Familya
|
LTb
|
Protein product
|
Namec
|
SPd
|
Fold changee
|
Linear RPKM Valuesf
|
---|
B/YE
|
C/YE
|
G/YE
|
S/YE
|
M/YE
|
B
|
C
|
G
|
S
|
M
|
YE
|
---|
Barley β-glucan utilization
|
GH16
|
0951
|
laminarinase
|
Bgl16A
1
|
Yes
|
80.3
|
0.2
|
0.2
|
0.4
|
0.1
|
170.2
|
0.4
|
0.5
|
0.8
|
0.3
|
2.1
|
GH16
|
0952
|
endo-β-1,3-1,4 glucanase
|
Bgl16A
2
|
Yes
|
24.5
|
0.2
|
0.2
|
0.3
|
0.1
|
124.1
|
1.1
|
0.8
|
1.5
|
0.6
|
5.1
|
GH16
|
0824
|
laminarinase
|
Bgl16A
3
|
Yes
|
0.4
|
0.5
|
0.6
|
0.6
|
0.6
|
1.7
|
2.2
|
2.7
|
2.4
|
2.4
|
4.1
|
GH3g
|
0317
|
glycoside hydrolase
| |
No
|
2.7
|
2.7
|
0.5
|
NS
|
2.4
|
379.0
|
376.6
|
70.7
|
156.1
|
338.1
|
141.5
|
Barley β-glucan induced xylanases
|
GH67
|
1323
|
α-glucuronidase
|
Agu67A
|
No
|
20.6
|
0.8
|
0.4
|
0.6
|
0.4
|
120.2
|
4.4
|
2.1
|
3.5
|
2.5
|
5.8
|
GH8
|
1182
|
exooligoxylanase
|
Xyn8
|
No
|
39.3
|
0.4
|
0.4
|
0.7
|
0.5
|
297.2
|
3.3
|
3.1
|
5.1
|
3.5
|
7.6
|
GH11
|
4664
|
endoxylanase
|
Xyn11
|
Yes
|
3.7
|
0.4*
|
0.2
|
0.3*
|
0.2
|
7.5
|
0.8
|
0.4
|
0.5
|
0.4
|
2.1
|
GH10
|
0221
|
endoxylanase
|
Xyn10A
1
|
Yes
|
8.8
|
0.2
|
0.1
|
0.3
|
0.1
|
52.0
|
1.2
|
0.8
|
1.6
|
0.6
|
5.9
|
GH10
|
1324
|
endoxylanase
|
Xyn10A
2
|
No
|
24.0
|
0.8*
|
0.5
|
0.6*
|
0.6
|
185.3
|
6.2
|
3.5
|
4.7
|
4.4
|
7.7
|
GH43
|
1325
|
xylosidase
|
Xyn43B1
|
No
|
19.6
|
0.9*
|
0.5
|
0.7*
|
0.8*
|
222.1
|
9.9
|
5.9
|
7.6
|
8.6
|
11.3
|
GH43
|
0750
|
xylosidase
|
Xyn43B2
|
No
|
3.2
|
176.6
|
NS
|
NS
|
NS
|
5.0
|
276.7
|
2.7
|
2.6
|
1.8
|
1.6
|
GH43
|
1907
|
xylosidase
|
Xyn43B3
|
No
|
111.5
|
2.3
|
NS
|
NS
|
0.6
|
1410.9
|
29.6
|
12.2
|
13.5
|
7.6
|
12.7
|
Starch utilization
|
GH13
|
0774
|
α-amylase
|
Amy13A1
|
Yes
|
0.2
|
0.2
|
0.1
|
114.1
|
69.7
|
2.0
|
1.8
|
1.3
|
1127.3
|
688.4
|
9.9
|
GH13
|
5200
|
α-amylase
|
Amy13A2
|
Yes
|
0.2
|
0.2
|
0.2
|
56.8
|
4.2
|
1.5
|
1.5
|
1.2
|
395.7
|
29.3
|
7.0
|
GH13
|
0783
|
α-amylase
|
Amy13A3
|
No
|
1.5
|
NS
|
NS
|
112.2
|
95.6
|
7.8
|
5.7
|
6.5
|
584.3
|
497.9
|
5.2
|
GH13
|
1045
|
α-amylase
|
Amy13A4
|
No
|
NS
|
2.7
|
3.8
|
NS
|
NS
|
2.6
|
4.7
|
6.6
|
1.5
|
1.4
|
1.7
|
GTg
|
1149
|
α-glucan phosphorylase
|
MalP
|
No
|
0.3
|
0.1
|
0.5
|
NS
|
0.2
|
2.4
|
0.9
|
0.7
|
6.6
|
1.5
|
8.9
|
Maltose utilization
|
ND
|
5587
|
oxidoreductase
|
ThuB
|
No
|
NS
|
NS
|
NS
|
NS
|
8.8
|
7.4
|
7.0
|
7.3
|
9.0
|
73.8
|
8.4
|
GATase1
|
5588
|
hypothetical protein
|
ThuA
|
No
|
0.7
|
0.7
|
NS
|
NS
|
8.1
|
7.1
|
2.6
|
2.5
|
2.5
|
30.3
|
3.8
|
-
aGH, glycoside hydrolase; GT, glycosyltransferase; ND, not determined; GATase1, type 1 glutamine amidotransferase (GATase1)-like domain
-
b LT, locus tag annotated as Pjdr2_#### abbreviated to only consist of the numeric portion, ####
-
cThe name assigned to gene candidates with enzymes characterized in our laboratory in bold
-
dSP, sequence encodes a predicted signal peptide for secretion
-
eTranscript levels of candidate genes that were expressed 2-fold greater (underlined) and those that were expressed 4-fold greater (bold) than the yeast extract without carbohydrate growth are indicated. The growth substrates are shown as follows: B, barley β-glucan; C, cellobiose; G, glucose; S, starch; M, maltose; YE, yeast extract. Significance of fold change data is judged by having a p-value no more than 0.01. Data with p-values between 0.01 and 0.05 are denoted with an asterisk, and those with p-values greater than 0.05 are designated as not significant (NS)
-
fRPKM values are defined as Reads Per Kilobase per Million reads sequenced
-
gGene 0317 and gene 1149 are included in this table as genes of interest in barley β-glucan and starch utilization pathways, respectively. Gene 0317 is increased 5.4-fold on barley β-glucan (p-value < 0.0002) and gene 1149 is increased 9.4-fold on starch (p-value < 0.037) relative to growth on glucose