Identification of microRNA-like RNAs from Trichoderma asperellum DQ-1 during its interaction with tomato roots using bioinformatic analysis and high-throughput sequencing.
Identification of microRNA-like RNAs from Trichoderma asperellum DQ-1 during its interaction with tomato roots using bioinformatic analysis and high-throughput sequencing.
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使用生物信息学分析和高通量测序鉴定木霉 DQ-1 与番茄根相互作用过程中的 microRNA 样 RNA
DOI：
10.1371/journal.pone.0254808
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发表时间：
2021
期刊：
影响因子：
3.7
通讯作者：
Liu T
中科院分区：
文献类型：
--
作者：
Wang W;Zhang F;Cui J;Chen D;Liu Z;Hou J;Zhang R;Liu T
microRNA-like small RNAs（milRNAs）及其在植物与真菌相互作用中的调控作用近年来引起了植物病理学家的极大兴趣。木霉属，广泛分布的生防真菌之一，能促进植物生长，诱导植物抗病性。为了研究可能参与木霉与番茄根相互作用的milRNA，构建了木霉与番茄根相互作用过程中表达的小RNA（sRNA）文库。构建了Asperellum DQ-1和番茄根的DNA序列，并使用Illumina HiSeqTM 2500测序平台进行测序。从13，464，142个sRNA读段中，我们鉴定了21个与miRBase数据库中其他已知microRNA相似的milRNA候选物和22个具有稳定microRNA前体发夹结构的新milRNA候选物。茎环RT-PCR结果显示，其中3个milRNA候选基因在木霉与番茄根互作中表现出不同的表达水平，表明这些milRNA可能在木霉与番茄根互作中发挥不同的调控作用。从T.通过生物信息学分析，预测了番茄中的Asperellum及其靶基因。研究结果表明，在植物的生长发育、抗病性、种子成熟和渗透胁迫信号转导等过程中，有几个重要的蛋白质可能受到跨界milRNA的调控。据我们所知，这是首次报道milRNA参与T.与促进植物生长和抗病性有关。研究结果为阐明木霉与番茄互作的机理提供了理论依据。
MicroRNA-like small RNAs (milRNAs) and their regulatory roles in the interaction between plant and fungus have recently aroused keen interest of plant pathologists. Trichoderma spp., one of the widespread biocontrol fungi, can promote plant growth and induce plant disease resistance. To investigate milRNAs potentially involved in the interaction between Trichoderma and tomato roots, a small RNA (sRNA) library expressed during the interaction of T. asperellum DQ-1 and tomato roots was constructed and sequenced using the Illumina HiSeqTM 2500 sequencing platform. From 13,464,142 sRNA reads, we identified 21 milRNA candidates that were similar to other known microRNAs in the miRBase database and 22 novel milRNA candidates that possessed a stable microRNA precursor hairpin structure. Among them, three milRNA candidates showed different expression level in the interaction according to the result of stem-loop RT-PCR indicating that these milRNAs may play a distinct regulatory role in the interaction between Trichoderma and tomato roots. The potential transboundary milRNAs from T. asperellum and their target genes in tomato were predicted by bioinformatics analysis. The results revealed that several interesting proteins involved in plant growth and development, disease resistance, seed maturation, and osmotic stress signal transduction might be regulated by the transboundary milRNAs. To our knowledge, this is the first report of milRNAs taking part in the process of interaction of T. asperellum and tomato roots and associated with plant promotion and disease resistance. The results might be useful to unravel the mechanism of interaction between Trichoderma and tomato.
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