Malik Chanchal, Dwivedi Sudhanshu, Rabuma Tilahun, Kumar Ravinder, Singh Nitesh, Kumar Anil, Yogi Rajesh, Chhokar Vinod
Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, India.
Department of Biotechnology, College of Natural and Computational Science, Wolkite University, Wolkite, Ethiopia.
Front Genet. 2023 Sep 7;14:1236517. doi: 10.3389/fgene.2023.1236517. eCollection 2023.
is known for its diverse content of secondary metabolites, i.e., saponins, alkaloids, and a wide range of flavonoids. Flavonoids, including phenols and polyphenols, have a significant role in plant physiology and are synthesized in several tissues. Despite the diverse role of flavonoids, genetic information is limited for flavonoid biosynthesis pathways in . The current study explores full-scale functional genomics information of by transcriptome sequencing using Illumina paired-end sequencing technology to elucidate the genes involved in flavonoid biosynthesis pathways. The assembly of high-quality paired-end reads resulted in ∼2.3 million high-quality reads with a pooled transcript of 45,647 comprising ∼76 Mb transcriptome with a mean length (bp) of 1,674 and N50 of 1,868bp. Furthermore, the coding sequence (CDS) prediction analysis from 45,647 pooled transcripts resulted in 45,444 CDS with a total length and mean length of 76,398,686 and 1,674, respectively. The Gene Ontology (GO) analysis resulted in a high number of CDSs assigned to 25,342 GO terms, which grouped the predicted CDS into three main domains, i.e., Biological Process (19,550), Molecular Function (19,873), and Cellular Component (14,577). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database was used to categorize 6,353 CDS into 25 distinct biological pathway categories, in which the majority of mapped CDS were shown to be related to translation (645), followed by signal transduction (532), carbohydrate metabolism (524), folding, sorting, and degradation (522). Among these, only ∼64 and 14 CDSs were found to be involved in the phenylpropanoid and flavonoid biosynthesis pathways, respectively. Quantitative Real-time PCR was used to check the expression profile of fourteen potential flavonoid biosynthesis pathway genes. The qRT-PCR analysis result matches the transcriptome sequence data validating the Illumina sequence results. Moreover, a large number of genes associated with the flavonoids biosynthesis pathway were found to be upregulated under the induction of methyl jasmonate. The present-day study on transcriptome sequence data of can be utilized for characterizing genes involved in flavonoid biosynthesis pathways and for functional genomics analysis in using the reverse genetics approach (CRISPR/Cas9 technology).
以其多样的次生代谢产物而闻名，即皂苷、生物碱和多种黄酮类化合物。黄酮类化合物，包括酚类和多酚类，在植物生理学中具有重要作用，并在多个组织中合成。尽管黄酮类化合物具有多种作用，但关于其黄酮类生物合成途径的遗传信息在[具体物种名称未给出]中却很有限。当前的研究利用Illumina双末端测序技术对[具体物种名称未给出]进行转录组测序，探索其全面的功能基因组学信息，以阐明参与黄酮类生物合成途径的基因。高质量双末端reads的组装产生了约230万个高质量reads，汇集转录本有45,647个，组成了约76 Mb的转录组（平均长度为1,674 bp，N50为1,868 bp）。此外，对45,647个汇集转录本进行编码序列（CDS）预测分析，得到45,444个CDS，总长度和平均长度分别为76,398,686和1,674。基因本体（GO）分析结果显示大量CDS被分配到25,342个GO术语中，这些术语将预测的CDS分为三个主要领域，即生物过程（19,550个）、分子功能（19,873个）和细胞成分（14,577个）。京都基因与基因组百科全书（KEGG）通路数据库用于将6,353个CDS分类到25个不同的生物通路类别中，其中大多数映射的CDS显示与翻译相关（645个），其次是信号转导（532个）、碳水化合物代谢（524个）、折叠、分选和降解（522个）。其中，分别仅发现约64个和14个CDS参与苯丙烷类和黄酮类生物合成途径。使用定量实时PCR来检测14个潜在黄酮类生物合成途径基因的表达谱。qRT-PCR分析结果与转录组序列数据匹配，验证了Illumina测序结果。此外，发现大量与黄酮类生物合成途径相关的基因在茉莉酸甲酯诱导下上调。当前对[具体物种名称未给出]转录组序列数据的研究可用于表征参与黄酮类生物合成途径的基因，并使用反向遗传学方法（CRISPR/Cas9技术）在[具体物种名称未给出]中进行功能基因组学分析。
