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56
Seema TRIVEDI
SSR search
Replication, repair and recombination related
gene sequences of all thirteen mycoplasmas were
subjected to repeat search programme SPUTNIK
(http://espressosoftware.com/sputnik/index.html).
SPUTNIK looks for di-, tri-, tetra- and pentanucleotide
repeats; tolerates insertions, mismatch
es and deletions but these affect the overall score.
Repeats found through this search were not
grouped i.e. the 5’ to 3’ or vice-a versa and the
complements were not put together. For example,
dinucleotide repeat CA was not grouped with AC,
TG or GT. Hence, each repeat was treated as
separate motif.
SSR CG richness and length
Length of an SSR was measured in nucleotides
(base pairs). However, repeat length given as
output from SPUTNIK was adjusted to nearest
divisible value i.e. dinucleotide repeat length
should be divisible by 2, trinucleotide by 3,
tetranucleotide repeat by 4 and pentanucleotide
repeat by 5. For example, if repeat length for
dinucleotide repeats was indicated as 11nt by
SPUTNIK output; this was adjusted to 10nt, for
trinucleotide repeats if the length was 14nt it was
adjusted to 15nt or if it was 16nt or 17nt it was
considered as 15nt.
Statistical analysis
For statistical analysis, SPSS (Version 16.0) was
used. One way ANOVA followed by Tukey’s
HSD at 95% confidence level was done to seek
significant difference in between the thirteen
species repeat number as well different replica
tion, repair and recombination genes.
Pearson’s ‘r’ two tailed correlation analysis of
genome size and CG richness, sequence lengths
of replication, repair and recombination genes and
CG richness vis-à-vis repeat numbers, length and
.
CG richness of total repeats and repeat types was
done.
Results
Total SSRs, repeat types and motifs in thirteen
mycoplasmas replication, repair and recombination
genes
Figure 1 shows total numbers of SSRs and repeat
types present in replication, repair and recombination
genes in genomes of thirteen mycoplasmas where M.
pulmonis has the maximum number of repeats
followed by M. capricolum and M. synoviae (5, 4
and 3 respectively).
Among repeat types, dinucleotides (five) are
present only in M. pulmonis. Maximum numbers of
tri nucleotides are in M. capricolum. Presence of
other repeat types in replication, repair and
recombination genes of mycoplasmas are given in
Figure 1.
There is diversity in repeat motifs found in the
present study among which maximum frequency
(four) is of tetranucleotide repeat ATTT followed by
dinucleotide repeat motifs AG (Table-2).
Total replication, repair and recombination genes
associated with SSRs in mycoplasmas
Methylase genes have maximum number of total
repeats (eight) followed by DNA polymerase,
excinuclease and topoisomerase genes (three in each)
among replication, repair and recombination genes in
thirteen mycoplasmas (Figure 2). Among repeat
types total dinucleotide followed by tetra nucleotide
repeats as well as the motifs AG and ATTT have
maximum frequency (all in methylase genes)
(Figures 2 and 3).
Comparison of total repeats and repeat types in
replication, repair and recombination genes of each
Mycoplasma is given in Figure 4 and motifs in Table
3, where once again methylase genes in M. pulmonis
have maximum repeats.