TY - JOUR
T1 - Comparative transcriptomics uncovers differences in photoautotrophic versus photoheterotrophic modes of nutrition in relation to secondary metabolites biosynthesis in Swertia chirayita
AU - Pal, Tarun
AU - Padhan, Jibesh Kumar
AU - Kumar, Pawan
AU - Sood, Hemant
AU - Chauhan, Rajinder S.
N1 - Publisher Copyright:
© Springer Science+Business Media B.V., part of Springer Nature 2018.
PY - 2018/4/1
Y1 - 2018/4/1
N2 - Swertia chirayita is a high-value medicinal herb exhibiting antidiabetic, hepatoprotective, anticancer, antiediematogenic and antipyretic properties. Scarcity of its plant material has necessitated in vitro production of therapeutic metabolites; however, their yields were low compared to field grown plants. Possible reasons for this could be differences in physiological and biochemical processes between plants grown in photoautotrophic versus photoheterotrophic modes of nutrition. Comparative transcriptomes of S. chirayita were generated to decipher the crucial molecular components associated with the secondary metabolites biosynthesis. Illumina HiSeq sequencing yielded 57,460 and 43,702 transcripts for green house grown (SCFG) and tissue cultured (SCTC) plants, respectively. Biological role analysis (GO and COG assignments) revealed major differences in SCFG and SCTC transcriptomes. KEGG orthology mapped 351 and 341 transcripts onto secondary metabolites biosynthesis pathways for SCFG and SCTC transcriptomes, respectively. Nineteen out of 30 genes from primary metabolism showed higher in silico expression (FPKM) in SCFG versus SCTC, possibly indicating their involvement in regulating the central carbon pool. In silico data were validated by RT-qPCR using a set of 16 genes, wherein 10 genes showed similar expression pattern across both the methods. Comparative transcriptomes identified differentially expressed transcription factors and ABC-type transporters putatively associated with secondary metabolism in S. chirayita. Additionally, functional classification was performed using NCBI Biosystems database. This study identified the molecular components implicated in differential modes of nutrition (photoautotrophic vs. photoheterotrophic) in relation to secondary metabolites production in S. chirayita.
AB - Swertia chirayita is a high-value medicinal herb exhibiting antidiabetic, hepatoprotective, anticancer, antiediematogenic and antipyretic properties. Scarcity of its plant material has necessitated in vitro production of therapeutic metabolites; however, their yields were low compared to field grown plants. Possible reasons for this could be differences in physiological and biochemical processes between plants grown in photoautotrophic versus photoheterotrophic modes of nutrition. Comparative transcriptomes of S. chirayita were generated to decipher the crucial molecular components associated with the secondary metabolites biosynthesis. Illumina HiSeq sequencing yielded 57,460 and 43,702 transcripts for green house grown (SCFG) and tissue cultured (SCTC) plants, respectively. Biological role analysis (GO and COG assignments) revealed major differences in SCFG and SCTC transcriptomes. KEGG orthology mapped 351 and 341 transcripts onto secondary metabolites biosynthesis pathways for SCFG and SCTC transcriptomes, respectively. Nineteen out of 30 genes from primary metabolism showed higher in silico expression (FPKM) in SCFG versus SCTC, possibly indicating their involvement in regulating the central carbon pool. In silico data were validated by RT-qPCR using a set of 16 genes, wherein 10 genes showed similar expression pattern across both the methods. Comparative transcriptomes identified differentially expressed transcription factors and ABC-type transporters putatively associated with secondary metabolism in S. chirayita. Additionally, functional classification was performed using NCBI Biosystems database. This study identified the molecular components implicated in differential modes of nutrition (photoautotrophic vs. photoheterotrophic) in relation to secondary metabolites production in S. chirayita.
KW - Next generation sequencing
KW - Photoautotrophic
KW - Photoheterotrophic
KW - Secondary metabolites
KW - Swertia chirayita
KW - Transcriptome
UR - http://www.scopus.com/inward/record.url?scp=85040790029&partnerID=8YFLogxK
U2 - 10.1007/s11033-017-4135-y
DO - 10.1007/s11033-017-4135-y
M3 - Article
C2 - 29349608
AN - SCOPUS:85040790029
SN - 0301-4851
VL - 45
SP - 77
EP - 98
JO - Molecular Biology Reports
JF - Molecular Biology Reports
IS - 2
ER -