A chromosome‐level genome assembly provides new insights into paternal genome elimination in the cotton mealybug Phenacoccus solenopsis
A chromosome‐level genome assembly provides new insights into paternal genome elimination in the cotton mealybug Phenacoccus solenopsis
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DOI：
10.1111/1755-0998.13232
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发表时间：
2020-08
影响因子：
7.7
通讯作者：
Mei-zhen Li;H. Tong;Shuping Wang;Wanyi Ye;Zicheng Li;Mohamed A. A. Omar-Mohamed-A.-A.-Omar-144770483;Y. Ao;Simin Ding;Zihao Li;Ying Wang;Chuanlin Yin;Xianxin Zhao;K. He;Feiling Liu;Xi Chen;Yang Mei;James R. Walters;M. Jiang;Fei Li
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文献类型：
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作者：
Mei-zhen Li;H. Tong;Shuping Wang;Wanyi Ye;Zicheng Li;Mohamed A. A. Omar-Mohamed-A.-A.-Omar-144770483;Y. Ao;Simin Ding;Zihao Li;Ying Wang;Chuanlin Yin;Xianxin Zhao;K. He;Feiling Liu;Xi Chen;Yang Mei;James R. Walters;M. Jiang;Fei Li
粉蚧（半翅目：假蚧科（Pseudococcusae）是经济上重要的农业害虫，具有几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和不寻常的生物现象的全面理解。在这里，我们通过结合Illumina短读段、PacBio长读段和Hi-C支架，产生了棉花粉蚧（Phenacoccus solenopsis）的染色体水平的基因组组装。组装的基因组为292.54 Mb，重叠群N50为489.8 kb，支架N50为49.0 Mb。Hi-C支架将84.42%的碱基分配给5条染色体。共预测110.75 Mb（37.9%）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转录物被独特地映射到组装的支架上，表明基因组组装的高质量。我们通过分析雄性和雌性的基因组重测序数据发现，棉花粉蚧缺乏分化的性染色体。DAPI染色证实，雄性中的一组染色体在早期胚胎阶段变成异染色质。染色质免疫沉淀分析与测序分析表明，表观遗传修饰H3 K9 me 3和H3 K27 me 3分布在整个基因组中的男性，这表明这两个修饰可能参与维持异染色质状态。两个标记更可能分布在重复区域，而H3 K27 me 3具有更高的总体富集。我们的研究结果提供了一个宝贵的基因组资源，并阐明了棉花粉蚧中PGE的基因组和表观遗传基础。
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.