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Bioscience Methods 2014, Vol.6, No.1, 1-13
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Table 1 Transcript sequence structure of the eleven
OSM
genes in potato
PGSC locus
gene
chro.
5’UTR
3’UTR
CDS
No.Intron
PGSC0003DMG400013227
OSM-8E
1
17
211
663(220 aa)
0
PGSC0003DMG400000573
OSM-297
3
0
0
894(297 aa)
2
PGSC0003DMG400026926
OSM-306
6
120
167
921(306 aa)
2
PGSC0003DMG400003040
OSM-1G
8
5
41
693(230 aa)
0
PGSC0003DMG400003041
OSM-182
8
0
0
549(182 aa)
2
PGSC0003DMG400003042
OSM-5A
8
12
211
744(247 aa)
0
PGSC0003DMG400003043
OSM-3B
8
12
201
744(247 aa)
0
PGSC0003DMG400003044
OSM-3F
8
36
138
741(246 aa)
0
PGSC0003DMG400003057
OSM-3C
8
24
183
753(250 aa)
0
PGSC0003DMG400003058
OSM-2D
8
24
157
753(250 aa)
0
PGSC0003DMG400000402
OSM-251
11
40
220
756(251 aa)
0
Overall, eleven
StOSM
genes were distributed on five of
twelve potato chromosomes (Figure 3). Seven of the
eleven
StOSM
genes are near 54277k–54230k on
chromosome 08 (Figure 4). The other four are located on
chromosomes 01, 03, 06 and 11 (Figure 3 and Table 1).
Figure 3 Genomic distribution of the
StOSM
genes throughout
the potato chromosomes. The chromosome number is given at
the top of each bar. The triangles next to the gene names
indicate the direction of transcription
The seven
StOSM
genes on chromosome 08 identified
from the PGSC database were not identical with the
eight
StOSM
genes on chromosome 08 distinguished
(Castillo et al. 2005). The extra
StOSM
gene on
chromosome 08 identified by Castillo et al. is most likely
due to two hybridised signals observed for
StOSM
-182
(PR-5X) on chromosome 08 because it contains two
exons. The
StOSM
gene on chromosome 11 identified by
Castillo et al.
is
StOSM
-251, as shown in Figure 3.
1.1.3 Phylogeny of the putative StOSM amino acid
sequences
The eleven putative amino acid sequences encoded
by these
StOSM
genes were used to construct a
phylogenetic tree (Figure 5). The eleven osmotins
Figure 5 Phylogenetic relationship of the eleven putative potato
osmotin peptides. These data were organised into a
phylogenetic tree using the MEGA5.02 package and the
neighbour-joining program. The numbers listed at the
branching points are boot-strapping values that indicate the
percentage significance for the separation of the two branches.
The length of the branch line indicates the extent of the
difference according to the scale on the lower left-hand side.
Putative functions are listed for each gene
Figure 4 Distribution of the seven
StOSM
s located on chromosome 08