马尔尼菲Talaromyces marneffei中基于rRNA探针的高效特异性DNA寡核苷酸rRNA去除

IF 4.6 2区 生物学 Q1 MYCOLOGY Mycology Pub Date : 2022-01-03 DOI:10.1080/21501203.2021.2017045
Xueyan Hu, Yun Zhang, Minghao Du, E. Yang
{"title":"马尔尼菲Talaromyces marneffei中基于rRNA探针的高效特异性DNA寡核苷酸rRNA去除","authors":"Xueyan Hu, Yun Zhang, Minghao Du, E. Yang","doi":"10.1080/21501203.2021.2017045","DOIUrl":null,"url":null,"abstract":"ABSTRACT Emerging evidence showed that lncRNAs play important roles in a wide range of biological processes of fungi such as Saccharomyces cerevisiae. However, systemic identification of lncRNAs in non-model fungi is a challenging task as the efficiency of rRNA removal has been proved to be affected by mismatches of universal rRNA-targeting probes of commercial kits, which forces deeper sequencing depth and increases costs. Here, we developed a low-cost and simple rRNA depletion method (rProbe) that could efficiently remove more than 99% rRNA in both yeast and mycelium samples of Talaromyces marneffei. The efficiency and robustness of rProbe were demonstrated to outperform the Illumina Ribo-Zero kit. Using rProbe RNA-seq, we identified 115 differentially expressed lncRNAs and constructed lncRNA-mRNA co-expression network related to dimorphic switch of T. marneffei. Our rRNA removal method has the potential to be a useful tool to explore non-coding transcriptomes of non-model fungi by adjusting rRNA probe sequences species specifically.","PeriodicalId":18833,"journal":{"name":"Mycology","volume":"13 1","pages":"106 - 118"},"PeriodicalIF":4.6000,"publicationDate":"2022-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Efficient and specific DNA oligonucleotide rRNA probe-based rRNA removal in Talaromyces marneffei\",\"authors\":\"Xueyan Hu, Yun Zhang, Minghao Du, E. Yang\",\"doi\":\"10.1080/21501203.2021.2017045\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"ABSTRACT Emerging evidence showed that lncRNAs play important roles in a wide range of biological processes of fungi such as Saccharomyces cerevisiae. However, systemic identification of lncRNAs in non-model fungi is a challenging task as the efficiency of rRNA removal has been proved to be affected by mismatches of universal rRNA-targeting probes of commercial kits, which forces deeper sequencing depth and increases costs. Here, we developed a low-cost and simple rRNA depletion method (rProbe) that could efficiently remove more than 99% rRNA in both yeast and mycelium samples of Talaromyces marneffei. The efficiency and robustness of rProbe were demonstrated to outperform the Illumina Ribo-Zero kit. Using rProbe RNA-seq, we identified 115 differentially expressed lncRNAs and constructed lncRNA-mRNA co-expression network related to dimorphic switch of T. marneffei. Our rRNA removal method has the potential to be a useful tool to explore non-coding transcriptomes of non-model fungi by adjusting rRNA probe sequences species specifically.\",\"PeriodicalId\":18833,\"journal\":{\"name\":\"Mycology\",\"volume\":\"13 1\",\"pages\":\"106 - 118\"},\"PeriodicalIF\":4.6000,\"publicationDate\":\"2022-01-03\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Mycology\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1080/21501203.2021.2017045\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"MYCOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Mycology","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1080/21501203.2021.2017045","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"MYCOLOGY","Score":null,"Total":0}
引用次数: 0

摘要

越来越多的证据表明,lncrna在酿酒酵母等真菌的广泛生物学过程中发挥着重要作用。然而,非模式真菌中lncrna的系统鉴定是一项具有挑战性的任务,因为rRNA去除的效率已被证明受到商业试剂盒中通用rRNA靶向探针的不匹配的影响,这迫使更深的测序深度并增加了成本。本研究开发了一种低成本、简单的rRNA去除方法(rProbe),该方法可以有效去除马尔尼菲Talaromyces marneffei酵母和菌丝体样品中99%以上的rRNA。rProbe的效率和鲁棒性优于Illumina Ribo-Zero试剂盒。利用rProbe RNA-seq技术,我们鉴定出115个差异表达的lncrna,并构建了与T. marneffei二态开关相关的lncRNA-mRNA共表达网络。我们的rRNA去除方法有可能成为一种有用的工具,通过特异性调节rRNA探针序列来探索非模式真菌的非编码转录组。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
Efficient and specific DNA oligonucleotide rRNA probe-based rRNA removal in Talaromyces marneffei
ABSTRACT Emerging evidence showed that lncRNAs play important roles in a wide range of biological processes of fungi such as Saccharomyces cerevisiae. However, systemic identification of lncRNAs in non-model fungi is a challenging task as the efficiency of rRNA removal has been proved to be affected by mismatches of universal rRNA-targeting probes of commercial kits, which forces deeper sequencing depth and increases costs. Here, we developed a low-cost and simple rRNA depletion method (rProbe) that could efficiently remove more than 99% rRNA in both yeast and mycelium samples of Talaromyces marneffei. The efficiency and robustness of rProbe were demonstrated to outperform the Illumina Ribo-Zero kit. Using rProbe RNA-seq, we identified 115 differentially expressed lncRNAs and constructed lncRNA-mRNA co-expression network related to dimorphic switch of T. marneffei. Our rRNA removal method has the potential to be a useful tool to explore non-coding transcriptomes of non-model fungi by adjusting rRNA probe sequences species specifically.
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
Mycology
Mycology Medicine-Infectious Diseases
CiteScore
9.10
自引率
0.00%
发文量
18
审稿时长
13 weeks
期刊最新文献
Isolation of triazole-resistant Aspergillus fumigatus harbouring cyp51A mutations from five patients with invasive pulmonary aspergillosis in Yunnan, China Analytical and clinical validation of multiplex droplet digital PCR assay for detecting pathogenic fungal infection in lungs Optimisation of hypocrellin production in Shiraia -like fungi via genetic modification involving a transcription factor gene and a putative monooxygenase gene Call me by your name: Considerations of DNA sequences as types within wider discussions on fungal nomenclature A comprehensive review of secondary metabolites from the genus Agrocybe : Biological activities and pharmacological implications
×
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
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 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 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1