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Tree Genetics and Molecular Breeding 2012, Vol.2, No.1, 1
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trees found that microsatellite abundances in eucalyptus
and poplar were very close except the abundance of 5
base repeat unit microsatellites, but quite different in
pine (Table 1). The results also showed that the
frequency of microsatellite with three-base repeat unit
were more than other types of microsatellites in three
tested trees. It is noteworthy that the abundance of
other three repeat unit microsatellites except
microsatellites with three-base repeat unit in eucalyptus
and poplar reduced with the increases of the length of
repeat units, whereas increased along with the increase
of length of repeating unit in pine. Genetic code
consists of three base nucleotides. Generally speaking,
gene would have higher fault-tolerant to mutations
of three base insertion or deletion, long-term selection
might lead to enrich the microsatellites with three-base
repeat unit in the gene region, the results of this study
might provide new direct evidence for this statement.
We also noted that enrichment of three-base repeat
unit microsatellites in pine (64.0%) were greater than
that in poplar (45.2%) and eucalyptus (48.2%), the
reason might be that the time of pine genome formation
was far earlier than that of poplar and eucalyptus, this
indicated that the pine genome might be subjected
to a very strong impact in codon selection during the
gene evolution.
Table 1 Comparative analysis of different types of microsatellites in expressed sequences in pine, poplar and eucalyptus
Type of microsatellite
Pine
Poplar
Eucalyptus
Di-nucleotide
285 (10.1%)
1 532 (27.0%)
2 208 (30.1%)
Tri-nucleotide
1 809 (64.0%)
2 559 (45.2%)
3 539 (48.2%)
Tetra-nucleotide
330 (11.7%)
806 (14.2%)
1 031 (14.0%)
Penta-nucleotide
400 (14.2%)
772 (13.6%)
567 (7.7%)
Percentage of ESTs containing microsatellites
2 465 (8.2%)
4 599 (15.3%)
5 612 (18.7%)
Note: The percentage values in this table are the ratio of the microsatellites with different lengths of repeat units accounting for the
total numbers of microsatellites detected in the tested tree species
Law of abundance of microsatellite in gene region and
in different types varied with the length of repeat unit
was significantly differences in pine from eucalyptus
and poplar; it is yet to be identified in many tree
species whether this is common differences of
microsatellite in gene region among needle trees and
broad-leaf trees. Although we couldn’t give a definitive
conclusion to the puzzle due to EST sequences of
other species at present very limited, the results of this
study revealed a very interesting phenomenon.
1.2 Nucleotide composition of pine dominant repeat
unit of EST-SSR in pine poplar and eucalyptus
Studies have shown that SSR site is a hotspot region
of gene recombination occurring (Jeffreys et al., 1998),
some repeat sequences of microsatellite such as repeat
units of GT, CA, CT, and GA often direct impact on
the DNA recombination through affecting the structure
of DNA (Biet et al., 1999). And also variations of the
numbers of repeat units of microsatellite in expressed
sequences facilitate the open reading frame changing,
thus affecting the gene encoded product. So, because
of the influence of the selection, the differentiation of
nucleotide composition in dominant repeat unit in
different species will occur in the long-term evolutionary
process.
Analysis on nucleotide composition of microsatellite
repeat unit in expression sequence (repeat motif) in
three species showed that the base composition of
microsatellite with highest frequency were two base
repeat unit of AG/TC in poplar and eucalyptus, while
TA/AT in the pine. Whereas the three-base repeat unit
of AAG/TTC occurred in the three species with the
highest frequency. The composition of dominant four
repeating unit was AAAG/TTTC in pine and poplar,
but AGTG/TCAC in the eucalyptus. There were different
base compositions of dominant penta-nucleotide repeat
unit in three tree, CTGCG in pine, AAAAG/TTTTC
in poplar and CAAAG in eucalyptus. So overall, the
base compositions of dominant repeat units with
different length had species-specific characteristics,
there was no any significant regularity of differentiation
in pine, poplar and eucalyptus (Table 2).
As the variations of the repeating numbers of repeat