Comparative analysis of the complete mitochondrial genomes of three geographical topmouth culter (Culter alburnus) groups and implications for their phylogenetics

Figures & data

Fig. 1. The map of the locations of samples collected of C. alburnus individuals.

Table 1. PCR primers in the analysis of the C. alburnus mitochondrial genomes.

Primer	Forward primer sequence (5′-3′)	Reverse primer sequence (5′-3′)	Product length (bp)	Amplified region
1	L1 = GCTAGCGTAGCTTAATACAAAGCAT	H1 = TTAATGTTGTGTTTTTTGATTTGGG	1530	1–1530
2	L2 = CCTATTTAAATTTAGGGCTAACCCG	H2 = CTAGGGGGTTGATTAGGTGGTTTAT	1491	1398–2888
3	L3 = TAGTACGAAAGGATCGGAAAAGAGG	H3 = GGTGTTGTGCTATTAGGGGGATAAT	1506	2675–4180
4	L4 = TCTAAGATGGGGTCAGCTAATCAAG	H4 = CCGAAGACAGAGGTTTAAGTCCTCT	1445	3989–5433
5	L5 = ATCCATCTACTTTTCCCGCCTAAAG	H5 = CCCGATGGATGATACTGTATTTCAC	1530	5314–6843
6	L6 = TGTCAATAGGTGCTGTATTTGCCAT	H6 = CGAATTGGTCGAAAAAGCTTACTAT	1502	6638–8139
7	L7 = CTCATGAATCGTCTTTCTCACCATT	H7 = GATGTAAAGTGGTACTGGATTTGGC	1459	8022–9480
8	L8 = GGGTATACGGCTCTACATTCTTCGT	H8 = GCCAGGGTGTAGAATAGGAAGTAGG	1438	9390–10827
9	L9 = ACCTTTCTAATTATAGCATTCGGCG	H9 = CTGTCAGTTTGTGGTGATGCTTTCT	1474	10697–12170
10	L10 = CCTAAACCACAAAAACCAGAATGAG	H10 = TTGTGGGGGTAATTTTGACTTGTTT	1462	12063–13524
11	L11 = TCCTACCCTCAAAAACACCCATTAT	H11 = TCTACTGAGAAGCCACCTCAGATTC	1483	13411–14893
12	L12 = TATGATAACAGCCTTCGTTGGCTAC	H12 = CTATGCATATAAAAGAATGCTCGGC	1370	14774–16143
13	L13 = ACTTGCATCTGGCTTCTATCTCAGG	H13 = GGTTGCTGAGACTTGCATGTGTAAG	701	16032–110

Fig. 2. Circular representation of the complete mitochondrial genomes of C. alburnus. Circles display (from inside to outside): LZH-female, LZH-male, TH-male, TH-female, PYH-male, and PYH-female. Different color rods and dots represent the variable sites and the same nucleotides, respectively. L1–L13: the location of forward primers. H1–H13: the location of reverse Primer.

Table 2. Similarity of 16 homolog genes among C. alburnus (retention three significant digits).

Species
Similarity	LZH-female	LZH-male	TH-female	TH-male	PYH-female	PYH-male
Whole genome sequence
LZH-female	–	0.999	0.993	0.993	0.993	0.992
LZH-male	0.999	–	0.993	0.994	0.993	0.993
TH-female	0.993	0.993	–	0.998	0.999	0.999
TH-male	0.993	0.994	0.998	–	0.998	0.998
PYH-female	0.993	0.993	0.999	0.998	–	0.998
PYH-male	0.992	0.993	0.999	0.998	0.998	–
Nad1
LZH-female	–	1	0.989	0.990	0.989	0.988
LZH-male	1	–	0.998	1	0.998	0.997
TH-female	0.989	0.998	–	0.996	1	0.998
TH-male	0.990	1	0.996	–	0.996	0.995
PYH-female	0.989	0.998	1	0.996	–	0.998
PYH-male	0.988	0.997	0.998	0.995	0.998	–
Nad2
LZH-female	–	0.998	0.988	0.990	0.989	0.986
LZH-male	0.998	–	0.990	0.992	0.991	0.988
TH-female	0.988	0.990	–	0.998	0.999	0.998
TH-male	0.990	0.992	0.998	–	0.999	0.996
PYH-female	0.989	0.991	0.999	0.999	–	0.997
PYH-male	0.986	0.988	0.998	0.996	0.997	–
Nad3
LZH-female	–	1	0.994	0.991	0.994	0.991
LZH-male	1	–	0.994	0.991	0.994	0.991
TH-female	0.994	0.994	–	0.997	1	0.997
TH-male	0.991	0.991	0.997	–	0.997	0.994
PYH-female	0.994	0.994	1	0.997	–	0.997
PYH-male	0.991	0.991	0.997	0.994	0.997	–
Nad4
LZH-female	–	1	0.992	0.994	0.992	0.992
LZH-male	1	–	0.992	0.994	0.992	0.992
TH-female	0.992	0.992	–	0.994	0.997	0.997
TH-male	0.994	0.994	0.994	–	0.994	0.994
PYH-female	0.992	0.992	0.997	0.994	–	0.996
PYH-male	0.992	0.992	0.997	0.994	0.996	–
Nad4l
LZH-female	–	1	1	1	1	1
LZH-male	1	–	1	1	1	1
TH-female	1	1	–	1	1	1
TH-male	1	1	1	–	1	1
PYH-female	1	1	1	1	–	1
PYH-male	1	1	1	1	1	–
Nad5
LZH-female	–	1	0.993	0.993	0.995	0.995
LZH-male	1	–	0.993	0.993	0.995	0.995
TH-female	0.993	0.993	–	0.997	0.998	0.998
TH-male	0.993	0.993	0.997	–	0.998	0.998
PYH-female	0.995	0.995	0.998	0.998	–	0.999
PYH-male	0.995	0.995	0.998	0.998	0.999	–
Nad6
LZH-female	–	1	0.984	0.984	0.984	0.984
LZH-male	1	–	0.984	0.984	0.984	0.984
TH-female	0.984	0.984	–	1	1	1
TH-male	0.984	0.984	1	–	1	1
PYH-female	0.984	0.984	1	1	–	1
PYH-male	0.984	0.984	1	1	1	–
Cox1
LZH-female	–	1	0.995	0.994	0.994	0.994
LZH-male	1	–	0.995	0.994	0.994	0.994
TH-female	0.995	0.995	–	0.999	0.999	0.999
TH-male	0.994	0.994	0.999	–	0.999	1
PYH-female	0.994	0.994	0.999	0.999	–	0.999
PYH-male	0.994	0.994	0.999	1	0.999	–
Cox2
LZH-female	–	1	0.994	0.994	0.994	0.994
LZH-male	1	–	0.994	0.994	0.994	0.994
TH-female	0.994	0.994	–	1	1	1
TH-male	0.994	0.994	1	–	1	1
PYH-female	0.994	0.994	1	1	–	1
PYH-male	0.994	0.994	1	1	1	–
Cox3
LZH-female	–	1	0.993	0.992	0.992	0.992
LZH-male	1	–	0.993	0.992	0.992	0.992
TH-female	0.993	0.993	–	0.998	0.998	0.998
TH-male	0.992	0.992	0.998	–	0.997	0.997
PYH-female	0.992	0.992	0.998	0.997	–	0.997
PYH-male	0.992	0.992	0.998	0.997	0.997	–
Atp6
LZH-female	–	1	0.997	0.997	0.997	0.997
LZH-male	1	–	0.997	0.997	0.997	0.997
TH-female	0.997	0.997	–	1	1	1
TH-male	0.997	0.997	1	–	1	1
PYH-female	0.997	0.997	1	1	–	1
PYH-male	0.997	0.997	1	1	1	–
Atp8
LZH-female	–	1	1	1	1	1
LZH-male	1	–	1	1	1	1
TH-female	1	1	–	1	1	1
TH-male	1	1	1	–	1	1
PYH-female	1	1	1	1	–	1
PYH-male	1	1	1	1	1	–
Cob
LZH-female	–	1	0.984	0.984	0.984	0.982
LZH-male	1	–	0.984	0.984	0.984	0.982
TH-female	0.984	0.984	–	0.996	0.998	0.998
TH-male	0.984	0.984	0.996	–	0.998	0.996
PYH-female	0.984	0.984	0.998	0.998	–	0.998
PYH-male	0.982	0.982	0.998	0.996	0.998	–
12S rRNA
LZH-female	–	1	0.991	0.989	0.991	0.989
LZH-male	1	–	0.991	0.989	0.991	0.989
TH-female	0.991	0.991	–	0.997	1	0.997
TH-male	0.989	0.989	0.997	–	0.997	0.997
PYH-female	0.991	0.991	1	0.997	–	0.997
PYH-male	0.989	0.989	0.997	0.997	0.997	–
16S rRNA
LZH-female	–	1	0.995	0.996	0.995	0.995
LZH-male	1	–	0.995	0.996	0.995	0.995
TH-female	0.995	0.995	–	0.998	0.998	0.998
TH-male	0.996	0.996	0.998	–	0.999	0.999
PYH-female	0.995	0.995	0.998	0.999	–	0.999
PYH-male	0.995	0.995	0.998	0.999	0.999	–
D-loop
LZH-female	–	1	0.993	0.992	0.991	0.990
LZH-male	1	–	0.993	0.992	0.991	0.990
TH-female	0.993	0.993	–	0.996	0.995	0.996
TH-male	0.992	0.992	0.996	–	0.996	0.997
PYH-female	0.991	0.991	0.995	0.996	–	0.994
PYH-male	0.990	0.990	0.996	0.997	0.994	–

Fig. 3. The complete control regions of three geographical groups. Termination associated sequences (TAS) as well as conserved sequence blocks (CSB-D, CSB-E, CSB-F CSB-1, CSB-2, and CSB-3) were underlined. Dots and dashes indicated the same nucleotides and gaps, respectively. Shaded region designated the motif of TGCAT and TACAT. ATGTA were bold. The number on the right side of alignment shows the nucleotide positions.

Fig. 4. Phylogenetic analysis based on the complete mitochondrial DNA sequences of various fish. Numbers at tree nodes refers to percent bootstrap values after 1000 replicates. The LZH-female, LZH-male, TH-female, TH-male, PYH-female, and PYH-male were boxed in the phylogenetic tree. Culter alburnus (XKH, KF039719.1), Ancherythroculter lini (KR864861.1), Ancherythroculter nigrocauda (KC513573.1), Chanodichthys dabryi (KC526217.1), Chanodichthys mongolicus (KC701385.1), Culter erythropterus (KJ801524.1), Culter recurviceps (KJ609181.1), Distoechodon tumirostris voucher (DQ026431.1), Hypophthalmichthys molitrix (KJ746944.1), Megalobrama pellegrini (KP262030.1), Megalobrama skolkovii (KJ630486.1), Megalobrama terminalis (AB626850.1), Mylopharyngodon piceus (EU979305.1), Parabramis pekinensis (JX242531.1), Sinibrama macrops (KC122916.1), Sinibrama taeniatus (KM272589.1), Xenocypris argentea (AP009059.1), Xenocypris davidi (KF039718.1).