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霜霉病病原体转录组微卫星分析及其在群体特征描述中的应用

Analysis of microsatellites from the transcriptome of downy mildew pathogens and their application for characterization of populations.

作者信息

Wallace Emma C, Quesada-Ocampo Lina M

机构信息

Department of Plant Pathology, North Carolina State University, Raleigh, NC, United States.

出版信息

PeerJ. 2017 May 2;5:e3266. doi: 10.7717/peerj.3266. eCollection 2017.

DOI:10.7717/peerj.3266
PMID:28480143
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5417063/
Abstract

Downy mildew pathogens affect several economically important crops worldwide but, due to their obligate nature, few genetic resources are available for genomic and population analyses. Draft genomes for emergent downy mildew pathogens such as the oomycete , causal agent of cucurbit downy mildew, have been published and can be used to perform comparative genomic analysis and develop tools such as microsatellites to characterize pathogen population structure. We used bioinformatics to identify 2,738 microsatellites in the predicted transcriptome and evaluate them for transferability to the hop downy mildew pathogen, , since no draft genome is available for this species. We also compared the microsatellite repertoire of to that of the model organism , which causes downy mildew in Arabidopsis. Although trends in frequency of motif-type were similar, the percentage of SSRs identified from transcripts differed significantly from . The majority of a subset of microsatellites selected for laboratory validation (92%) produced a product in isolates, and 83 microsatellites demonstrated transferability to . Eleven microsatellites were found to be polymorphic and consistently amplified in isolates. Analysis of isolates from diverse hosts and locations revealed higher diversity in compared to isolates. These microsatellites will be useful in efforts to better understand relationships within species and on a population level.

摘要

霜霉病病原体影响着全球几种具有重要经济价值的作物，但由于它们的专性本质，可用于基因组和群体分析的遗传资源很少。已公布了一些新兴霜霉病病原体的基因组草图，如引起葫芦科霜霉病的卵菌纲病原菌，可用于进行比较基因组分析，并开发如微卫星等工具来表征病原体群体结构。由于该物种没有基因组草图，我们利用生物信息学在预测转录组中鉴定了2738个微卫星，并评估它们向啤酒花霜霉病病原体的可转移性。我们还比较了该病原体与在拟南芥中引起霜霉病的模式生物的微卫星库。尽管基序类型频率的趋势相似，但从该病原体转录本中鉴定出的简单序列重复（SSR）百分比与模式生物有显著差异。为实验室验证而选择的一部分微卫星（92%）在该病原体分离株中产生了产物，并且83个微卫星证明可转移到该病原体。发现11个微卫星具有多态性，并在该病原体分离株中持续扩增。对来自不同宿主和地点的该病原体分离株的分析表明，与模式生物分离株相比，该病原体具有更高的多样性。这些微卫星将有助于更好地理解该病原体物种内以及群体水平上的关系。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/831d/5417063/bbcad95fae57/peerj-05-3266-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/831d/5417063/7d0cf0039b5f/peerj-05-3266-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/831d/5417063/caa4904362ef/peerj-05-3266-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/831d/5417063/ab6c4f4a13a9/peerj-05-3266-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/831d/5417063/44640f10b6bb/peerj-05-3266-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/831d/5417063/bbcad95fae57/peerj-05-3266-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/831d/5417063/7d0cf0039b5f/peerj-05-3266-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/831d/5417063/caa4904362ef/peerj-05-3266-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/831d/5417063/ab6c4f4a13a9/peerj-05-3266-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/831d/5417063/44640f10b6bb/peerj-05-3266-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/831d/5417063/bbcad95fae57/peerj-05-3266-g005.jpg

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