Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, India.
Sci Rep. 2018 Oct 18;8(1):15375. doi: 10.1038/s41598-018-33693-4.
Solanum trilobatum L. is an important medicinal plant in traditional Indian system of medicine belonging to Solanaceae family. However, non-availability of genomic resources hinders its research at the molecular level. We have analyzed the S. trilobatum leaf transcriptome using high throughput RNA sequencing. The de novo assembly of 136,220,612 reads produced 128,934 non-redundant unigenes with N50 value of 1347 bp. Annotation of unigenes was performed against databases such as NCBI nr database, Gene Ontology, KEGG, Uniprot, Pfam, and plnTFDB. A total of 60,097 unigenes were annotated including 48 Transcription Factor families and 14,490 unigenes were assigned to 138 pathways using KEGG database. The pathway analysis revealed the transcripts involved in the biosynthesis of important secondary metabolites contributing for its medicinal value such as Flavonoids. Further, the transcripts were quantified using RSEM to identify the highly regulated genes for secondary metabolism. Reverse-Transcription PCR was performed to validate the de novo assembled unigenes. The expression profile of selected unigenes from flavonoid biosynthesis pathway was analyzed using qRT-PCR. We have also identified 13,262 Simple Sequence Repeats, which could help in molecular breeding. This is the first report of comprehensive transcriptome analysis in S. trilobatum and this will be an invaluable resource to understand the molecular basis related to the medicinal attributes of S. trilobatum in further studies.
三叶茄（Solanum trilobatum L.）是茄科茄属的一种植物，是印度传统医学体系中的一种重要药用植物。然而，由于缺乏基因组资源，其分子水平的研究受到了阻碍。我们使用高通量 RNA 测序技术对三叶茄叶片的转录组进行了分析。对 136,220,612 条reads 的从头组装产生了 128,934 个非冗余的 unigenes，其 N50 值为 1347bp。对 unigenes 的注释是针对 NCBI nr 数据库、基因本体论（GO）、KEGG、UniProt、Pfam 和 plnTFDB 等数据库进行的。共有 60,097 个 unigenes被注释，包括 48 个转录因子家族，14,490 个 unigenes被分配到 138 个途径，使用 KEGG 数据库。途径分析显示，参与生物合成重要次生代谢物的转录本，如类黄酮，为其药用价值做出了贡献。此外，使用 RSEM 对转录本进行定量，以鉴定次生代谢物的高度调控基因。进行了逆转录 PCR（RT-PCR）以验证从头组装的 unigenes。使用 qRT-PCR 分析了类黄酮生物合成途径中选定 unigenes 的表达谱。我们还鉴定了 13,262 个简单序列重复（SSR），这有助于进行分子育种。这是三叶茄综合转录组分析的首次报道，这将是进一步研究三叶茄药用属性相关分子基础的宝贵资源。
