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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Autores principales:	Adil Lateef, Sudheesh K. Prabhudas, Purushothaman Natarajan
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Solanum Trilobatum Unigenes RNA-Seq By Expectation-Maximization (RSEM) Flavonoid Biosynthesis Pathway Kyoto Encyclopedia Of Genes And Genomes (KEGG) Medicine R Science Q
Acceso en línea:	https://doaj.org/article/5e2a3c7ba5364472975c88f24e479150
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spelling	oai:doaj.org-article:5e2a3c7ba5364472975c88f24e4791502021-12-02T15:09:03ZRNA sequencing and de novo assembly of Solanum trilobatum leaf transcriptome to identify putative transcripts for major metabolic pathways10.1038/s41598-018-33693-42045-2322https://doaj.org/article/5e2a3c7ba5364472975c88f24e4791502018-10-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-33693-4https://doaj.org/toc/2045-2322Abstract 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.Adil LateefSudheesh K. PrabhudasPurushothaman NatarajanNature PortfolioarticleSolanum TrilobatumUnigenesRNA-Seq By Expectation-Maximization (RSEM)Flavonoid Biosynthesis PathwayKyoto Encyclopedia Of Genes And Genomes (KEGG)MedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-13 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Solanum Trilobatum Unigenes RNA-Seq By Expectation-Maximization (RSEM) Flavonoid Biosynthesis Pathway Kyoto Encyclopedia Of Genes And Genomes (KEGG) Medicine R Science Q
spellingShingle	Solanum Trilobatum Unigenes RNA-Seq By Expectation-Maximization (RSEM) Flavonoid Biosynthesis Pathway Kyoto Encyclopedia Of Genes And Genomes (KEGG) Medicine R Science Q 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
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.
format	article
author	Adil Lateef Sudheesh K. Prabhudas Purushothaman Natarajan
author_facet	Adil Lateef Sudheesh K. Prabhudas Purushothaman Natarajan
author_sort	Adil Lateef
title	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_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_sort	rna sequencing and de novo assembly of solanum trilobatum leaf transcriptome to identify putative transcripts for major metabolic pathways
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/5e2a3c7ba5364472975c88f24e479150
work_keys_str_mv	AT adillateef rnasequencinganddenovoassemblyofsolanumtrilobatumleaftranscriptometoidentifyputativetranscriptsformajormetabolicpathways AT sudheeshkprabhudas rnasequencinganddenovoassemblyofsolanumtrilobatumleaftranscriptometoidentifyputativetranscriptsformajormetabolicpathways AT purushothamannatarajan rnasequencinganddenovoassemblyofsolanumtrilobatumleaftranscriptometoidentifyputativetranscriptsformajormetabolicpathways
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RNA sequencing and de novo assembly of Solanum trilobatum leaf transcriptome to identify putative transcripts for major metabolic pathways

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