De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments
IR@IHBT: CSIR-Institute of Himalayan Bioresource Technology, Palampur
View Archive InfoField | Value | |
Title |
De novo sequencing and characterization of
Picrorhiza kurrooa transcriptome at two
temperatures showed major transcriptome
adjustments
|
|
Creator |
Gahlan, P
Singh, H R Shanker, R Sharma, N Kumari, A Chawla, V Ahuja, Paramvir Singh Kumar, Sanjay |
|
Subject |
Plant sciences
Plant Biotechnology |
|
Description |
Background: Picrorhiza kurrooa Royle ex Benth. is an endangered plant species of medicinal importance. The
medicinal property is attributed to monoterpenoids picroside I and II, which are modulated by temperature. The
transcriptome information of this species is limited with the availability of few hundreds of expressed sequence
tags (ESTs) in the public databases. In order to gain insight into temperature mediated molecular changes, high
throughput de novo transcriptome sequencing and analyses were carried out at 15°C and 25°C, the temperatures
known to modulate picrosides content.
Results: Using paired-end (PE) Illumina sequencing technology, a total of 20,593,412 and 44,229,272 PE reads were
obtained after quality filtering for 15°C and 25°C, respectively. Available (e.g., De-Bruijn/Eulerian graph) and in-house
developed bioinformatics tools were used for assembly and annotation of transcriptome. A total of 74,336
assembled transcript sequences were obtained, with an average coverage of 76.6 and average length of 439.5.
Guanine-cytosine (GC) content was observed to be 44.6%, while the transcriptome exhibited abundance of
trinucleotide simple sequence repeat (SSR; 45.63%) markers.
Large scale expression profiling through “read per exon kilobase per million (RPKM)”, showed changes in several
biological processes and metabolic pathways including cytochrome P450s (CYPs), UDP-glycosyltransferases (UGTs) and
those associated with picrosides biosynthesis. RPKM data were validated by reverse transcriptase-polymerase chain
reaction using a set of 19 genes, wherein 11 genes behaved in accordance with the two expression methods.
Conclusions: Study generated transcriptome of P. kurrooa at two different temperatures. Large scale expression
profiling through RPKM showed major transcriptome changes in response to temperature reflecting alterations in
major biological processes and metabolic pathways, and provided insight of GC content and SSR markers. Analysis
also identified putative CYPs and UGTs that could help in discovering the hitherto unknown genes associated with
picrosides biosynthesis.
|
|
Date |
2012
|
|
Type |
Article
PeerReviewed |
|
Format |
application/pdf
|
|
Identifier |
http://ihbt.csircentral.net/1207/1/10_De_novo.pdf
Gahlan, P and Singh, H R and Shanker, R and Sharma, N and Kumari, A and Chawla, V and Ahuja, Paramvir Singh and Kumar, Sanjay (2012) De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments. BMC Genomics, 13. p. 126. |
|
Relation |
http://ihbt.csircentral.net/1207/
|
|