RNA sequencing and de novo assembly of Solanum trilobatum leaf transcriptome to identify putative transcripts for major metabolic pathways
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 through...
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Nature Portfolio
2018-10-01
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| Series: | Scientific Reports |
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| Online Access: | https://doi.org/10.1038/s41598-018-33693-4 |
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| author | Adil Lateef Sudheesh K. Prabhudas Purushothaman Natarajan |
| author_facet | Adil Lateef Sudheesh K. Prabhudas Purushothaman Natarajan |
| author_sort | Adil Lateef |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-20T21:52:11Z |
| format | Article |
| id | doaj.art-5e2a3c7ba5364472975c88f24e479150 |
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| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-20T21:52:11Z |
| publishDate | 2018-10-01 |
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| spelling | doaj.art-5e2a3c7ba5364472975c88f24e4791502022-12-21T19:25:31ZengNature PortfolioScientific Reports2045-23222018-10-018111310.1038/s41598-018-33693-4RNA sequencing and de novo assembly of Solanum trilobatum leaf transcriptome to identify putative transcripts for major metabolic pathwaysAdil Lateef0Sudheesh K. Prabhudas1Purushothaman Natarajan2Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and TechnologyDepartment of Genetic Engineering, School of Bioengineering, SRM Institute of Science and TechnologyDepartment of Genetic Engineering, School of Bioengineering, SRM Institute of Science and TechnologyAbstract 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.https://doi.org/10.1038/s41598-018-33693-4Solanum TrilobatumUnigenesRNA-Seq By Expectation-Maximization (RSEM)Flavonoid Biosynthesis PathwayKyoto Encyclopedia Of Genes And Genomes (KEGG) |
| spellingShingle | Adil Lateef Sudheesh K. Prabhudas Purushothaman Natarajan RNA sequencing and de novo assembly of Solanum trilobatum leaf transcriptome to identify putative transcripts for major metabolic pathways Scientific Reports Solanum Trilobatum Unigenes RNA-Seq By Expectation-Maximization (RSEM) Flavonoid Biosynthesis Pathway Kyoto Encyclopedia Of Genes And Genomes (KEGG) |
| title | RNA sequencing and de novo assembly of Solanum trilobatum leaf transcriptome to identify putative transcripts for major metabolic pathways |
| title_full | RNA sequencing and de novo assembly of Solanum trilobatum leaf transcriptome to identify putative transcripts for major metabolic pathways |
| title_fullStr | RNA sequencing and de novo assembly of Solanum trilobatum leaf transcriptome to identify putative transcripts for major metabolic pathways |
| title_full_unstemmed | RNA sequencing and de novo assembly of Solanum trilobatum leaf transcriptome to identify putative transcripts for major metabolic pathways |
| title_short | RNA sequencing and de novo assembly of Solanum trilobatum leaf transcriptome to identify putative transcripts for major metabolic pathways |
| title_sort | rna sequencing and de novo assembly of solanum trilobatum leaf transcriptome to identify putative transcripts for major metabolic pathways |
| topic | Solanum Trilobatum Unigenes RNA-Seq By Expectation-Maximization (RSEM) Flavonoid Biosynthesis Pathway Kyoto Encyclopedia Of Genes And Genomes (KEGG) |
| url | https://doi.org/10.1038/s41598-018-33693-4 |
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