IN SILICO DATA MINING FOR DEVELOPMENT OF CAPSICUM MICROSATELLITES

A.G. İnce, A.N. Onus, S.Y. Elmasulu, M. Bilgen, M. Karaca
Tandemly repeated DNAs play important roles in evolution and regulatory processes. Tandem Repeats (TRs) exist in coding and non-coding portion of genomes. Simple Sequence Repeats (SSRs) or microsatellites are stretches of DNA consisting of exact and inexact simple tandemly repeated DNA. In this study, distribution and frequency of TRs and SSRs in Capsicum annuum Expressed Sequence Tags (ESTs) were investigated. Results demonstrated that TR’s and SSR’s content of C. annuum were quite high in the family Solanaceae. There were considerable variations in the occurrence of the individual SSR motif in Capsicum annuum. SSR motifs of mono A/T, di CT/GA, tri CTT/GAA, tetra AAAT/TTTA, penta TTTTC and hexa CTGCTC nucleotides were abundant in Capsicum. Exact and inexact SSRs also differed in frequency and distribution in Capsicum. Results indicated that frequency and distribution of SSRs differing in tissue/organ ESTs of Capsicum indicated that repeats distribution and frequency may not be random in the coding portion of genome differing from the non-coding portion of genomes. Exact and inexact SSR contents of several organs/tissues differed. A total of 300 Capsicum EST-SSR primer pairs, of which 124 were tissue/organ specific, were developed.
İnce, A.G., Onus, A.N., Elmasulu, S.Y., Bilgen, M. and Karaca, M. (2007). IN SILICO DATA MINING FOR DEVELOPMENT OF CAPSICUM MICROSATELLITES. Acta Hortic. 729, 123-127
DOI: 10.17660/ActaHortic.2007.729.18
https://doi.org/10.17660/ActaHortic.2007.729.18
data mining, SSR, microsatellites and EST-SSR primers
English

Acta Horticulturae