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Jonathan H Badger¹, Rosanna Giordano², Aleksey Zimin³

¹Genetics and Microbiome Core, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.

Current opinion in insect science

|November 5, 2023

概括

牛津纳米孔适应采样有效地从虫中测序了昆虫共生体基因组,包括线粒体,Buchnera和Wolbachia. 这种方法有助于研究共感染,但对低度共生生物来说效果不佳.

科学领域:

基因组学就是基因组学.
昆虫微生物学昆虫微生物学
生物信息学是一种生物信息学.

背景情况:

昆虫共生体显著影响宿主表型,其影响范围从有益到致病.
昆虫的同时感染对研究共生体相互作用提出了重大挑战.
昆虫及其共生体的高质量,参考基因组很少,限制了研究.

研究的目的:

开发和评估一种用于测序昆虫共生体基因组的新方法.
评估牛津纳米孔 (ONT) 适应性采样在宿主和共生体基因组的共同测序中的实用性.
在特定的虫物种中获得线粒体,布克内拉和沃尔巴基亚的完整基因组.

主要方法:

利用牛津纳米孔 (ONT) 适应性采样 (减法方法) 进行实时序列选择.
应用该方法对两种虫物种的基因组进行测序:Aphis glycines和Pentalonia nigronervosa.
专注于检索线粒体的基因组,布克内拉 (包括等离子体) 和沃尔巴基亚.

主要成果:

在两种虫物种中成功测序了线粒体,Buchnera (pLeu,pTrp等离子体) 和Wolbachia的完整基因组.
证明了ONT适应性采样对像Buchnera和Wolbachia这样的高度代表的共生体的有效性.
观察到在低度存在的共生体获取方面的限制.

结论:

ONT适应性采样为获得高质量的昆虫共生体基因组提供了一种有效的方法,特别是丰富的共生体.
这种技术有助于研究昆虫与微生物的相互作用和共感染.
对于低丰度的共生体恢复,需要进一步优化.

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