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哈普洛型解析基因组组装和VitExpress的实施,这是葡萄藤的一个开放的交互式转录基因平台

Anis Djari¹, Guillaume Madignier^1,2, Olivia Di Valentin¹

¹Laboratoire de Recherche en Sciences Végétales-Génomique et Biotechnologie des Fruits-UMR5546, Université de Toulouse, CNRS, Université Paul Sabatier, Institut Polytechnique de Toulouse, Auzeville Tolosan 31326, France.

Proceedings of the National Academy of Sciences of the United States of America

|May 28, 2024

概括

葡萄藤 (Vitis vinifera) 的高保真性基因组测序产生了哈普类型解析组件. 这些组合揭示了结构变异,并改善了基因组注释,为葡萄酒研究建立了一个新的参考基因组.

科学领域:

基因组学就是基因组学.
植物科学植物科学
生物信息学是一种生物信息学.

背景情况:

葡萄藤 (Vitis vinifera) 基因组研究一直受到异合体品种复杂性的限制.
准确的基因组组合对于理解遗传变异和进化历史至关重要.

研究的目的:

为两个葡萄酒品种 (Chasselas 和 Ugni Blanc) 生成以哈普罗类型解决的基因组组.
揭示品种内部的结构变异,并改进基因组注释.
为葡萄酒研究开发新的生物信息学工具.

主要方法:

结合高准确度的长读测序与染色体构造捕获 (Hi-C) 进行端粒到端粒基因组组装.
使用Iso-Seq (全长转录异形序列) 进行增强的基因组注释.
开发VitExpress平台,使用基因组浏览和表达式分析工具.

主要成果:

成功组装了查塞拉斯和乌格尼布朗克的单独的半基因组,揭示了删除,反转和转位等结构变异.
查塞拉斯组件实现了高连续性和强大的注释,满足了参考基因组的标准.
通过表达特征和相关性分析,确定了参与安东素代谢的候选基因.

结论:

开发的哈普洛型解析组合和注释为Vitis vinifera提供了一个强大的参考.
新的生物信息学工具 (VitExpress,StatTools) 便于对葡萄藤转录组数据进行高级分析.
这些资源将加速葡萄藤遗传学,进化和育种方面的研究.

关键词:

葡萄酒 (Vitis vinifera) 是一种葡萄酒.哈普洛型解析的基因组组合.一个转录基因平台

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