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which leads to variability in number of SSR motifs at a locus (Levinson and
Gutman
1987
; Richards and Sutherland
1992
). SSRs show highest variability among
DNA sequences within the genome (Weber
1990
), and the rate of mutation and type
mainly depends upon the number of repeat motifs (Wierdl et al.
1997
). However,
the rates of mutations differ among loci, among alleles, and between species
(Ellegren
2000
). Among the earlier studies the anonymous DNA fragments (isolated
from genomic libraries) were utilized for the development of SSR markers. How-
ever, recently SSRs are being developed computationally from the sequencing data
generated from large-scale EST sequencing projects. The EST-SSR markers are
superior and informative than anonymous DNA markers because they are gene-
tagged and are associated with the expressed gene and hence linked to quantitative
and qualitative trait loci (QTLs) (Andersen and Lübberstedt
2003
). The
Fusarium
genomes have been conserved and are well documented, and to compare genetic
information from model to related species comparative genomics has become nec-
essary. In short, EST-SSRs derived from expressed genes are conserved with higher
transferability to related species in comparison to anonymous DNA markers, thus,
are very useful as strong markers for evolutionary studies comparative genomics
and comparative mapping across species (Torben 2007).
Fusarium
Databases
The comparative analysis among the fungal species is facilitated by the Fusarium
database which gives accesses to various sequenced genomes of Fusarium simul-
taneously. The three most important
Fusarium
spp, which have been studied exten-
sively due to their devastating impact on crops, are
F. oxysporum, F. verticillioides
and F. graminearum.
Over the last decade there has been enormous advancement
in genomic technology and sequencing of various species has been completed and
thus there arose the need for comparative projects. Thus, the Fusarium Compara-
tive project (http://www.broad.mit.edu/annotation/genome/fusarium_group/Multi-
Home.html) is one such effort which compared the above three species. This project
improved gene annotations and identifying non-coding elements. As these species
are biologically distinct evolutionary studies were done among these above spe-
cies and it was found that
F. oxysporum
and
F. verticillioides
genomes have di-
verged from
F. graminearum
, and thus the comparative of these offers a platform
for interaction studies in plant-fungi (pathogenicity, virulence factors and evolu-
tion). The comparative genomics among these have highlighted the presence of
lineage-specific chromosomes comprising the transposable elements (TEs) and en-
coding pathogenicity related (PR) genes. These projects have also helped in explor-
ing the genetic composition of these chromosomes among the strains of the above
Fusarium
species. The
F. oxysporum
spp. are ubiquitous plant and soil inhabiting
microbes causing the wilt and root rot diseases in over 120 plant species (Michielse
and Rep
2009
). It has been reported that many of the strains don't show apparent
symptoms on the plant and can even protect them from subsequent infections (Al-
abouvette et al.
2009
). Further, some strains have also been identified as pathogenic
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