一种基于k-mer计数的蜘蛛螨品种PCR引物设计方法。

IF 2.6 3区 综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES
PLoS ONE Pub Date : 2025-06-09 eCollection Date: 2025-01-01 DOI:10.1371/journal.pone.0321199
Tomoko Matsuda, Hironori Sakamoto, Takumi Kayukawa, Yasuki Kitashima, Toshinori Kozaki, Tetsuo Gotoh
{"title":"一种基于k-mer计数的蜘蛛螨品种PCR引物设计方法。","authors":"Tomoko Matsuda, Hironori Sakamoto, Takumi Kayukawa, Yasuki Kitashima, Toshinori Kozaki, Tetsuo Gotoh","doi":"10.1371/journal.pone.0321199","DOIUrl":null,"url":null,"abstract":"<p><p>Using PCR to distinguish closely related species can be difficult because they may have very similar genomes. Advances in bioinformatics make it possible to design PCR primers that are species-specific. In this study, we developed a bioinformatics method for extracting species-specific primer candidate sequences (i.e., unpaired primers that were specific to a single species) from RNA-Seq data sets of 19 species of spider mites (Acari, Tetranychidae). Using k-mer counting, we obtained between 257 and 48,621 species-specific unpaired primer candidates for the 19 species. We then manually obtained a second primer that was also species-specific. The primer pairs were then confirmed to work in the target species and not to work in the non-target species. Finally, species-specific primer pairs were obtained for 17 of the 19 species tested. Such species-specific primers may be used for practical species discrimination by optimizing multiplex PCR. Our primer design method is expected to be applicable to other taxa.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 6","pages":"e0321199"},"PeriodicalIF":2.6000,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12148119/pdf/","citationCount":"0","resultStr":"{\"title\":\"A PCR primer design method for identifying spider mite species using k-mer counting.\",\"authors\":\"Tomoko Matsuda, Hironori Sakamoto, Takumi Kayukawa, Yasuki Kitashima, Toshinori Kozaki, Tetsuo Gotoh\",\"doi\":\"10.1371/journal.pone.0321199\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Using PCR to distinguish closely related species can be difficult because they may have very similar genomes. Advances in bioinformatics make it possible to design PCR primers that are species-specific. In this study, we developed a bioinformatics method for extracting species-specific primer candidate sequences (i.e., unpaired primers that were specific to a single species) from RNA-Seq data sets of 19 species of spider mites (Acari, Tetranychidae). Using k-mer counting, we obtained between 257 and 48,621 species-specific unpaired primer candidates for the 19 species. We then manually obtained a second primer that was also species-specific. The primer pairs were then confirmed to work in the target species and not to work in the non-target species. Finally, species-specific primer pairs were obtained for 17 of the 19 species tested. Such species-specific primers may be used for practical species discrimination by optimizing multiplex PCR. Our primer design method is expected to be applicable to other taxa.</p>\",\"PeriodicalId\":20189,\"journal\":{\"name\":\"PLoS ONE\",\"volume\":\"20 6\",\"pages\":\"e0321199\"},\"PeriodicalIF\":2.6000,\"publicationDate\":\"2025-06-09\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12148119/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"PLoS ONE\",\"FirstCategoryId\":\"103\",\"ListUrlMain\":\"https://doi.org/10.1371/journal.pone.0321199\",\"RegionNum\":3,\"RegionCategory\":\"综合性期刊\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2025/1/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"Q1\",\"JCRName\":\"MULTIDISCIPLINARY SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"PLoS ONE","FirstCategoryId":"103","ListUrlMain":"https://doi.org/10.1371/journal.pone.0321199","RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/1/1 0:00:00","PubModel":"eCollection","JCR":"Q1","JCRName":"MULTIDISCIPLINARY SCIENCES","Score":null,"Total":0}
引用次数: 0

摘要

利用聚合酶链反应(PCR)来区分近亲物种可能很困难,因为它们可能具有非常相似的基因组。生物信息学的进步使设计具有物种特异性的PCR引物成为可能。在本研究中,我们开发了一种生物信息学方法,用于从19种螨(蜱螨、叶螨科)的RNA-Seq数据集中提取物种特异性引物候选序列(即单个物种特异性的未配对引物)。通过k-mer计数,我们获得了19个物种的257 ~ 48,621个物种特异性的未配对引物候选物。然后我们手动获得了第二个引物,也是物种特异性的。然后确认引物对在目标物种中起作用,而在非目标物种中不起作用。最后,对19个被测物种中的17个获得了物种特异性引物对。这种物种特异性引物可以通过优化多重PCR用于实际的物种鉴别。我们的引物设计方法有望应用于其他分类群。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

A PCR primer design method for identifying spider mite species using k-mer counting.

A PCR primer design method for identifying spider mite species using k-mer counting.

A PCR primer design method for identifying spider mite species using k-mer counting.

A PCR primer design method for identifying spider mite species using k-mer counting.

Using PCR to distinguish closely related species can be difficult because they may have very similar genomes. Advances in bioinformatics make it possible to design PCR primers that are species-specific. In this study, we developed a bioinformatics method for extracting species-specific primer candidate sequences (i.e., unpaired primers that were specific to a single species) from RNA-Seq data sets of 19 species of spider mites (Acari, Tetranychidae). Using k-mer counting, we obtained between 257 and 48,621 species-specific unpaired primer candidates for the 19 species. We then manually obtained a second primer that was also species-specific. The primer pairs were then confirmed to work in the target species and not to work in the non-target species. Finally, species-specific primer pairs were obtained for 17 of the 19 species tested. Such species-specific primers may be used for practical species discrimination by optimizing multiplex PCR. Our primer design method is expected to be applicable to other taxa.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
PLoS ONE
PLoS ONE 生物-生物学
CiteScore
6.20
自引率
5.40%
发文量
14242
审稿时长
3.7 months
期刊介绍: PLOS ONE is an international, peer-reviewed, open-access, online publication. PLOS ONE welcomes reports on primary research from any scientific discipline. It provides: * Open-access—freely accessible online, authors retain copyright * Fast publication times * Peer review by expert, practicing researchers * Post-publication tools to indicate quality and impact * Community-based dialogue on articles * Worldwide media coverage
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术官方微信