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两种茶尺蠖近缘种基因组草图比较分析
Comparative analysis of the draft genome of two sibling tea geometrids, Ectropis grisescens and Ectropis obliqua
程梓淇;李佳琦;叶昕海;李 飞; 贺 康
点击:1016次 下载:61次
DOI:10.7679/j.issn.2095-1353.2022.076
作者单位:浙江大学昆虫科学研究所,浙江省作物病虫生物学重点实验室,杭州 310058; 浙江大学茶叶科学研究所,杭州 310058
中文关键词:茶尺蠖;基因组;近缘种;基因组大小;适应性;特异性引物
英文关键词:tea geometrid; genome; sibling species; genome size; adaption; specific primer
中文摘要:
【目的】 灰茶尺蠖Ectropis grisescens和茶尺蠖E. obliqua是东南亚茶园中重要的鳞翅目害虫,二者形态相似,但茶尺蠖核型多角体病毒(Ectropis obliqua nuclear polyhedrosis virus,EoNPV)对二者的防效存在差异。为深入解析灰茶尺蠖和茶尺蠖基因组水平物种差异特性,本研究利用全基因组测序,组装和注释了灰茶尺蠖和茶尺蠖基因组草图,并开展比较基因组分析。【方法】 通过流式细胞术测定灰茶尺蠖和茶尺蠖的基因组大小;采用Illumina二代测序技术获得2个近缘种低覆盖度基因组测序数据,完成基因组组装和注释后对其进行系统进化和基因共线性分析以及1 018个单拷贝同源基因的正选择分析。同时分析了2种茶尺蠖的病毒抗性基因和化学感受相关基因家族,并对灰茶尺蠖和茶尺蠖的物种特异性序列进行鉴定和验证。【结果】 利用低覆盖度基因组测序数据,组装构建了灰茶尺蠖和茶尺蠖的基因组草图,二者基因组大小约为770 Mb。比较基因组学分析显示,灰茶尺蠖和茶尺蠖的基因数量相似,但重复序列存在差异,分别为52.62%和49.67%。系统发育分析和全基因组共线性分析表明,二者分化时间为318万年前,但未发生明显的染色体重排事件。灰茶尺蠖中与EoNPV抗性相关基因载脂蛋白和组织蛋白酶基因发生了扩增,包括小分子代谢过程通路(GO: 0044281)显著正向选择。【结论】 本研究获得了灰茶尺蠖和茶尺蠖的基因组草图数据,分析结果为研究2个近缘种的适应性进化策略提供了依据,同时也为减少农药的使用和开发绿色茶树害虫防治技术提供了参考。
英文摘要:
[Objectives]  To analyze genome-level species differences between two sibling species of tea geometrids, Ectropis grisescens and E. obliqua, two major lepidopteran pests in southeast Asian tea plantations with very similar morphology, but different susceptibility to the E. obliqua nuclear polyhedrosis virus (EoNPV), a common biological pesticide. [Methods]  We assembled and annotated the draft genomes of E. grisescens and E. obliqua by whole-genome sequencing data and conducted comparative genomic analysis. Flow cytometry was used to estimate the genome size of each species, after which low-coverage genome sequencing data were obtained using Illumina next-generation sequencing technology. After genome assembly and annotation, we conducted phylogenetic and synteny analysis. Positive selection analysis of 1 018 single-copy homologous genes was also conducted. We then analyzed chemosensory genes and those involved in EoNPV resistance and identified and verified species-specific sequences. [Results]  We used low-coverage genome survey sequencing to successfully assemble and annotate the draft genomes of E. grisescens and E. obliqua, which have a similar genome size of 770 megabase (Mb) pairs. Comparative genomics indicates a similar length of contigs, scaffolds and gene number, but a different number of repeat sequences (52.62% for E. grisescens and 49.67% for E. obliqua). Phylogenetic and whole-genome synteny analysis indicates that these sibling species diverged 318 million year ago with no obvious chromosome rearrangement. Gene expansion of apolipophorin and cathepsin has occurred, including significant positive selection on the GO pathway 0044281 (small molecule metabolic process) in E. grisescens. [Conclusion]  We successfully used genome survey sequencing to assemble and annotate draft genomes of E. grisescens and E. obliqua. The results provide fundamental data for genetic comparison between these tea geometrids, thereby facilitating understanding of the adaptive evolution of sibling species, and may also allow reduced pesticide use and promote more environmentally friendly methods of controlling these pests.
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