MINING OF EXPRESSED SEQUENCE TAG (EST) LIBRARIES AND CORE NUCLEOTIDE SEQUENCES FOR SIMPLE SEQUENCE REPEATS (SSR) IN PAPAYA

Papaya, an economically important fruit plant, is polygamous in nature. Carica papaya is a native of tropical America and a member of the family Caricaceae.
Expressed Sequence Tags (ESTs) are fragments of gene transcripts that provide researchers a quick and inexpensive route for discovering new genes.
Available EST resources (1283) and core nucleotide (303) sequences were mined to develop Sequences for Simple Sequence Repeat (SSR) maker and its abundance in the papaya genome.
Computational tools MISA and ETRA were employed to find the microsatellite repeats or SSRs ranging from monomer to decamer from assembled ESTs, singlets as well as core nucleotide sequences.
A total of 1301 and 1134 SSR were reported in EST and core nucleotide respectively.
Class I type SSR were found in papaya genome at a frequency of 1 SSR/8.7 kbp and Class II SSRs were very highly frequent at 1 SSR/552 bp.
Pentanucleotide repeats and mononucleotide repeats were found to be abundant in EST sequences and monomer repeats and dinulceotide repeats are abundant in core nucleotide sequences.
A database was generated http://www.riju.mybioscience.com/papaya.

II International Symposium on Papaya

V. Arumugam, A. Riju, V. Arunachalam

Carica, fruit, in silico, molecular marker, transcriptome

https://doi.org/10.17660/ActaHortic.2010.851.28