High Throughput Sequencing of Small RNAs in the Two Cucurbita Germplasm with Different Sodium Accumulation Patterns Identifies Novel MicroRNAs Involved in Salt Stress Response.
High Throughput Sequencing of Small RNAs in the Two Cucurbita Germplasm with Different Sodium Accumulation Patterns Identifies Novel MicroRNAs Involved in Salt Stress Response.
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对具有不同钠积累模式的两种葫芦种质中的小 RNA 进行高通量测序，鉴定出参与盐胁迫响应的新型 MicroRNA
DOI：
10.1371/journal.pone.0127412
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Bie Z
中科院分区：
文献类型：
--
作者：
Xie J;Lei B;Niu M;Huang Y;Kong Q;Bie Z
MicroRNA（miRNAs）是一类小的非编码RNA，能够根据序列的互补性识别mRNA靶分子。miRNAs在植物暴露于胁迫后导致基因表达发生更广泛的变化。高通量测序是一种有效的方法来识别和分析盐胁迫下的非模式植物中的小RNA群体，显着提高我们的知识，在耐盐性的miRNA功能。瓜类植物对土壤盐分敏感，葫芦科植物被用作其他瓜类植物的砧木以增强其耐盐性。一些葫芦科作物已被用于miRNA测序，但葫芦科物种中盐胁迫相关的miRNA尚未报道。本研究以南瓜属（Cucurbita.）maxima Duch.）和N15（Cucurbita. moschata Duch.），与不同的钠积累模式，以Illumina测序，以确定在盐处理和对照4小时后根组织中的小RNA群体。分别从对照和盐处理的N12根组织产生总共21，548，326和19，394，108个读数。相比之下，分别从对照和盐处理的N15根组织获得19，108，240和20，546，052个读数。在这两份南瓜种质中共鉴定出58个保守的miRNA家族和33个新的miRNA家族。在盐处理的N12和N15样品中，七种miRNA（六种保守的miRNA和一种新的miRNA）被上调。差异表达的新miRNAs的靶基因主要是转录因子和盐胁迫响应蛋白，包括脱水诱导蛋白、阳离子/H+逆向转运蛋白18和CBL相互作用丝氨酸/苏氨酸蛋白激酶。盐胁迫条件下两种南瓜种质及其靶基因的差异表达表明，新的miRNAs在两种南瓜种质对盐胁迫的响应中起重要作用。本研究初步探讨了小分子RNA在南瓜盐胁迫响应中的作用，为南瓜属植物中新的miRNAs及其靶基因的研究提供了有价值的信息。
MicroRNAs (miRNAs), a class of small non-coding RNAs, recognize their mRNA targets based on perfect sequence complementarity. MiRNAs lead to broader changes in gene expression after plants are exposed to stress. High-throughput sequencing is an effective method to identify and profile small RNA populations in non-model plants under salt stresses, significantly improving our knowledge regarding miRNA functions in salt tolerance. Cucurbits are sensitive to soil salinity, and the Cucurbita genus is used as the rootstock of other cucurbits to enhance salt tolerance. Several cucurbit crops have been used for miRNA sequencing but salt stress-related miRNAs in cucurbit species have not been reported. In this study, we subjected two Cucurbita germplasm, namely, N12 (Cucurbita. maxima Duch.) and N15 (Cucurbita. moschata Duch.), with different sodium accumulation patterns, to Illumina sequencing to determine small RNA populations in root tissues after 4 h of salt treatment and control. A total of 21,548,326 and 19,394,108 reads were generated from the control and salt-treated N12 root tissues, respectively. By contrast, 19,108,240 and 20,546,052 reads were obtained from the control and salt-treated N15 root tissues, respectively. Fifty-eight conserved miRNA families and 33 novel miRNAs were identified in the two Cucurbita germplasm. Seven miRNAs (six conserved miRNAs and one novel miRNAs) were up-regulated in salt-treated N12 and N15 samples. Most target genes of differentially expressed novel miRNAs were transcription factors and salt stress-responsive proteins, including dehydration-induced protein, cation/H+ antiporter 18, and CBL-interacting serine/threonine-protein kinase. The differential expression of miRNAs between the two Cucurbita germplasm under salt stress conditions and their target genes demonstrated that novel miRNAs play an important role in the response of the two Cucurbita germplasm to salt stress. The present study initially explored small RNAs in the response of pumpkin to salt stress, and provided valuable information on novel miRNAs and their target genes in Cucurbita.
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