©1996-2008 All
Rights Reserved.
Online Journal of Bioinformatics . You may not store these pages in any form except
for your own personal use. All other usage or distribution is illegal under
international copyright treaties. Permission to use any of these pages in any
other way besides the before mentioned must be
gained in writing from the publisher. This article is exclusively copyrighted
in its entirety to OJB publications. This article may be copied once but may
not be, reproduced or re-transmitted without the
express permission of the editors. This
journal satisfies the refereeing requirements (DEST) for the Higher Education
Research Data Collection (Australia). Linking:To
link to this page or any pages linking to this page you must link directly to
this page only here rather than put up your own page.
OJBTM
Online Journal of Bioinformatics ©
Identification of SSR-ESTs
corresponding to alkaloid, phenylpropanoid and terpenoid biosynthesis in MAP’s
Bioinformatics & In
Silico Biology Division, Central Institute of
Medicinal & Aromatic Plants (CSIR), P.O. CIMAP, Lucknow-226015 (UP),
ABSTRACT
Tripathi KP, Roy S, Khan F, Shasany
AK, Sharma A, Khanuja SPS Identification of SSR-ESTs corresponding to alkaloid, phenylpropanoid
and terpenoid biosynthesis in MAP’s,
Online Journal of Bioinformatics, 9 (1):
78-91, 2008. Simple sequence
repeats (SSRs) are repetitions of nucleotide motifs
of 1 to 5 bases and are currently the markers of choice in many plants and
animals genomes. SSRs are the DNA regions where a few
bases are tandemly repeated. SSRs
have been proven to be the markers of choice in plants genetics research and
for breeding purposes because of their hyper-variability and ease of detection.
However, development of these markers is expensive, labour
intensive and time consuming, if they are being developed from genomic
libraries. In this study, SSRs were mined in silico from ESTs of medicinal
and aromatic plants (MAPs) corresponding to secondary
metabolites e.g. Alkaloids, Phenylpropanoids and Terpenoids. SSRs are potential
candidates for markers, gene tagging, comparative genomics research and
breeding purposes. For this, comparative genomic study was performed for
finding the corresponding genes to these SSR-ESTs
using Arabidopsis thaliana as a model organism. Results revealed
that the SSRs e.g., 941 trinucleotides,
213 dinucleotides, 157 tetranucleotides
and 179 pentanucleotides were distributed throughout
the studied datasets of ESTs in medicinal plants viz.,
Coptis japonica, Oryza
sativa, Papaver somniferum,
Catharanthus roseus, Phaseolus vulgaris, Capsicum annuum, Mentha piperita and Euphorbia tirucalli.
Primers associated with the SSR-ESTs were also
designed successfully. Moreover, functional perspectives of these SSRs suggest that microsatellites
are more than mere repetitive sequences and their role have been attributed to
many biological functions. Because of their abundance and high polymorphism, microsatellites could be widely used to develop genetic
markers for the construction of linkage maps of medicinal crops.
Keywords: ESTs, SSRs, Microsatellites,
Primers, Markers, Secondary metabolites, Alkaloids, Phenylpropanoids,
Terpenoids, Medicinal & Aromatic Plants.
FULL-TEXT(SUBSCRIPTION
OR SINGLE ARTICLE)