Regulation of coconut somatic embryogenesis: decoding the role of long non-coding RNAs

IF 1.7 4区 生物学 Q4 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
A. A. Sabana, Ginny Antony, K. P. Gangaraj, Tony Grace, M. K. Rajesh
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Abstract

Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides that lack significant protein coding potential and have been shown to regulate various biological processes. This study was designed to identify lncRNAs in coconut and their role in the process of somatic embryogenesis in coconut, a crop with high recalcitrance to in vitro culture. RNA-Seq data of coconut embryogenic calli of the West Coast Tall cultivar was exploited for in silico prediction of lncRNA. From a total of 6328 transcripts, which were annotated as uncharacterised or with no homology hits with the existing database, 5110 putative lncRNAs are identified. We also studied the relationship between lncRNAs, microRNAs (miRNAs) and mRNAs and found that some of the lncRNAs act as miRNA precursors, some as potential miRNA targets and some function as endogenous target mimics (eTMs) for miRNAs. Real-time quantitative PCR confirmed that 10 selected lncRNAs showed significant differences in the expression pattern in different stages of coconut somatic embryogenesis. Our results suggest the existence of diverse lncRNAs in coconut embryogenic calli, some of which are differentially expressed. The information generated in this study could be of great value in understanding the molecular mechanisms governing somatic embryogenesis in coconut.

Abstract Image

椰子体细胞胚胎发生的调控:解码长非编码 RNA 的作用
长非编码 RNA(lncRNA)是指长度超过 200 个核苷酸的转录本,它们缺乏显著的蛋白质编码潜能,已被证明可调控各种生物过程。本研究旨在鉴定椰子中的lncRNA及其在椰子体细胞胚胎发生过程中的作用。研究利用西海岸高秆栽培品种椰子胚胎发生胼胝体的 RNA-Seq 数据对 lncRNA 进行了硅预测。从总共 6328 个转录本中(这些转录本被注释为未表征或与现有数据库没有同源性命中),鉴定出 5110 个推测的 lncRNA。我们还研究了lncRNA、microRNA(miRNA)和mRNA之间的关系,发现一些lncRNA是miRNA的前体,一些是潜在的miRNA靶标,还有一些是miRNA的内源性靶标模拟物(eTM)。实时定量 PCR 证实,所选的 10 个 lncRNA 在椰子体细胞胚胎发生的不同阶段表现出显著的表达模式差异。我们的研究结果表明,在椰子胚胎发生的胼胝体中存在多种lncRNA,其中一些存在差异表达。本研究获得的信息对了解椰子体细胞胚胎发生的分子机制具有重要价值。
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来源期刊
Plant Biotechnology Reports
Plant Biotechnology Reports 生物-生物工程与应用微生物
CiteScore
4.10
自引率
4.20%
发文量
72
审稿时长
>12 weeks
期刊介绍: Plant Biotechnology Reports publishes original, peer-reviewed articles dealing with all aspects of fundamental and applied research in the field of plant biotechnology, which includes molecular biology, genetics, biochemistry, cell and tissue culture, production of secondary metabolites, metabolic engineering, genomics, proteomics, and metabolomics. Plant Biotechnology Reports emphasizes studies on plants indigenous to the Asia-Pacific region and studies related to commercialization of plant biotechnology. Plant Biotechnology Reports does not exclude studies on lower plants including algae and cyanobacteria if studies are carried out within the aspects described above.
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