Chromosome-level Assembly, Dosage Compensation and Sex-biased Gene Expression in the Small Brown Planthopper, Laodelphax striatellus.

In insects, sex chromosome differentiation often results in unequal gene dosages between sexes. Dosage compensation mechanisms evolve to balance gene expression, but the degree and mechanism of regulation often vary by insect species. In hemipteran species, the small brown planthopper (SBPH), Laodelphax striatellus, is an injurious crop pest, with a sex chromosome type XX in females and XO in males. This species offers the opportunity to study dosage compensation and sex-biased gene expression. In this study, we generated a chromosome-level genome of SBPH using Oxford Nanopore Technologies and high-throughput chromatin conformation capture (Hi-C) technology. We also sequenced RNA-seq data from 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 16,160 protein-coding genes based on full-length cDNA 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. This study not only provides a high-quality genome assembly but also lays a foundation for a better understanding of the sexual regulatory network in hemipteran insects.

在昆虫中，性染色体分化常常导致两性之间基因剂量不平等。剂量补偿机制随之进化以平衡基因表达，但调节的程度和机制往往因昆虫种类而异。在半翅目昆虫中，灰飞虱是一种有害的农作物害虫，雌性性染色体为XX型，雄性为XO型。该物种为研究剂量补偿和性别偏向基因表达提供了机会。在本研究中，我们利用牛津纳米孔技术和高通量染色质构象捕获（Hi - C）技术构建了灰飞虱的染色体水平基因组。我们还对16个组织样本进行了RNA - seq测序，以注释基因组并分析基因剂量补偿。最终我们获得了一个510.2兆碱基（Mb）的基因组，其中99.12%的支架锚定在15条染色体上（14条常染色体和1条X染色体），并基于全长cDNA测序数据注释了16160个蛋白质编码基因。此外，我们发现灰飞虱所有体细胞组织中存在完全的剂量补偿，但在性腺组织睾丸中缺乏剂量补偿。我们还发现，在所有组织中，雌性偏向基因在X染色体上显著富集，而性腺组织中的雄性偏向基因在常染色体上富集。这项研究不仅提供了高质量的基因组组装，还为更好地理解半翅目昆虫的性别调控网络奠定了基础。