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Next Generation Sequencing and Transcriptome Analysis Predicts Biosynthetic Pathway of Sennosides from Senna (Cassia angustifolia Vahl.), a Non-Model Plant with Potent Laxative Properties.

Rama Reddy NR, Mehta RH, Soni PH, Makasana J, Gajbhiye NA, Ponnuchamy M, Kumar J - PLoS ONE (2015)

Bottom Line: A total of 10,763 CDS differentially expressing in both young and mature leaf libraries of which 2,343 (21.7%) CDS were up-regulated in young compared to mature leaf.Several differentially expressed genes found functionally associated with sennoside biosynthesis.We have identified a set of putative genes involved in various secondary metabolite pathways, especially those related to the synthesis of sennosides which will serve as an important platform for public information about gene expression, genomics, and functional genomics in senna.

View Article: PubMed Central - PubMed

Affiliation: ICAR-Directorate of Medicinal and Aromatic Plants Research (DMAPR), Anand, Gujarat, India.

ABSTRACT
Senna (Cassia angustifolia Vahl.) is a world's natural laxative medicinal plant. Laxative properties are due to sennosides (anthraquinone glycosides) natural products. However, little genetic information is available for this species, especially concerning the biosynthetic pathways of sennosides. We present here the transcriptome sequencing of young and mature leaf tissue of Cassia angustifolia using Illumina MiSeq platform that resulted in a total of 6.34 Gb of raw nucleotide sequence. The sequence assembly resulted in 42230 and 37174 transcripts with an average length of 1119 bp and 1467 bp for young and mature leaf, respectively. The transcripts were annotated using NCBI BLAST with 'green plant database (txid 33090)', Swiss Prot, Kyoto Encylcopedia of Genes & Genomes (KEGG), Cluster of Orthologous Gene (COG) and Gene Ontology (GO). Out of the total transcripts, 40138 (95.0%) and 36349 (97.7%) from young and mature leaf, respectively, were annotated by BLASTX against green plant database of NCBI. We used InterProscan to see protein similarity at domain level, a total of 34031 (young leaf) and 32077 (mature leaf) transcripts were annotated against the Pfam domains. All transcripts from young and mature leaf were assigned to 191 KEGG pathways. There were 166 and 159 CDS, respectively, from young and mature leaf involved in metabolism of terpenoids and polyketides. Many CDS encoding enzymes leading to biosynthesis of sennosides were identified. A total of 10,763 CDS differentially expressing in both young and mature leaf libraries of which 2,343 (21.7%) CDS were up-regulated in young compared to mature leaf. Several differentially expressed genes found functionally associated with sennoside biosynthesis. CDS encoding for many CYPs and TF families were identified having probable roles in metabolism of primary as well as secondary metabolites. We developed SSR markers for molecular breeding of senna. We have identified a set of putative genes involved in various secondary metabolite pathways, especially those related to the synthesis of sennosides which will serve as an important platform for public information about gene expression, genomics, and functional genomics in senna.

No MeSH data available.


KEGG pathway analysis of CDS in the young and mature leaf transcriptome of Cassia angustifolia.
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pone.0129422.g006: KEGG pathway analysis of CDS in the young and mature leaf transcriptome of Cassia angustifolia.

Mentions: Pathway based analysis can help us further understand the biological significance of genes. The Koyto Encyclopedia of Genes and Genomes (KEGG) pathway database contains systematic analysis of inner-cell metabolic pathways and functions of gene products, which aid in studying the complex biological behavior of genes. Ortholog assignment and mapping of the CDS to the biological pathways were performed using KEGG automatic annotation server (KAAS). All the CDS were compared against the KEGG database using BLASTX with threshold bit-score value of 60 (default). A total of 7,504 and 7,618 CDS were enriched in 24 different functional KASS pathway categories in young and mature leaf, respectively (Fig 6). The mapped CDS represented metabolic pathways of major biomolecules such as carbon, carbohydrates, lipids, nucleotides, amino acids, glycans, cofactors, vitamins, terpenoids, polyketides, and others. The mapped CDS also represented the genes involved in genetic information processing, environmental information processing, cellular processes, and organizational systems. In total, all CDS from young and mature leaf were assigned to 191 KEGG pathways (S1 Table and S2 Table). In young leaf, the pathways with most representation by the CDS were translation (955) followed by folding, sorting and degradation (730), and signal transduction (617). While in mature leaf, translation (846) followed by folding, sorting and degradation (721), and carbohydrate metabolism (669) were the most represented pathways by the CDS. The least represented pathways include ‘signal molecules and interaction’, and membrane transport. Interestingly, 166 and 159 CDS, from young and mature leaf libraries, respectively, were found to be involved in metabolism of terpenoids and polyketides. Within this category, the cluster for ‘Terpenoid backbone biosynthesis [PATH:ko00900]’ represented the largest cluster with 58 and 66 CDS in young and mature leaf libraries, respectively. Similarly, there were 102 and 122 CDS from young and mature leaves, respectively, were found to be involved in the biosynthesis of other secondary metabolites. The ‘Phenylpropanoid biosynthesis [PATH: ko00940]’ cluster represented the largest group with 48 and 60 CDS in young and mature leaf libraries, respectively.


Next Generation Sequencing and Transcriptome Analysis Predicts Biosynthetic Pathway of Sennosides from Senna (Cassia angustifolia Vahl.), a Non-Model Plant with Potent Laxative Properties.

Rama Reddy NR, Mehta RH, Soni PH, Makasana J, Gajbhiye NA, Ponnuchamy M, Kumar J - PLoS ONE (2015)

KEGG pathway analysis of CDS in the young and mature leaf transcriptome of Cassia angustifolia.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4476680&req=5

pone.0129422.g006: KEGG pathway analysis of CDS in the young and mature leaf transcriptome of Cassia angustifolia.
Mentions: Pathway based analysis can help us further understand the biological significance of genes. The Koyto Encyclopedia of Genes and Genomes (KEGG) pathway database contains systematic analysis of inner-cell metabolic pathways and functions of gene products, which aid in studying the complex biological behavior of genes. Ortholog assignment and mapping of the CDS to the biological pathways were performed using KEGG automatic annotation server (KAAS). All the CDS were compared against the KEGG database using BLASTX with threshold bit-score value of 60 (default). A total of 7,504 and 7,618 CDS were enriched in 24 different functional KASS pathway categories in young and mature leaf, respectively (Fig 6). The mapped CDS represented metabolic pathways of major biomolecules such as carbon, carbohydrates, lipids, nucleotides, amino acids, glycans, cofactors, vitamins, terpenoids, polyketides, and others. The mapped CDS also represented the genes involved in genetic information processing, environmental information processing, cellular processes, and organizational systems. In total, all CDS from young and mature leaf were assigned to 191 KEGG pathways (S1 Table and S2 Table). In young leaf, the pathways with most representation by the CDS were translation (955) followed by folding, sorting and degradation (730), and signal transduction (617). While in mature leaf, translation (846) followed by folding, sorting and degradation (721), and carbohydrate metabolism (669) were the most represented pathways by the CDS. The least represented pathways include ‘signal molecules and interaction’, and membrane transport. Interestingly, 166 and 159 CDS, from young and mature leaf libraries, respectively, were found to be involved in metabolism of terpenoids and polyketides. Within this category, the cluster for ‘Terpenoid backbone biosynthesis [PATH:ko00900]’ represented the largest cluster with 58 and 66 CDS in young and mature leaf libraries, respectively. Similarly, there were 102 and 122 CDS from young and mature leaves, respectively, were found to be involved in the biosynthesis of other secondary metabolites. The ‘Phenylpropanoid biosynthesis [PATH: ko00940]’ cluster represented the largest group with 48 and 60 CDS in young and mature leaf libraries, respectively.

Bottom Line: A total of 10,763 CDS differentially expressing in both young and mature leaf libraries of which 2,343 (21.7%) CDS were up-regulated in young compared to mature leaf.Several differentially expressed genes found functionally associated with sennoside biosynthesis.We have identified a set of putative genes involved in various secondary metabolite pathways, especially those related to the synthesis of sennosides which will serve as an important platform for public information about gene expression, genomics, and functional genomics in senna.

View Article: PubMed Central - PubMed

Affiliation: ICAR-Directorate of Medicinal and Aromatic Plants Research (DMAPR), Anand, Gujarat, India.

ABSTRACT
Senna (Cassia angustifolia Vahl.) is a world's natural laxative medicinal plant. Laxative properties are due to sennosides (anthraquinone glycosides) natural products. However, little genetic information is available for this species, especially concerning the biosynthetic pathways of sennosides. We present here the transcriptome sequencing of young and mature leaf tissue of Cassia angustifolia using Illumina MiSeq platform that resulted in a total of 6.34 Gb of raw nucleotide sequence. The sequence assembly resulted in 42230 and 37174 transcripts with an average length of 1119 bp and 1467 bp for young and mature leaf, respectively. The transcripts were annotated using NCBI BLAST with 'green plant database (txid 33090)', Swiss Prot, Kyoto Encylcopedia of Genes & Genomes (KEGG), Cluster of Orthologous Gene (COG) and Gene Ontology (GO). Out of the total transcripts, 40138 (95.0%) and 36349 (97.7%) from young and mature leaf, respectively, were annotated by BLASTX against green plant database of NCBI. We used InterProscan to see protein similarity at domain level, a total of 34031 (young leaf) and 32077 (mature leaf) transcripts were annotated against the Pfam domains. All transcripts from young and mature leaf were assigned to 191 KEGG pathways. There were 166 and 159 CDS, respectively, from young and mature leaf involved in metabolism of terpenoids and polyketides. Many CDS encoding enzymes leading to biosynthesis of sennosides were identified. A total of 10,763 CDS differentially expressing in both young and mature leaf libraries of which 2,343 (21.7%) CDS were up-regulated in young compared to mature leaf. Several differentially expressed genes found functionally associated with sennoside biosynthesis. CDS encoding for many CYPs and TF families were identified having probable roles in metabolism of primary as well as secondary metabolites. We developed SSR markers for molecular breeding of senna. We have identified a set of putative genes involved in various secondary metabolite pathways, especially those related to the synthesis of sennosides which will serve as an important platform for public information about gene expression, genomics, and functional genomics in senna.

No MeSH data available.