Thesis
In Silico Est Datamining for Elucidation of Repeats Biology and Functional Annotation in Sorghum [Sorghum Bicolor (L.) Moench.]
(2006)
Abstract
A database of available sorghum ESTs was constructed and used to identify microsatellites or
SSRs. A total of 2,32,921 ESTs from public databases, representing 35 different transcriptomes were
downloaded. Repeat scan analysis identified 12,235 ESTs with repeats of varied type and length,
which accounted for 5.25 per cent of all the ESTs in a redundant dataset. Clustering of this dataset
removed redundancy, leaving a total of 3,281 unique genes containing microsatellites. TNRs
(50.37%) were the most abundant types, followed by DNRs (42.9%) and TTNRs (6.72%). Among the
DNRs, AG/CT was the most abundant type, accounting for 55.23 per cent of all DNRs, followed by
AC/GT (21.94%). The CG repeats were rare at 6.63 per cent. Among TNRs, most abundant type was
ATG/TAC (34.67%) followed by ATC/TAG (17.42%). The frequency of individual TTNRs varied from
9.11 per cent for ACGT/TGCA to 0.24% for ACCC/TGGG. Pairs of primers could be designed for 520
of the 3281 ESTs. The parental lines, IS22380 and E36-1 were scanned with a random set of 20
genic SSRs. All the 20 primer pairs produced the expected amplicon from the genomic DNA of both
genotypes, of which 4 were polymorphic. The database constructed for the EST-SSRs was named as
‘Jowar GenRepeat database’ with 3281 ESTs with SSRs as records. Each record has complete
information about the repeats, functional annotation and primers information in addition to information
available in respective source database. This database is compatible for seach, using keywords in all
fields, updateable and user friendly. Each EST was compared to annotated proteins in the databases
with BLASTx algorithm and tentative function was assigned for 687 (20.93%) of the 3281 ESTs
containing repeats. Of this lot of 687 ESTs, primer pairs have been designd for 135 annotated ESTs,
which can be used for further applications in functional genomics.
Disciplines
Publication Date
2006
Degree
Master of Science (Agriculture)
Field of study
Plant Biotechnology
Department
Biotechnology
Advisor
B. Fakrudin
Comments
Copyright 2006 The Author
Citation Information
Arun S. Seetharam. "In Silico Est Datamining for Elucidation of Repeats Biology and Functional Annotation in Sorghum [Sorghum Bicolor (L.) Moench.]" (2006) Available at: http://works.bepress.com/arun-seetharam/7/