Match!

RNA sequencing and de novo assembly of Solanum trilobatum leaf transcriptome to identify putative transcripts for major metabolic pathways

Published on Dec 1, 2018in Scientific Reports4.011
· DOI :10.1038/s41598-018-33693-4
Adil Lateef1
Estimated H-index: 1
,
Sudheesh K. Prabhudas2
Estimated H-index: 2
,
Purushothaman Natarajan3
Estimated H-index: 3
Sources
Abstract
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.
Figures & Tables
  • References (55)
  • Citations (2)
📖 Papers frequently viewed together
8 Citations
20162.78PLOS ONE
2 Citations
20182.78PLOS ONE
7 Authors (Dian-Yun Hou, ..., Hua-Wei Xu)
1 Citations
78% of Scinapse members use related papers. After signing in, all features are FREE.
References55
Newest
#1Kumar GanesanH-Index: 7
Last. Baojun XuH-Index: 30
view all 3 authors...
Solanum trilobatum L. (Solanaceae) has been well known as nightshade, commonly used by diverse populations to heal several disorders. Earlier studies in Solanum trilobatum were focused on different pharmacological activities and a few were concerned with antioxidant and hepatoprotective effects. Thus, the current study was focused to evaluate the antioxidant potential and hepatoprotective effects of S. trilobatum L. on thioacetamide (TAA) intoxication in Wistar albino rats. The rats were kept in...
5 CitationsSource
#1Mostafa Abdelrahman (Science College)H-Index: 10
#2Magdi A. El-Sayed (Aswan University)H-Index: 15
Last. Masayoshi Shigyo (Science College)H-Index: 4
view all 11 authors...
The genus Allium is a rich source of steroidal saponins, and its medicinal properties have been attributed to these bioactive compounds. The saponin compounds with diverse structures play a pivotal role in Allium’s defense mechanism. Despite numerous studies on the occurrence and chemical structure of steroidal saponins, their biosynthetic pathway in Allium species is poorly understood. The monosomic addition lines (MALs) of the Japanese bunching onion (A. fistulosum, FF) with an extra chromosom...
17 CitationsSource
#1Minoru Kanehisa (Kyoto University)H-Index: 71
#2Miho Furumichi (Kyoto University)H-Index: 7
Last. Kanae Morishima (Kyoto University)H-Index: 3
view all 5 authors...
1,651 CitationsSource
#1Aparupa Bose Mazumdar (Council for Scientific and Industrial Research)H-Index: 1
#2Sharmila Chattopadhyay (Council for Scientific and Industrial Research)H-Index: 1
Phyllanthus amarus Schum. & Thonn., a widely distributed annual medicinal herb has a long history of use in the traditional system of medicine for over 2000 years. However, the lack of genomic data for P. amarus, a non-model organism hinders research at the molecular level. In the present study, high-throughput sequencing technology has been employed to enhance better understanding of this herb and provide comprehensive genomic information for future work. Here P. amarus leaf transcriptome was s...
10 CitationsSource
#1Minoru Kanehisa (Kyoto University)H-Index: 71
#2Yoko Sato (Fujitsu)H-Index: 9
Last. Mao Tanabe (Kyoto University)H-Index: 11
view all 5 authors...
KEGG (http://www.kegg.jp/ or http://www.genome.jp/kegg/) is an integrated database resource for biological interpretation of genome sequences and other high-throughput data. Molecular functions of genes and proteins are associated with ortholog groups and stored in the KEGG Orthology (KO) database. The KEGG pathway maps, BRITE hierarchies and KEGG modules are developed as networks of KO nodes, representing high-level functions of the cell and the organism. Currently, more than 4000 complete geno...
1,861 CitationsSource
#1Qiang Dang (Xi'an Jiaotong University)H-Index: 10
#2Wenbin Song (Xi'an Jiaotong University)H-Index: 9
Last. Lei Li (Xi'an Jiaotong University)H-Index: 28
view all 11 authors...
The effects of the flavonoid compound, kaempferol, which is an inhibitor of cancer cell proliferation and an inducer of cell apoptosis have been shown in various cancers, including lung, pancreatic, and ovarian, but its effect has never been studied in bladder cancer. Here, we investigated the effects of kaempferol on bladder cancer using multiple in vitro cell lines and in vivo mice studies. The MTT assay results on various bladder cancer cell lines showed that kaempferol enhanced bladder cance...
36 CitationsSource
In the present study, seed crude extracts of Solanum trilobatum was studied for its ability to inhibit the growth of dental (bacterial) pathogens (Staphylococcus aureus, Streptococcus mutans, Streptococcus salivarius, Streptococcus sanguinis and Lactobacillus acidophilus). Collected seeds of S. trilobatum were properly washed and shade dried at room temperature, crushed and extracted in acetone, petroleum ether and chloroform. The antibacterial activity of extracts was examined by ager well diff...
1 Citations
Introduction: Vyaghriharitaki Avaleha (VHA), a polyherbal classical Ayurvedic formulation has been used in Kasa (cough), Swasa (asthma), Rajayakshma (tuberculosis) etc., conditions. Aim: To evaluate the clinical efficacy of VHA in the management of chronic bronchitis. Materials and Methods: Patients of chronic bronchitis were given 10 g of VHA twice a day with lukewarm water before meals for 12 weeks. Improvement in clinical symptoms of chronic bronchitis as the primary outcome measures and St. ...
1 CitationsSource
#1Er-Jiang LinH-Index: 1
#2Xian ZhangH-Index: 2
Last. Lei-Yu LiH-Index: 1
view all 5 authors...
Metastasis is a multifactorial condition that complicates cancer treatment options and widens the target of treatment. Matrix mettalopriteinases (MMPs) of the extracellular matrix (ECM) are involved in metastasis, thus they present as potential targets in halting cancer metastasis. The study was undertaken to investigate the influence of naringenin, a naturally occurring flavonoid on the metastasis of human prostate cancer cells (PC-3 and DU145). Naringenin was observed to be effective in reduci...
6 CitationsSource
#1Amr A. Fouad (King Faisal University)H-Index: 16
#2Waleed H. Albuali (King Faisal University)H-Index: 10
Last. Wafaey Gomaa (KAU: King Abdulaziz University)H-Index: 9
view all 4 authors...
Abstract The protective effect of naringenin, a flavonoid compound isolated from citrus fruits, was investigated against nephrotoxicity induced by gentamicin (80 mg kg −1 /day, i.p., for eight days) in rats. Naringenin treatment (50 mg kg −1 /day, p.o.) was administered for eight days, starting on the same day of gentamicin administration. Gentamicin caused significant elevations of serum creatinine, and kidney tissue levels of malondialdehyde, nitric oxide, and interleukin-8, and a significant ...
20 CitationsSource
Cited By2
Newest
#1Garima N. AyachitH-Index: 2
#2Inayatullah ShaikhH-Index: 2
Last. Jayashankar DasH-Index: 6
view all 9 authors...
Source
#2Soumyashant NayakH-Index: 3
Last. Gregory R. Grant (UPenn: University of Pennsylvania)H-Index: 15
view all 5 authors...
Full-length isoform quantification from RNA-Seq is a key goal in transcriptomics analyses and an area of active development. The fundamental difficulty stems from the fact that RNA transcripts are long, while RNA-Seq reads are typically short. We have generated realistic benchmarking data, and have performed a comprehensive comparative analysis of isoform quantification, including evaluating them on the level of differential expression analysis. Genome, transcriptome and pseudo alignment-based m...
Source