Single nucleotide polymorphisms (SNPs) and indels in expressed sequence tag libraries of turmeric (Curcuma longa L.):Online Journal of Bioinformatics.

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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 K², Anoop S³, Santhosh J Eapen*¹

¹Bioinformatics Centre, Indian Institute of Spices Research, Marikunnu P.O, Calicut – 673012, Kerala, India,²Kandiyl House, Makkada (P.O), Kakkodi, Calicut – 673617. Kerala. India. ³Ottankulam, Athicode (P.O), Palakkad (Dist), Kerala – 678554. India. *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.), Onl J Bioinform., 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

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