Limits...
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.


Clusters of orthologous groups (COG) functional classification of CDS in the young and mature leaf transcriptome of Cassia angustifolia.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4476680&req=5

pone.0129422.g003: Clusters of orthologous groups (COG) functional classification of CDS in the young and mature leaf transcriptome of Cassia angustifolia.

Mentions: To further predict the function of the CDS, all 42,230 and 37,174 CDS of young and mature leaves, respectively were subjected to classification into different protein families based on Clusters of Orthologus Groups (COG) of protein databases. Overall 15,592 and 15,215 CDS of young and mature leaves, respectively showed significant homology and assigned to the appropriate COG clusters. The COG annotated putative proteins were distributed functionally into at least 24 protein families (Fig 3), of which the cluster for “general function prediction” represented the largest group (4411 and 4534), followed by “transcription” (1927 and 2054), “signal transduction” (1806 and 1932), “replication and repair” (1653 and 1976) and “post translational modification, protein turnover (1598 and 1505) in young and mature leaf samples. The least represented groups include “cell motility” (16 and 12) and “nuclear structure” (3 and 3) in young and mature leaves, 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)

Clusters of orthologous groups (COG) functional classification 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.g003: Clusters of orthologous groups (COG) functional classification of CDS in the young and mature leaf transcriptome of Cassia angustifolia.
Mentions: To further predict the function of the CDS, all 42,230 and 37,174 CDS of young and mature leaves, respectively were subjected to classification into different protein families based on Clusters of Orthologus Groups (COG) of protein databases. Overall 15,592 and 15,215 CDS of young and mature leaves, respectively showed significant homology and assigned to the appropriate COG clusters. The COG annotated putative proteins were distributed functionally into at least 24 protein families (Fig 3), of which the cluster for “general function prediction” represented the largest group (4411 and 4534), followed by “transcription” (1927 and 2054), “signal transduction” (1806 and 1932), “replication and repair” (1653 and 1976) and “post translational modification, protein turnover (1598 and 1505) in young and mature leaf samples. The least represented groups include “cell motility” (16 and 12) and “nuclear structure” (3 and 3) in young and mature leaves, 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.