Genomics and Applied Biology 2018, Vol.9, No.5, 24-31
26
AnTrk4
were compared with Trk1 and Trk2, respectively. The results showed that
AnTrk2
experienced a
purification selection, while the other TRK gene family members in
Aspergillus niger
were positively selected
(Table 2).
Table 2 The analysis of evolutionary selection pressure for TRK
Gene pairs
S
N
dS
dN
dS/dN
Selection class
AnTrk1vsTrk1
780.9
1697.1
7.1628
15.6859
2.1899
Positive selection
AnTrk2vsTrk1
374.5
1728.5
23.5957
4.5115
0.1912
Purification selection
AnTrk3vsTrk1
578.4
1272.6
4.0152
17.0841
4.2549
Positive selection
AnTrk4vsTrk1
626.7
1416.3
3.4852
17.2098
4.9380
Positive selection
AnTrk1vsTrk2
675.9
1802.1
0.1625
16.0866
99.0000
Positive selection
AnTrk2vsTrk2
566.7
1536.3
0.2281
17.7113
77.6535
Positive selection
AnTrk3vsTrk2
374.7
1476.3
0.1343
13.2916
99.0000
Positive selection
AnTrk4vsTrk2
418.1
1624.9
0.1474
14.5938
99.0000
Positive selection
Note: S: Number of synonymous sites; N: Number of non-synonymous sites;
dS
:Synonymous substitution rate;
dN:
Non-synonymous substitution rate; dS/dN: Synonymous substitution rate/ Non-synonymous substitution rate
1.3 Phylogenetic Tree Construction of
TRK
Genes
Based on the multiple sequence alignment of the
TRK
genes, phylogenetic relationship was analyzed using the
MEGA software.
AnTrk1
,
AnTrk2
, and
Trk1
,
Trk2
in yeast were clustered together, while
AnTrk3
and
AnTrk4
were
clustered together (Figure 1). This result shows that the phylogenetic relationship between
AnTrk1
,
AnTrk2
and
Trk1
,
Trk2
is closer, and we speculated that there is an intersection from their origins.
AnTrk3
and
AnTrk4
are
relatively far apart, but they all belong to one big branch and were considered to be coordinative relationship. This
also shows that there is a certain degree of phylogenetic relationship between them. The small branches appeared
after large branches, which indicated that these subfamilies have undergone evolutionary losses and amplification
events. Furthermore, the structure and function of genes are more disproportionate, revealing the diversity of gene
expression and function in this gene family. Since the research of function of the
TRK
family genes in
Aspergillus
niger
are limited, this result referred from the
TRK
genes in yeast which were studied more deeply can provide
guidance for the functional studies and regulatory networks of the
Aspergillus niger TRK
family.
Figure 1 The phylogenetic tree construction of
TRK
gene
1.4 Motif Analysis of the
TRK
Gene Family in
Aspergillus niger
Motif analysis of four
TRK
genes in
Aspergillus niger
and two
TRK
genes in yeast was performed by the MEME
program. The result shows that
AnTrk1
,
AnTrk2
and
TRK
genes in yeast all contained eight conserved motifs, but
the positions of them are inconsistent (Figure 2A). On the other hand,
AnTrk3
contains only six motifs and
AnTrk4
contains only seven motifs. The results further confirmed the reliability of the phylogenetic analysis of the
TRK
genes. From the analysis of codon usage in each motif, it is obviously observed that the codons used by each motif
are quite different among different genes (Figure 2B).
