Mining of expressed sequence tag libraries of cacao for microsatellite markers using five computational tools.
Expressed sequence tags (ESTs) provide researchers with a quick and inexpensive route for discovering new genes, data on gene expression and regulation, and also provide genic markers that help in constructing genome maps. Cacao is an important perennial crop of humid tropics. Cacao EST sequences, as available in the public domain, were downloaded and made into contigs. Microsatellites were located in these ESTs and contigs using five softwares (MISA, TRA, TROLL, SSRIT and SSR primer). MISA gave maximum coverage of SSRs in cacao ESTs and contigs, although TRA was able to detect higher order (5-mer) repeats. The frequency of SSRs was one per 26.9 kb in the known set of ESTs. One-third of the repeats in EST-contigs were found to be trimeric. A few rare repeats like 21-mer repeat were also located. A/T repeats were most abundant among the mononucleotide repeats and the AG/GA/TC/CT type was the most frequent among dimerics. Flanking primers were designed using Primer3 program and verified experimentally for PCR amplification. The results of the study are made available freely online database (http://riju.byethost31.com/cocoa/). Seven primer pairs amplified genomic DNA isolated from leaves were used to screen a representative set of 12 accessions of cacao.
Riju
Aikkal
A
Central Plantation Crops Research Institute, Kasaragod 671 124, India.
Rajesh
M K
MK
Sherin
P T P Fasila
PT
Chandrasekar
A
A
Apshara
S Elain
SE
Arunachalam
Vadivel
V
D001483:Base Sequence; D002099:Cacao / Q000235:genetics*; D017931:DNA Primers; D020224:Expressed Sequence Tags; D005819:Genetic Markers; D018895:Microsatellite Repeats / Q000235:genetics*; D016133:Polymerase Chain Reaction
D017931:DNA Primers; D005819:Genetic Markers
Bioinformatics. 2004 Dec 12;20(18):3379-86
15256410
Plant Mol Biol. 2002 Mar-Apr;48(5-6):501-10
11999831
Trends Biotechnol. 2005 Jan;23(1):48-55
15629858
Nucleic Acids Res. 2001 Jan 1;29(1):159-64
11125077
Plant Physiol. 2006 May;141(1):147-66
16531485
Genome Res. 2000 Jan;10(1):72-80
10645952
Theor Appl Genet. 2003 Feb;106(3):411-22
12589540
Theor Appl Genet. 2007 Jan;114(2):359-72
17115127
Theor Appl Genet. 2004 Apr;108(6):1151-61
14760486
J Biosci. 2007 Jan;32(1):3-15
17426376
Genome Biol. 2006;7(2):R14
16507170
Genome. 2005 Dec;48(6):985-98
16391668
Genome Res. 2001 Aug;11(8):1441-52
11483586
J Mol Evol. 1995 Feb;40(2):120-6
7699718
J Genet. 2008 Apr;87(1):21-5
18560170
BMC Plant Biol. 2006 May 30;6:9
16734891
Plant Cell Rep. 2004 Nov;23(6):404-13
15340758
Syst Biol. 1998 Mar;47(1):147-58; discussion 159-67
12064235
Nucleic Acids Res. 2006 Feb 21;34(4):e31
16493138
Genome Res. 1998 Mar;8(3):186-94
9521922
Bioinformatics. 2004 Jun 12;20(9):1475-6
14962913
Mol Biol Evol. 2001 Jul;18(7):1161-7
11420357
Mol Gen Genet. 1993 Feb;237(1-2):123-8
8455550
Genetics. 2000 Oct;156(2):847-54
11014830
Cell Mol Biol Lett. 2002;7(2A):537-46
12378259
Mol Genet Genomics. 2004 Jul;271(6):742-51
15197579