HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes.
HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes.
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DOI：
10.1186/s12859-023-05335-8
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发表时间：
2023-05-17
影响因子：
3
通讯作者：
中科院分区：
文献类型：
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自RenSeq协议首次发表以来的十年里，该方法已被证明是研究植物抗病和为育种计划提供目标基因的强大工具。自最初发表该方法以来，随着新技术的出现和计算能力的增加使新的生物信息学方法成为可能，该方法一直在不断发展。最近，这包括开发基于k-mer的关联遗传学方法，使用PacBio HiFi数据，以及使用诊断RenSeq进行图形基因分型。然而，目前还没有统一的工作流程可用，研究人员必须自己配置各种来源的方法。这使得重复性和版本控制成为一个挑战，并将执行这些分析的能力限制在那些具有生物信息学专业知识的人身上。在这里，我们介绍HISS，由三个工作流程组成，从原始的RenSeq读取到鉴定抗病基因的候选基因。这些工作流程从具有感兴趣的抗性表型的登录物中进行丰富的HiFi读数的组装。一组既有抗性又没有抗性的材料随后被用于联合遗传学方法(AgRenSeq)来鉴定与抗性表型正相关的重叠群。然后在这些重叠群上识别候选基因，并使用使用dRenSeq的图形基因分型方法评估它们在小组中的存在或不存在。这些工作流是通过Snakemake实现的，Snakemake是一个基于Python的工作流管理器。软件依赖关系要么随发行版一起提供，要么与Conda一起处理。所有代码都是免费提供的，并在GNU GPL-3.0许可下分发。HISS为鉴定植物中新的抗病基因提供了一种用户友好、便携和易于定制的方法。它很容易安装，所有的依赖关系都可以在内部处理或随版本一起提供，并且在这些生物信息学分析的易用性方面有了显著的改进。网上版载有补充材料，可在10.1186/s12859-023-05335-8查阅。
In the ten years since the initial publication of the RenSeq protocol, the method has proved to be a powerful tool for studying disease resistance in plants and providing target genes for breeding programmes. Since the initial publication of the methodology, it has continued to be developed as new technologies have become available and the increased availability of computing power has made new bioinformatic approaches possible. Most recently, this has included the development of a k-mer based association genetics approach, the use of PacBio HiFi data, and graphical genotyping with diagnostic RenSeq. However, there is not yet a unified workflow available and researchers must instead configure approaches from various sources themselves. This makes reproducibility and version control a challenge and limits the ability to perform these analyses to those with bioinformatics expertise. Here we present HISS, consisting of three workflows which take a user from raw RenSeq reads to the identification of candidates for disease resistance genes. These workflows conduct the assembly of enriched HiFi reads from an accession with the resistance phenotype of interest. A panel of accessions both possessing and lacking the resistance are then used in an association genetics approach (AgRenSeq) to identify contigs positively associated with the resistance phenotype. Candidate genes are then identified on these contigs and assessed for their presence or absence in the panel with a graphical genotyping approach that uses dRenSeq. These workflows are implemented via Snakemake, a python-based workflow manager. Software dependencies are either shipped with the release or handled with conda. All code is freely available and is distributed under the GNU GPL-3.0 license. HISS provides a user-friendly, portable, and easily customised approach for identifying novel disease resistance genes in plants. It is easily installed with all dependencies handled internally or shipped with the release and represents a significant improvement in the ease of use of these bioinformatics analyses. The online version contains supplementary material available at 10.1186/s12859-023-05335-8.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
9.2
作者：
Pham GM;Hamilton JP;Wood JC;Burke JT;Zhao H;Vaillancourt B;Ou S;Jiang J;Buell CR
通讯作者：
Buell CR
影响因子：
7.2
作者：
Huang, SW;van der Vossen, EAG;Visser, RGF
通讯作者：
Visser, RGF
影响因子：
7.2
作者：
Ballvora, A;Ercolano, MR;Gebhardt, C
通讯作者：
Gebhardt, C