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为研究野桑蚕(Bombyx mandarina)全基因组甲基化特性及蛹滞育与基因组DNA甲基化关系，本研究首先测序组装了秦巴野桑蚕基因组，在此基础上对不同时期的蛹滞育材料进行基因组甲基化测序，分析DNA甲基化特征，鉴定差异甲基化区域及相关基因。结果表明，秦巴野桑蚕基因组大小为457.85 Mb,蛋白编码基因12 280个，rRNA、 sRNA、 tRNA分别为158、 6 951和778个，同时鉴定获得672个扩张基因家族和1 894个收缩基因家族。全基因组DNA甲基化分析表明，不同时期的全基因组mC水平均在0.69%以下，甲基化形式以mCG为主，甲基化主要分布于编码基因体上游、下游2 kb及基因体中，未在转座子及其上下游区域内检测到甲基化现象。差异甲基化区域分析表明，蛹滞育中期vs早期、蛹滞育晚期vs早期和蛹滞育中期vs晚期的差异区域分别为807、 1 545和804个，基因组在蛹滞育的解除过程存在去甲基化事件。差异甲基化区域相关基因分析共鉴定获得1 496个相关基因，功能富集分析发现Foxo、 Hippo、 Jak-STAT、 mTOR、 Wnt等多个细胞信号转导途径的组成元件参与调控野桑蚕蛹滞育。本研究为深入研究表观遗传在蛹滞育调控中的作用机制提供参考。
Abstract：Aimed to investigate the relationship between diapause and genomic DNA methylation in the wild silkworm(Bombyx mandarina), this study conducted genome-wide methylation sequencing on diapause pupae at different stages based on the genome assembly of B. mandarina from the Qinba region. The analysis included examining DNA methylation patterns, identifying differentially methylated regions, and annotating related genes. The results showed that the genome size of B. mandarina is approximately 457.85 Mb, with 12 280 protein-coding genes, 158 rRNAs, 6 951 sRNAs, and 778 tRNAs. Additionally, 672 expanded gene families and 1 894 contracted gene families were identified. Whole-genome methylation profiling revealed that the global mC levels across different stages remained below 0.69%, with mCG being the predominant methylation form. Methylation was primarily located within 2 kb upstream and downstream of coding genes, as well as within the gene bodies themselves, while no methylation was detected in transposons or their adjacent regions. Analysis of differentially methylated regions indicated that there were 807, 1 545, and 804 differential regions in mid-diapause vs early diapause, late diapause vs early diapause, and mid-diapause vs late diapause, respectively. This indicated that the genome underwent demethylation events during the termination of pupal diapause. A total of 1 496 genes associated with these differential regions were identified through differential methylation region analysis. Functional enrichment analysis revealed that components of multiple cellular signal transduction pathway, including Foxo, Hippo, Jak-STAT, mTOR, Wnt, were involved in regulating diapause in wild mulberry silkworm pupae. This study provided insights into the role of epigenetic mechanisms in the regulation of diapause.
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基本信息:
DOI：10.13417/j.gab.044.000381
中图分类号:S88
引用信息:
[1]孟刚,楚渠,王瑞娴,等.秦巴野桑蚕(Bombyx mandarina)基因组测序组装与蛹滞育时期的全基因组甲基化分析[J].基因组学与应用生物学,2025,44(04):381-396.DOI:10.13417/j.gab.044.000381.
基金信息:
陕西省重点研发计划(2023-JC-YB-206); 陕西省教育厅重点科学研究计划(20JS002); 家蚕基因组生物学国家重点实验室开放课题(SKLSQB1819-4); 安康学院科研计划项目(2022AYZD02)共同资助
2025-04-25
2025-04-25