Table 1 The number of genes encoding proteins associated with alkaliphily in two neutrophile and
two alkaliphile fungi according to the eukaryotic orthologous groups (KOGs) annotations obtained
from the MycoCosm fungal genomic resource (https://genome.jgi.doe.gov/programs/fungi/index.
jsf)
KOG annotation
A. oryzae P. cucumerina S. alkalinus A. alcalophilum
KOG0672 halotolerance protein
HAL3
3
2
19
20
KOG4126 alkaline phosphatase
3
4
4
2
KOG1397 Ca
2+ /H
+ antiporter
VCX1 and related proteins
8
4
4
4
KOG2493 Na
+ /P i symporter
4
6
4
4
KOG4505 Na
+ /H
+ antiporter
5
5
2
3
KOG1341 Na
+ /K
+ transporter
5
5
2
2
KOG1650 predicted K
+ /H
+ -
antiporter
3
2
2
1
KOG2399 K
+ -dependent Na
+ /
Ca
2+ antiporter
1
1
1
1
KOG0205 plasma membrane H
+ -
transporting ATPase
3
1
1
1
KOG3126 Porin/voltagedependent anion-selective channel protein
1
1
1
1
KOG3182 predicted cation
transporter
1
1
1
1
Table 2 Extrachromosomal plasmids present in representative strains of alkaliphilic bacteria and
archaea
Species
Plasmids
Size (bp)
GC % Nr. genes
Listeria monocytogenes 08-5923
pLM5578
77,054 36.59
79
Thermobacillus composti KWC4
pTHECO01
149,182 47.3
149
Kineococcus radiotolerans SRS30216
pKRAD01
182,572 69.4
183
pKRAD02
12,917 72.3
17
Halobacillus halophilus DSM 2266
pL16
16,047 43
19
pL3
3,329 36.5
2
Natranaerobius thermophilus JW/NM-WN-LF pNTHE01
17,207 34.2
17
pNTHE02
8,689 35.7
9
Chroococcidiopsis thermalis PCC 7203
pCHRO.01
370,830 45.1
335
pCHRO.02
2,779 44.1
2
Bacillus pseudofirmus OF4
pBpOF4-01
285,222 36
260
pBpOF4-02
105,029 35.5
113
Sinorhizobium medicae WSM419
pSMED01
1,570,951 61.5
1,441
pSMED02
1,245,408 59.9
1,094
pSMED03
219,313 60.1
149
Natronococcus occultus DSM 3396
Plasmid 1
12,939 54.8
20
Plasmid 2
287,963 61.3
238
142
P. H. Lebre and D. A. Cowan
two alkaliphile fungi according to the eukaryotic orthologous groups (KOGs) annotations obtained
from the MycoCosm fungal genomic resource (https://genome.jgi.doe.gov/programs/fungi/index.
jsf)
KOG annotation
A. oryzae P. cucumerina S. alkalinus A. alcalophilum
KOG0672 halotolerance protein
HAL3
3
2
19
20
KOG4126 alkaline phosphatase
3
4
4
2
KOG1397 Ca
2+ /H
+ antiporter
VCX1 and related proteins
8
4
4
4
KOG2493 Na
+ /P i symporter
4
6
4
4
KOG4505 Na
+ /H
+ antiporter
5
5
2
3
KOG1341 Na
+ /K
+ transporter
5
5
2
2
KOG1650 predicted K
+ /H
+ -
antiporter
3
2
2
1
KOG2399 K
+ -dependent Na
+ /
Ca
2+ antiporter
1
1
1
1
KOG0205 plasma membrane H
+ -
transporting ATPase
3
1
1
1
KOG3126 Porin/voltagedependent anion-selective channel protein
1
1
1
1
KOG3182 predicted cation
transporter
1
1
1
1
Table 2 Extrachromosomal plasmids present in representative strains of alkaliphilic bacteria and
archaea
Species
Plasmids
Size (bp)
GC % Nr. genes
Listeria monocytogenes 08-5923
pLM5578
77,054 36.59
79
Thermobacillus composti KWC4
pTHECO01
149,182 47.3
149
Kineococcus radiotolerans SRS30216
pKRAD01
182,572 69.4
183
pKRAD02
12,917 72.3
17
Halobacillus halophilus DSM 2266
pL16
16,047 43
19
pL3
3,329 36.5
2
Natranaerobius thermophilus JW/NM-WN-LF pNTHE01
17,207 34.2
17
pNTHE02
8,689 35.7
9
Chroococcidiopsis thermalis PCC 7203
pCHRO.01
370,830 45.1
335
pCHRO.02
2,779 44.1
2
Bacillus pseudofirmus OF4
pBpOF4-01
285,222 36
260
pBpOF4-02
105,029 35.5
113
Sinorhizobium medicae WSM419
pSMED01
1,570,951 61.5
1,441
pSMED02
1,245,408 59.9
1,094
pSMED03
219,313 60.1
149
Natronococcus occultus DSM 3396
Plasmid 1
12,939 54.8
20
Plasmid 2
287,963 61.3
238
142
P. H. Lebre and D. A. Cowan