits development of modern pest control strategies.

中文翻译：

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三种稻飞虱的染色体水平基因组为性染色体进化提供了新的见解。

褐飞虱Nilaparvata lugens、白背飞虱Sogatella furcifera和小褐飞虱Laodelphax striatellus是水稻的三大害虫。他们在基因上很接近；然而，它们在一些生态特征上有所不同，例如寄主范围、迁移能力和它们的性染色体。虽然之前已经发布了这三种飞虱的基因组草图，但基因组组装的质量有待提高。染色体水平基因组资源的缺乏阻碍了对这三个物种的深入研究。在这里，我们对N. lugens进行了从头基因组组装使用 PacBio 和 Illumina 平台提高其基因组组装质量，将 contig N50 增加到 589.46 Kb。然后，利用新的褐飞虱基因组和先前报道的S. furcifera和L. striatellus基因组组装，我们使用 HiC 支架技术生成了这三种飞虱物种的染色体水平支架组装。对于N. lugens、S. furcifera和L. striatellus，支架 N50s 分别显着增加到 77.63 Mb、43.36 Mb 和 29.24 Mb 。为了鉴定这三种飞虱的性染色体，我们对雄性和雌性进行了基因组重测序，并成功确定了褐飞虱的 X 和 Y 染色体，以及S. furcifera和L. striatellus 的X 染色体。这三种飞虱的性染色体基因含量显示出高度的多样性，表明性连锁基因的快速进化，并且所有染色体都表现出高度的同线性。三种飞虱的染色体水平基因组组装将为分子生态学的广泛未来研究提供宝贵的资源，随后有利于现代害虫防治策略的发展。