Mealybugs (Hemiptera: Pseudococcidae) are economically important agricultural pests with several compelling biological phenomena including paternal genome elimination (PGE). However, limited high‐quality genome assemblies of mealybugs hinder a full understanding of this striking and unusual biological phenomenon. Here, we generated a chromosome‐level genome assembly of cotton mealybug, Phenacoccus solenopsis, by combining Illumina short reads, PacBio long reads and Hi‐C scaffolding. The assembled genome was 292.54 Mb with a contig N50 of 489.8 kb and a scaffold N50 of 49.0 Mb. Hi‐C scaffolding assigned 84.42% of the bases to five chromosomes. A total of 110.75 Mb (37.9%) repeat sequences and 11,880 protein‐coding genes were predicted. The completeness of the genome assembly was estimated to be 95.5% based on BUSCO genes. In addition, 27,086 (95.3%) full‐length PacBio transcripts were uniquely mapped to the assembled scaffolds, suggesting the high quality of the genome assembly. We showed that cotton mealybugs lack differentiated sex chromosomes by analysing genome resequencing data of males and females. DAPI staining confirmed that one chromosome set in males becomes heterochromatin at an early embryo stage. Chromatin immunoprecipitation assays with sequencing analysis demonstrated that the epigenetic modifications H3K9me3 and H3K27me3 are distributed across the whole genome in males, suggesting that these two modifications might be involved in maintaining heterochromatin status. Both markers were more likely to be distributed in repeat regions, while H3K27me3 had higher overall enrichment. Our results provide a valuable genomic resource and shed new light on the genomic and epigenetic basis of PGE in cotton mealybugs.

中文翻译：

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染色体水平的基因组组装为棉花粉蚧 Phenacoccus solenopsis 中父本基因组消除提供了新见解

粉蚧（半翅目：假球菌科）是经济上重要的农业害虫，具有多种引人注目的生物学现象，包括父本基因组消除 (PGE)。然而，粉蚧有限的高质量基因组组装阻碍了对这种惊人的、不寻常的生物现象的充分理解。在这里，我们生成了棉粉蚧Phenacoccus solenopsis的染色体水平基因组组装，通过结合 Illumina 短读长、PacBio 长读长和 Hi-C 支架。组装的基因组为 292.54 Mb，具有 489.8 kb 的重叠群 N50 和 49.0 Mb 的支架 N50。Hi-C 支架将 84.42% 的碱基分配给五个染色体。预测了总共 110.75 Mb (37.9%) 的重复序列和 11,880 个蛋白质编码基因。基于BUSCO基因，基因组组装的完整性估计为95.5%。此外，27,086 (95.3%) 个全长 PacBio 转录本被唯一映射到组装的支架上，表明基因组组装的质量很高。我们通过分析雄性和雌性的基因组重测序数据表明棉粉蚧缺乏分化的性染色体。DAPI 染色证实，雄性中的一条染色体在胚胎早期就变成了异染色质。染色质免疫沉淀分析和测序分析表明，表观遗传修饰 H3K9me3 和 H3K27me3 分布在男性的整个基因组中，表明这两种修饰可能与维持异染色质状态有关。这两个标记更可能分布在重复区域，而 H3K27me3 具有更高的整体富集度。我们的结果提供了宝贵的基因组资源，并为棉花粉蚧中 PGE 的基因组和表观遗传基础提供了新的线索。而 H3K27me3 具有更高的整体富集度。我们的结果提供了宝贵的基因组资源，并为棉花粉蚧中 PGE 的基因组和表观遗传基础提供了新的线索。而 H3K27me3 具有更高的整体富集度。我们的结果提供了宝贵的基因组资源，并为棉花粉蚧中 PGE 的基因组和表观遗传基础提供了新的线索。