Small RNA and Transcriptome Sequencing Reveal a Potential miRNA-Mediated Interaction Network That Functions during Somatic Embryogenesis in Lilium pumilum DC. Fisch.
Small RNA and Transcriptome Sequencing Reveal a Potential miRNA-Mediated Interaction Network That Functions during Somatic Embryogenesis in Lilium pumilum DC. Fisch.
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小 RNA 和转录组测序揭示了一个潜在的 miRNA 介导的相互作用网络，该网络在百合体细胞胚胎发生过程中发挥作用。
DOI：
10.3389/fpls.2017.00566
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发表时间：
2017
影响因子：
5.6
通讯作者：
Sun H
中科院分区：
文献类型：
--
作者：
Zhang J;Xue B;Gai M;Song S;Jia N;Sun H
植物体细胞胚在种质资源保护、基因工程育种和人工制种等领域有着广泛的应用。MicroRNAs （miRNAs）在体细胞胚胎发生（somatic embrgenesis， SE）调控中起着关键作用。然而，它们在SE各个阶段的调节作用尚不清楚。本研究对六种不同类型的百合胚性样品进行了研究。费斯。分别制备器官愈伤组织、诱导4周胚性愈伤组织、诱导6周胚性愈伤组织、球形胚、鱼雷胚和子叶胚，进行小RNA测序。结果显示，共有2,378,760个小RNA reads，其中最常见的大小为24nt。已知的452个miRNA属于86个家族，鉴定出57个新miRNA和40个miRNA*s。根据与24种陆地植物同源物的比对，将86个已知miRNA家族分为以下4类：23个高度保守，4个中等保守，15个不太保守和44个物种特异性miRNA。在SE的不同阶段鉴定出差异表达的已知mirna。随后，使用qRT-PCR验证12个差异表达mirna和4个靶点的表达水平。另外，将6个样本等量混合进行转录本测序，测序数据作为转录本用于miRNA靶点预测。从56,258,974个原始reads中，共组装了平均长度为800 bp的66,422个unigenes。基因本体（GO）和京都基因与基因组百科全书（KEGG）富集表明，分别成功地将38,004个和15,497个unique Genes分配到GO术语和KEGG途径上。在这些unigenes中，预计有2182个转录本是396个已知mirna的靶标。所鉴定的mirna的潜在靶标主要分为以下氧化石墨烯术语：细胞、结合和代谢过程。富集KEGG分析表明，碳水化合物代谢是百合的主要代谢途径。因此，我们对百合进行了系统表征、同源性比较和miRNA表达谱分析，并首次构建了百合生长过程中的miRNA靶点网络。本研究结果为百合SE关键基因的进一步探索和SE基因的解析奠定了基础。
Plant somatic embryos are widely used in the fields of germplasm conservation, breeding for genetic engineering and artificial seed production. MicroRNAs (miRNAs) play pivotal roles in somatic embryogenesis (SE) regulation. However, their regulatory roles during various stages of SE remain unclear. In this study, six types of embryogenic samples of Lilium pumilum DC. Fisch., including organogenic callus, embryogenic callus induced for 4 weeks, embryogenic callus induced for 6 weeks, globular embryos, torpedo embryos and cotyledon embryos, were prepared for small RNA sequencing. The results revealed a total of 2,378,760 small RNA reads, among which the most common size was 24 nt. Four hundred and fifty-two known miRNAs, belonging to more than 86 families, 57 novel miRNAs and 40 miRNA*s were identified. The 86 known miRNA families were sorted according to an alignment with their homologs across 24 land plants into the following four categories: 23 highly conserved, 4 moderately conserved, 15 less conserved and 44 species-specific miRNAs. Differentially expressed known miRNAs were identified during various stages of SE. Subsequently, the expression levels of 12 differentially expressed miRNAs and 4 targets were validated using qRT-PCR. In addition, six samples were mixed in equal amounts for transcript sequencing, and the sequencing data were used as transcripts for miRNA target prediction. A total of 66,422 unigenes with an average length of 800 bp were assembled from 56,258,974 raw reads. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment indicated that 38,004 and 15,497 unigenes were successfully assigned to GO terms and KEGG pathways, respectively. Among the unigenes, 2,182 transcripts were predicted to be targets for 396 known miRNAs. The potential targets of the identified miRNAs were mostly classified into the following GO terms: cell, binding and metabolic process. Enriched KEGG analysis demonstrated that carbohydrate metabolism was the predominant pathway in Lilium SE. Thus, we performed systemic characterization, homology comparisons and profiling of miRNA expression, and we constructed an miRNA-target network during Lilium SE for the first time. Our findings establish a foundation for the further exploration of critical genes and elucidation of SE in Lilium.