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 Info| Field | Value | |
| Title |
De novo sequencing and characterization of Picrorhiza
kurrooa transcriptome at two temperatures showed major
transcriptome adjustments
|
|
| Creator |
Gahlan, Parul
Singh, H R Shankar, R Sharma, N Kumari, A Chawla, V Ahuja, Paramvir Singh Kumar, Sanjay |
|
| Subject |
Plant sciences
Natural Product Chemistry |
|
| 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. Guaninecytosine
(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 at the two
temperatures 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 |
2011
|
|
| Type |
Article
PeerReviewed |
|
| Format |
application/pdf
|
|
| Identifier |
http://ihbt.csircentral.net/1104/1/43_de_novo.pdf
Gahlan, Parul and Singh, H R and Shankar, R and Sharma, N and Kumari, A and Chawla, V and Ahuja, Paramvir Singh and Kumar, Sanjay (2011) De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments. BMC Genomics, 12. p. 636. |
|
| Relation |
http://ihbt.csircentral.net/1104/
|
|