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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HISS：基于 Snakemake 的工作流程，用于执行 SMRT-RenSeq 组装、AgRenSeq 和 dRenSeq，用于发现新型植物抗病基因
DOI：
10.1101/2022.11.01.514708
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发表时间：
2022
期刊：
影响因子：
--
通讯作者：
Adams T
中科院分区：
文献类型：
--
作者：
Adams T
自RenSeq方案首次发表以来的十年中，该方法已被证明是研究植物抗病性和为育种计划提供靶基因的有力工具。自该方法首次发表以来，随着新技术的出现，以及计算能力的提高，新的生物信息学方法成为可能，该方法不断得到发展。最近，这包括开发基于ak-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，目前还没有一个统一的工作流程，研究人员必须自己配置各种来源的方法。这使得再现性和版本控制的挑战，并限制了那些与bioinformatics expertise. ResultsHISS进行这些分析的能力在这里，我们提出了三个工作流程，其中包括一个用户从原始RenSeq读取抗病基因的候选人的识别。这些工作流程进行来自具有感兴趣的抗性表型的登记的富集HiFi读段的组装。然后将一组具有和缺乏抗性的种质用于关联遗传学方法（AgRenSeq）以鉴定与抗性表型正相关的重叠群。然后在这些重叠群上鉴定候选基因，并使用使用dRenSeq的图形基因分型方法评估它们在面板中的存在或不存在。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，要么用conda处理。所有代码都是免费提供的，并根据GNU GPL-3.0 license.ConclusionsHISS提供了一个用户友好的，便携式的，易于定制的方法来识别植物中的新抗病基因。它很容易安装，所有依赖项都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着的改进。
BackgroundIn 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 ak-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.ResultsHere 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.ConclusionsHISS 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.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
14.9
作者：
NCBI Resource Coordinators
通讯作者：
NCBI Resource Coordinators
影响因子：
7.2
作者：
Ballvora, A;Ercolano, MR;Gebhardt, C
通讯作者：
Gebhardt, C
通过富集测序跟踪马铃薯育种中的抗病部署
DOI：
10.1101/360644
发表时间：
2018
期刊：
--
影响因子：
--
作者：
Armstrong M
通讯作者：
Armstrong M
影响因子：
5.4
作者：
Bendahmane, A;Kanyuka, K;Baulcombe, DC
通讯作者：
Baulcombe, DC