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
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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。
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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.
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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
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