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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.


Top 10 Pfam domains represented in InterProScan transcript annotations of the Cassia angustifolia leaf Transcriptome.
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pone.0129422.g005: Top 10 Pfam domains represented in InterProScan transcript annotations of the Cassia angustifolia leaf Transcriptome.

Mentions: We used InterProscan to see protein similarity at domain level, where the proteins have little similarity at sequence level but might share conserved structural domains. In total, 34,031 and 32,077 transcripts were annotated against the Pfam domains (Fig 5). Pentatricopeptide repeat (PPR) (PF01535.15) domain represented the most (2255 and 2935 transcripts in young and mature leaves, respectively) which was followed by PPR_3 (PF13812.1) (2081 and 2686 transcripts in young and mature leaves, respectively), PPR_2 (PF13041.1) (2007 and 2614 transcripts in young and mature leaves, respectively) and PPR_1 (PF12854.2) (1823 and 2422 transcripts in young and mature leaves, respectively). Other domains frequently represented in young and mature leaf libraries include TPR_14 (PF13428.1) (1721 and 2367), LRR_6 (PF13516.1) (2183 and 2237), LRR_1 (PF00560.28) (2056 and 2175) and WD40 (PF00400.27) (1983 and 2139) in the transcripts indicating strong signal transduction mechanisms.


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)

Top 10 Pfam domains represented in InterProScan transcript annotations of the Cassia angustifolia leaf Transcriptome.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0129422.g005: Top 10 Pfam domains represented in InterProScan transcript annotations of the Cassia angustifolia leaf Transcriptome.
Mentions: We used InterProscan to see protein similarity at domain level, where the proteins have little similarity at sequence level but might share conserved structural domains. In total, 34,031 and 32,077 transcripts were annotated against the Pfam domains (Fig 5). Pentatricopeptide repeat (PPR) (PF01535.15) domain represented the most (2255 and 2935 transcripts in young and mature leaves, respectively) which was followed by PPR_3 (PF13812.1) (2081 and 2686 transcripts in young and mature leaves, respectively), PPR_2 (PF13041.1) (2007 and 2614 transcripts in young and mature leaves, respectively) and PPR_1 (PF12854.2) (1823 and 2422 transcripts in young and mature leaves, respectively). Other domains frequently represented in young and mature leaf libraries include TPR_14 (PF13428.1) (1721 and 2367), LRR_6 (PF13516.1) (2183 and 2237), LRR_1 (PF00560.28) (2056 and 2175) and WD40 (PF00400.27) (1983 and 2139) in the transcripts indicating strong signal transduction mechanisms.

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.