基因组组合和注释的比较基于两种鸟类致病菌大肠杆菌的克隆

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Yufei Zhao¹, John Elmerdahl Olsen¹, Louise Poulsen¹

¹Department of Veterinary and Animal Sciences, University of Copenhagen, Denmark.

Research in microbiology

|October 1, 2025

概括

通过比较禽病原性大肠杆菌 (APEC) 的全基因组测序方法,这项研究发现Unicycler在混合组装方面优越. 像RAST和PROKKA这样的自动基因注释工具需要仔细控制,以尽量减少APEC菌株中的错误.

科学领域:

基因组学就是基因组学.
生物信息学是一种生物信息学.
微生物病原体的产生

背景情况:

禽类致病性大肠杆菌 (APEC) 对家禽健康构成重大威胁.
准确的全基因组测序和注释对于理解APEC病毒性和开发控制策略至关重要.

研究的目的:

为了比较APEC全基因组序列的不同组装和注释方法的性能.
评估短读和长读测序方法,包括混合组装.

主要方法:

六种APEC菌株 (PFGE类型65-ST95和PFGE类型47-ST131) 使用Illumina短读和Nanopore长读进行了测序.
通过使用SPAdes和CLC Genomic Workbench组装了短读数.
短读和长读的混合组装是使用Unicycler和Flye进行的.
用子系统技术 (RAST) 和PROKKA.使用快速注释来注释基因序列.

主要成果:

在短读组装方面,SPAdes和CLC Genomic Workbench没有显著差异.
与混合组装的Fly相比,Unicycler的结果是较少的连接和更高的NG50值.
在组装器之间没有观察到总基因组长度的显著差异.
至少有2.1%和0.9%的编码基因序列被RAST和PROKKA错误注释,错误集中在较短的CDS中.

结论:

建议在APEC基因组测序中使用Unicycler进行混合组装.
自动注释工具需要验证,特别是非K12/B系的假设蛋白质和移动元素.
需要进一步的研究,以提高各种大肠杆菌菌株的注释准确度.

关键词:

错误的注释错误的注释基因组组装组的基因组组装组打开阅读框架打开阅读框架

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