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组装和分析诺托利托卡普斯 (Notholithocarpus densiflorus) 的基因组

Ying Cai¹, Ellis Anderson¹, Wen Xue¹

¹Advanced Genomics Technology Laboratory, Complete Genomics Inc, San Jose, CA 95134, USA.

G3 (Bethesda, Md.)

|March 1, 2024

概括

我们组装了木 (Notholithocarpus densiflorus) 的第一个基因组草案,揭示了其独特的进化路径和遗传多样性. 这项基础工作有助于了解其对突然树死亡 (SOD) 的易感性.

科学领域:

基因组学就是基因组学.
植物进化生物学植物进化生物学
保护遗传学保护遗传学

背景情况:

塔诺克 (Notholithocarpus densiflorus) 是加利福尼亚州和俄勒冈州的一棵具有文化意义的树,历史上用于食物和日.
遗传学研究表明,tanoak代表了融合进化,与亚洲石树和太平洋西北方树不同.
塔诺克受到"突然树死亡" (SOD) 的严重威胁,这种疾病是由病原体Phytophthora ramorum引起的.

研究的目的:

为了生成Notholithocarpus densiflorus的高质量的参考基因组草案.
为了能够对有不同易受突然树死亡 (SOD) 的tanoak个体进行比较基因组研究.
在tanoak种群中识别遗传变异,包括单核酸多态 (SNP) 和小插入/删除 (indels).

主要方法:

使用MGI DNBSEQ-G400和牛津纳米孔长读序列的N. densiflorus的新基因组组装.
测序和映射11个基因上不同的Tanoak个体到参考基因组.
利用可编码的库处理来实现高效的测序和单元型生成.

主要成果:

产生了一个高度连续的基因组组件草案 (连续N50~1.2 Mb,支架N50~2.1 Mb) 具有95.5%的完整基因得分 (BUSCO).
在11个个体中发现了近2500万个单核酸多态 (SNP) 和大约440万个小插入/删除 (indels).
对于所有测序的tanoak基因组,生成了完整的单元型覆盖.

结论:

产生的tanoak基因组是迄今为止发表的最连续和最完整的树基因组之一.
这种基因组资源为了解木的进化及其对木突然死亡 (SOD) 的易感性提供了基础.
鉴定到的遗传变异将有助于未来对鱼保护和抗病能力的研究.

关键词:

这就是SOD的意义.在CobaCoding中,我们使用的是CobaCoding.stLFRFR 在线观看这就是TanoakTanoak.

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