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OJBTM
Online Journal of Bioinformatics ©
Volume 10 (2): 224-232,
2009.
Single
nucleotide
polymorphisms (SNPs) and indels in
expressed sequence
tag libraries of turmeric (Curcuma longa
L.)
Chandrasekar A1, Riju
A1, Sithara
1Bioinformatics
Centre,
Indian Institute of Spices Research, Marikunnu
P.O,
Calicut – 673012, Kerala, India, 2 Kandiyl
House, Makkada (P.O), Kakkodi,
Calicut
– 673617. Kerala.
*Corresponding
author: sjeapen@spices.res.in
ABSTRACT
Chandrasekar A, Riju A, Sithara K, Anoop S , Santhosh
J Eapen Single
nucleotide polymorphisms (SNPs) and indels
in
expressed sequence tag libraries of turmeric (Curcuma longa
L.), Online J Bioinformatics, Volume 10 (2): 224-232, 2009. Expressed sequence tag
(EST) sequencing
programs provide methods to identify novel genes. EST’s are a source of
biologically useful SNPs due to the relatively high redundancy of gene
sequences
and diversity of genotypes represented within databases. EST based SNPs
are
potential molecular markers for genetic improvement. 27599 and 2506
polymorphic
sites (SNPs and indels) were found in
turmeric, a
medicinal spice plant. Frequencies of SNPs and indels
were 1/91 bp and 1/998 bp,
respectively. The transition to transversion
ratio was
0.713, which showed a
relative increase in transversion type
mutation. The program is available
(http://spices.res.in/spicesnip).
Keywords:
Curcuma
longa, expressed
sequence
tag, mutation,
nucleotide, transition, transversion,
turmeric