Singh Ravi S, Kesari Ravi, Kumar Ujjwal, Jha Vikash Kumar, Kumar Anjani, Kumar Tribhuwan, Pal Awadhesh K, Singh Prabhash K
Department of Plant Breeding and Genetics, Bihar Agricultural College, Bihar Agricultural University, Sabour, Bhagalpur, Bihar, 813210, India.
Funct Integr Genomics. 2018 Sep;18(5):505-517. doi: 10.1007/s10142-018-0603-2. Epub 2018 Apr 18.
In the present study, de novo transcriptome analysis of Selaginella bryopteris in frond and root was performed to understand the regulation of flavonoid (FL) biosynthesis. High-quality data of 5.84 and 5.86 Gb was generated for frond and root, respectively, that assembled into 94,713 and 81,567 transcripts. A total of 87,471 and 73,395 unigenes were obtained from frond and root, respectively. A total of 41,267 and 31,048 CDS of frond and root, respectively, were annotated by BLASTX, which showed maximum hits against S. moellendorffii. Out of 11,285 differentially expressed genes, a total of 5639 genes were found to be down-regulated and 5628 genes up-regulated in frond as compared to those in root. In silico analysis of expression of genes in frond as compared to that in root was done for those related to phenylpropanoid (PP)/FL biosynthesis along with transcription factors (TFs) after DESeq and MapMan-based information. Results showed that genes of PP/FL biosynthesis pathway namely SbCHS, SbCHI, SbF3H, SbF3'H, SbDFR, SbUF3GT, SbCCOAMT, and SbCATOMT and TFs (SbMYB1, SbMYB2, SbMYB3, SbBHLH1, and SbWD40-5) were up-regulated in frond in comparison to those in root. Further, this in silico expression data was validated by RT-PCR analysis which showed predominant expression of most of these genes in frond and indicated their importance in the biosynthesis of flavonoids in S. bryopteris. A total of 9074 simple sequence repeats (SSRs) were also identified for frond and 3811 SSRs for root; these can be used for experimental validation.
在本研究中，对卷柏的叶片和根进行了从头转录组分析，以了解黄酮类化合物（FL）生物合成的调控机制。分别为叶片和根生成了5.84Gb和5.86Gb的高质量数据，这些数据组装成了94,713和81,567个转录本。分别从叶片和根中获得了87,471和73,395个单基因。通过BLASTX分别对叶片和根的41,267和31,048个编码序列（CDS）进行注释，结果显示与江南卷柏的匹配度最高。在11,285个差异表达基因中，与根相比，叶片中有5639个基因下调，5628个基因上调。基于DESeq和MapMan的信息，对与苯丙烷类（PP）/FL生物合成相关的基因以及转录因子（TFs）在叶片和根中的表达进行了电子分析。结果表明，与根相比，叶片中PP/FL生物合成途径的基因，即SbCHS、SbCHI、SbF3H、SbF3'H、SbDFR、SbUF3GT、SbCCOAMT和SbCATOMT以及TFs（SbMYB1、SbMYB2、SbMYB3、SbBHLH1和SbWD40-5）上调。此外，通过RT-PCR分析验证了这些电子表达数据，结果表明这些基因中的大多数在叶片中优势表达，表明它们在卷柏黄酮类化合物生物合成中的重要性。还分别为叶片和根鉴定出9074个简单序列重复（SSR）和3811个SSR；这些可用于实验验证。
