Biodiversity Data Journal :
Research Article
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Corresponding author: Chuanjiang Zhou (chuanjiang88@163.com)
Academic editor: Yahui Zhao
Received: 24 Aug 2022 | Accepted: 01 Feb 2023 | Published: 21 Feb 2023
© 2023 Jinhui Yu, Xin Chen, Ruyao Liu, Yongtao Tang, Guoxing Nie, Chuanjiang Zhou
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Yu J, Chen X, Liu R, Tang Y, Nie G, Zhou C (2023) Mitochondrial genome of Acheilognathus barbatulus (Cypriniformes, Cyprinidae, Acheilognathinae): characterisation and phylogenetic analysis. Biodiversity Data Journal 11: e93947. https://doi.org/10.3897/BDJ.11.e93947
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Acheilognathus barbatulus is distributed in Yangtze River, Yellow River and Pearl River systems in China. Genome data can help to understand the phylogenetic relationships of A. barbatulus, but its complete mitochondrial genome has not been published. We determined the complete mitochondrial genome structure and characteristics of this species and constructed a comprehensive phylogenetic tree, based on mitochondrial genome data of several species of Acheilognathus, Rhodeus and Pseudorasbora parva. The complete length of the mitochondrial genome of A. barbatulus is 16726 bp. The genome is a covalently closed double-stranded circular molecule containing 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, a D-loop and a light strand replication initiation region. The base composition of the complete mitochondrial genome is A (29.33%) > T (27.6%) > C (26.12%) > G (16.95%), showing a strong AT preference and anti-G bias. All 13 PCGs have different degrees of codon preference, except for cytochrome c oxidase 1, which uses GTG as the start codon. All the PCGs use ATG as the start codon and the stop codon is dominated by TAG. The encoded amino acids Leu and Ser exist in two types, whereas the rest are all present as one type, except for tRNASer (GCT), which lacks the D-arm and has an incomplete secondary structure, all other tRNAs can be folded to form a typical cloverleaf secondary structure. Based on the 13 PCG tandems, the Maximum Likelihood and Bayesian trees were constructed, based on the concatenated sequence of 13 PCGs for the genera Acheilognathus and Rhodeus, with Pseudorasbora parva as the outgroup. Acheilognathus barbatulus, Acheilognathus tonkinensis and Acheilognathus cf. macropterus were clustered together and the most closely related. The results of this study enrich the mitochondrial genomic data of Acheilognathus and provide molecular and genetic base information for species conservation, molecular identification and species evolution of Acheilognathinae.
Acheilognathus barbatulus, mitochondrial genome, phylogenetic relationships
Species in subfamily Acheilognathinae (Cypriniformes, Cyprinidae) mostly inhabit shallow and still water areas in rivers, lakes and reservoirs. Acheilognathus barbatulus Günther belongs to subfamily Acheilognathinae within Cyprinidae; Acheilognathinae comprises approximately 72 species (
The mitochondrion possesses a separate genome (mitochondrial genome, mtDNA) and a relatively independent genetic system (
The development of genomics has allowed the analysis of numerous mitochondrial genomes (mtDNA) and advancement of the study of population genetic structure, conservation biology and evolutionary genetics of fish (
A. barbatulus belongs to subfamily Acheilognathinae. This species is a small fish that lives in the Yangtze River, Yellow River, Pearl River and other river systems. It lays eggs in the gills of mussels and feeds on aquatic higher plants and algae. In previous studies, the phylogenetic relationship of A. barbatulus has not been unified in accordance with different classification methods. With the wide use of multi-site sequence analysis, we downloaded the existing mitochondrial genome data of Acheilognathus and Rhodeus fish species from the National Center for Biotechnology Information (NCBI). With Pseudorasbora parva as the outgroup, 13 PCGs were connected in series and Maximum Likelihood (ML) and Bayesian (Bayes) tree were constructed, based on the optimal nucleotide substitution model and optimal partition model, respectively. The description in this paper is expected to provide support and theoretical supports for the evolutionary development of Acheilognathinae in the future.
Samples of A. barbatulus were collected from Poyang Lake in northern Jiangxi Province, China. The experimental material for this study was provided by the Institute of Hydrobiology, Chinese Academy of Sciences. Specimens were stored in absolute ethanol at the College of Fisheries Henan Normal University. In the sampling process, the specific sampling location was not clearly marked, which led to the failure to obtain the latitude and longitude information of the sampling point. Samples from A. barbatulus were extracted using the phenol-chloroform protocol (
The complete mitochondrial genome sequence was obtained by comparing it to the published mitochondrial genome of subfamily Acheilognathinae in NCBI. The position of start transfer RNA (tRNAPhe) was determined using the MITOS website (http://mitos2.bioinf.uni-leipzig.de/index.py) (
To study the phylogenetic position of A. barbatulus, we selected a part of the fish in the Acheilognathus and Rhodeus data provided by NCBI. Given that subfamilies Gobioninae and Acheilognathae are sister groups (
GenBank Accession |
Speices |
Length |
AT (%) |
Acheilognathus tabira erythropterus |
16770 |
56 |
|
Acheilognathus tabira tohokuensis |
16774 |
56 |
|
Acheilognathus majusculus |
17155 |
56.8 |
|
Acheilognathus longipinnis |
16772 |
58 |
|
Acheilognathus cf. macropterus |
16761 |
57.6 |
|
Acheilognathus tabira jordani |
16765 |
56.4 |
|
Acheilognathus rhombeus |
16783 |
56.5 |
|
Acheilognathus typus |
16778 |
57 |
|
Acheilognathus sp. CBM ZF 11927 |
16254 |
56.2 |
|
Acheilognathus tabira nakamurae |
16343 |
56.6 |
|
Acheilognathus cyanostigma |
16454 |
58.9 |
|
Acheilognathus hypselonotus |
16706 |
57.1 |
|
Acheilognathus tonkinensis |
16767 |
56.5 |
|
Acheilognathus omeiensis |
16774 |
56.7 |
|
Acheilognathus rhombeus |
16780 |
56.9 |
|
Acheilognathus macropterus |
16773 |
57.6 |
|
Acheilognathus yamatsutae |
16703 |
56.7 |
|
Acheilognathus melanogaster |
16556 |
56.8 |
|
Acheilognathus meridianus |
16563 |
57.9 |
|
Acheilognathus tabira tabira |
16771 |
56.1 |
|
Rhodeus amarus |
16607 |
55.6 |
|
Rhodeus atremius atremius |
16734 |
55 |
|
Rhodeus ocellatus kurumeus |
16674 |
56.5 |
|
Rhodeus notatus |
16735 |
55.3 |
|
Rhodeus fangi |
16733 |
55.3 |
|
Rhodeus sericeus |
16581 |
55.5 |
|
Rhodeus lighti |
16677 |
56.1 |
|
Rhodeus ocellatus |
16574 |
52.9 |
|
Rhodeus suigensis |
16733 |
55.1 |
|
Rhodeus sinensis |
16677 |
56.3 |
|
Rhodeus cyanorostris |
16580 |
54.9 |
|
Rhodeus ocellatus |
16680 |
56.4 |
|
Pseudorasbora parva |
16600 |
58.9 |
The sequences were aligned, based on the mitochondrial genome by Phylosiute (
GenBank accession number ON815031
The complete mitochondrial genome (GenBank accession number ON815031) of A. barbatulus is 16726 bp in total length and a typical covalently closed double-stranded cyclic molecule (Fig.
Mitochondrial genes and associated features of Acheilognathus barbatulus. Intergenic space (IGS) described as intergenic (+) or overlapping nucleotides.
Locus |
Type |
One-letter code |
Strand |
Amino acids |
Position |
Codon |
|||||
Start |
Stop |
Length (bp) |
Start |
Stop |
Anti-condon |
Intergenic nucleotide |
|||||
tRNAPhe |
tRNA |
F |
H |
1 |
69 |
69 |
GAA |
0 |
|||
12S rRNA |
rRNA |
H |
70 |
1025 |
956 |
1 |
|||||
tRNAVal |
tRNA |
V |
H |
1027 |
1098 |
72 |
TAC |
16 |
|||
16S rRNA |
rRNA |
H |
1115 |
2774 |
1660 |
0 |
|||||
tRNALeu |
tRNA |
L2 |
H |
2775 |
2850 |
76 |
TAA |
0 |
|||
NAD1 |
Protein-coding |
H |
324 |
2851 |
3825 |
975 |
ATG |
TAA |
4 |
||
tRNAIle |
tRNA |
I |
H |
3830 |
3901 |
72 |
GAT |
-2 |
|||
tRNAGln |
tRNA |
Q |
L |
3900 |
3970 |
71 |
TTG |
1 |
|||
tRNAMet |
tRNA |
M |
H |
3972 |
4040 |
69 |
CAT |
0 |
|||
NAD2 |
Protein-coding |
H |
348 |
4041 |
5087 |
1047 |
ATG |
TAG |
-2 |
||
tRNATrp |
tRNA |
W |
H |
5086 |
5155 |
70 |
TCA |
1 |
|||
tRNAAla |
tRNA |
A |
L |
5157 |
5225 |
69 |
TGC |
1 |
|||
tRNAAsn |
tRNA |
N |
L |
5227 |
5299 |
73 |
GTT |
2 |
|||
OL |
H |
5302 |
5332 |
31 |
-2 |
||||||
tRNACys |
tRNA |
C |
L |
5331 |
5398 |
68 |
GCA |
0 |
|||
tRNATyr |
tRNA |
Y |
L |
5399 |
5469 |
71 |
GTA |
1 |
|||
COX1 |
Protein-coding |
H |
516 |
5471 |
7021 |
1551 |
GTG |
TAA |
0 |
||
tRNASer |
tRNA |
S2 |
L |
7022 |
7092 |
71 |
TGA |
2 |
|||
tRNAAsp |
tRNA |
D |
H |
7095 |
7165 |
71 |
GTC |
7 |
|||
COX2 |
Protein-coding |
H |
230 |
7173 |
7863 |
691 |
ATG |
T(AA) |
0 |
||
tRNALys |
tRNA |
K |
H |
7864 |
7939 |
76 |
TTT |
1 |
|||
ATP8 |
Protein-coding |
H |
54 |
7941 |
8105 |
165 |
ATG |
TAG |
-7 |
||
ATP6 |
Protein-coding |
H |
227 |
8099 |
8782 |
684 |
ATG |
TAA |
-1 |
||
COX3 |
Protein-coding |
H |
261 |
8782 |
9566 |
785 |
ATG |
TA(A) |
-1 |
||
tRNAGly |
tRNA |
G |
H |
9566 |
9636 |
71 |
TCC |
0 |
|||
NAD3 |
Protein-coding |
H |
116 |
9637 |
9987 |
351 |
ATG |
TAG |
-2 |
||
tRNAArg |
tRNA |
R |
H |
9986 |
10054 |
69 |
TCG |
0 |
|||
NAD4L |
Protein-coding |
H |
98 |
10055 |
10351 |
297 |
ATG |
TAA |
-7 |
||
NAD4 |
Protein-coding |
H |
460 |
10345 |
11725 |
1381 |
ATG |
T(AA) |
0 |
||
tRNAHis |
tRNA |
H |
H |
11726 |
11794 |
69 |
GTG |
0 |
|||
tRNASer |
tRNA |
S1 |
H |
11795 |
11863 |
69 |
GCT |
1 |
|||
tRNALeu |
tRNA |
LI |
H |
11865 |
11937 |
73 |
TAG |
0 |
|||
NAD5 |
Protein-coding |
H |
611 |
11938 |
13773 |
1836 |
ATG |
TAA |
-4 |
||
NAD6 |
Protein-coding |
L |
173 |
13770 |
14291 |
522 |
ATG |
TAA |
0 |
||
tRNAGlu |
tRNA |
E |
L |
14292 |
14360 |
69 |
TTC |
2 |
|||
CYTB |
Protein-coding |
H |
380 |
14363 |
15503 |
1141 |
ATG |
T(AA) |
0 |
||
tRNAThr |
tRNA |
T |
H |
15504 |
15576 |
73 |
TGT |
-1 |
|||
tRNAPro |
tRNA |
P |
L |
15576 |
15645 |
70 |
TGG |
406 |
|||
D-loop |
Non- coding |
H |
16052 |
16630 |
579 |
96 |
Gene map of the Acheilognathus barbatulus mitochondrial genomes. The genome contained two rRNA genes (in yellow), 13 coding genes (in black), 22 tRNA genes (in red) and a control region (D-loop) (in brown). The outer ring corresponds to the H- (outermost) and L-strands and depicts the location of PCGs (except for ND6 which is encoded in the L-strand and is portrayed in red). The inner ring (black sliding window) denotes GC content along the genome.
Similar to other bony fish, spacers and overlap between genes were present. Gene overlapping promotes miniaturisation of mitotic genes, shortens genome replication time and offers a natural selection advantage (
The highest base content in A. barbatulus was that of A (29.33%), followed by those of T (27.6%) > C (26.12%) > G (16.95%). The complete mitochondrial genome of A. barbatulus showed an anti-G bias and AT preference (Table
Nucleotide composition of the complete Acheilognathus barbatulus mitochondrial genomes (and concatenated PCGs, rRNA, D-loop) analysed in this study.
Region |
Base composition (%) |
|||||||
Total |
T |
C |
A |
G |
AT(%) |
ATskew |
GCskew |
|
ATPase 6 |
683 |
30.75 |
28.11 |
26.35 |
14.79 |
57.10 |
-0.08 |
-0.31 |
ATPase 8 |
165 |
27.27 |
24.24 |
34.55 |
13.94 |
61.82 |
0.12 |
-0.27 |
COI |
1551 |
30.82 |
26.05 |
25.02 |
18.12 |
55.83 |
-0.10 |
-0.18 |
COII |
691 |
29.09 |
25.47 |
29.52 |
15.92 |
58.61 |
0.01 |
-0.23 |
COIII |
784 |
29.97 |
26.28 |
25.13 |
18.62 |
55.10 |
-0.09 |
-0.17 |
Cyt b |
1141 |
31.11 |
26.12 |
27.70 |
15.07 |
58.81 |
-0.06 |
-0.27 |
ND1 |
975 |
30.67 |
27.49 |
25.74 |
16.10 |
56.41 |
-0.09 |
-0.26 |
ND2 |
1045 |
26.22 |
31.39 |
27.75 |
14.64 |
53.97 |
0.03 |
-0.36 |
ND3 |
349 |
30.37 |
28.08 |
25.50 |
16.05 |
55.87 |
-0.09 |
-0.27 |
ND4 |
1381 |
29.76 |
27.23 |
28.39 |
14.63 |
58.15 |
-0.02 |
-0.30 |
ND4L |
297 |
29.29 |
28.28 |
26.94 |
15.49 |
56.23 |
-0.04 |
-0.29 |
ND5 |
1836 |
29.74 |
26.96 |
28.70 |
14.60 |
58.44 |
-0.02 |
-0.30 |
ND6 |
522 |
37.93 |
13.60 |
15.52 |
32.95 |
53.45 |
-0.42 |
0.42 |
PCGs |
11420 |
30.17 |
26.58 |
26.73 |
16.52 |
56.89 |
-0.06 |
-0.23 |
tRNAs |
1561 |
27.35 |
21.33 |
28.76 |
22.55 |
56.12 |
0.03 |
0.03 |
D-loop |
579 |
29.53 |
24.01 |
28.32 |
18.13 |
57.86 |
-0.02 |
-0.14 |
12S rRNA |
957 |
19.54 |
26.96 |
31.03 |
22.47 |
50.57 |
0.23 |
-0.09 |
16S rRNA |
1676 |
21.30 |
22.49 |
34.84 |
21.36 |
56.15 |
0.24 |
-0.03 |
Complete genome |
16726 |
27.60 |
26.12 |
29.33 |
16.95 |
56.93 |
0.03 |
-0.21 |
The mitochondrial genome of A. barbatulus contains 13 PCGs with a total length of 11,420 bp, which accounts for 68.28% of the entire mitochondrial genome.
The PCGs of A. barbatulus encode 3798 amino acids and, amongst the encoded amino acids, the Leu, Ser, Pro and Thr exhibit high contents. Low contents of most amino acids, such as Arg, Cys, Glu and Asp, can be observed (Table
Results from the Relative Synonymous Codon Usage (RSCU) analysis for the PCGs of the mitochondrial genome of Acheilognathus barbatulus. * denotes stop codon.
AA |
Codon |
Count |
RSCU |
AA |
Codon |
Count |
RSCU |
Phe |
UUU(F) |
150 |
1.3 |
Tyr |
UAU(Y) |
145 |
1.08 |
UUC(F) |
81 |
0.7 |
UAC(Y) |
123 |
0.92 |
||
Leu |
UUA(L) |
127 |
1.24 |
UAA(*) |
155 |
1.53 |
|
UUG(L) |
104 |
1.01 |
UAG(*) |
96 |
0.95 |
||
CUU(L) |
114 |
1.11 |
His |
CAU(H) |
121 |
1.08 |
|
CUC(L) |
109 |
1.06 |
CAC(H) |
103 |
0.92 |
||
CUA(L) |
92 |
0.9 |
Gln |
CAA(Q) |
125 |
1.28 |
|
CUG(L) |
70 |
0.68 |
CAG(Q) |
70 |
0.72 |
||
Ile |
AUU(I) |
151 |
1.37 |
Asn |
AAU(N) |
160 |
1.08 |
AUC(I) |
69 |
0.63 |
AAC(N) |
135 |
0.92 |
||
Met |
AUA(M) |
107 |
1.14 |
Lys |
AAA(K) |
153 |
1.36 |
AUG(M) |
81 |
0.86 |
AAG(K) |
72 |
0.64 |
||
Val |
GUU(V) |
47 |
1.21 |
Asp |
GAU(D) |
71 |
1.06 |
GUC(V) |
30 |
0.77 |
GAC(D) |
63 |
0.94 |
||
GUA(V) |
48 |
1.24 |
Glu |
GAA(E) |
96 |
1.29 |
|
GUG(V) |
30 |
0.77 |
GAG(E) |
53 |
0.71 |
||
Ser |
UCU(S) |
128 |
1.46 |
Cys |
UGU(C) |
42 |
0.74 |
UCC(S) |
90 |
1.03 |
UGC(C) |
72 |
1.26 |
||
UCA(S) |
88 |
1.01 |
Trp |
UGA(W) |
84 |
1.11 |
|
UCG(S) |
40 |
0.46 |
UGG(W) |
67 |
0.89 |
||
Pro |
CCU(P) |
166 |
1.32 |
Arg |
CGU(R) |
39 |
1 |
CCC(P) |
149 |
1.18 |
CGC(R) |
45 |
1.15 |
||
CCA(P) |
113 |
0.9 |
CGA(R) |
25 |
0.64 |
||
CCG(P) |
75 |
0.6 |
CGG(R) |
47 |
1.21 |
||
Thr |
ACU(T) |
121 |
1.21 |
Ser |
AGU(S) |
68 |
0.78 |
ACC(T) |
133 |
1.33 |
AGC(S) |
111 |
1.27 |
||
ACA(T) |
95 |
0.95 |
AGA(*) |
75 |
0.74 |
||
ACG(T) |
52 |
0.52 |
AGG(*) |
80 |
0.79 |
||
Ala |
GCU(A) |
55 |
1.03 |
Gly |
GGU(G) |
36 |
0.7 |
GCC(A) |
74 |
1.38 |
GGC(G) |
55 |
1.07 |
||
GCA(A) |
66 |
1.23 |
GGA(G) |
52 |
1.01 |
||
GCG(A) |
19 |
0.36 |
GGG(G) |
62 |
1.21 |
Results from analysis of Relative Synonymous Codon Usage (RSCU) of the mitochondrial genome of Acheilognathus barbatulus. Codon families are plotted on the x-axis. The label for the 2, 4 or 6 codons that compose each family is shown in the boxes below the x-axis and the colours correspond to those in the stacked columns. RSCU values are shown on the y-axis.
Most of the start codons of A. barbatulus are ATG. Only the COX1 gene has GTG as the start codon. ND1, COX1, ATP6, ND4L, ND5 and ND6 use TAA as the complete stop codon. ND2, ATP8 and ND3 use TAG as the complete stop codon, whereas COX2, COX3, ND4 and CYTB use TA- and T-- as incomplete stop codons.
Codon usage bias (CUB) refers to the unequal use of synonymous codons in organisms. CUB is affected by mutation and selection pressure and is an important feature of biological evolution. It not only affects gene function and expression potential, but also the accuracy and efficiency of translation. The higher the gene expression level, the stronger the CUB. To investigate codon usage preference in the mitochondrial genomes of A. barbatulus, we calculated CAI, ENC, GC and GC3 using CodonW1.4.2.
Effective number of condon (ENC) can describe the extent to which codon usage deviates from random selection, with values generally varying from 20 to 61. The larger the ENC value, the lower bias of expression genes towards the use of rare codons. The smaller the ENC value, the greater the preference for codons of genes with high expressions. The ENC values of PCGs in the mitochondrial genome of A. barbatulus ranged from 39 to 55.71 (Table
Preference for codon usage of genes encoding proteins in mitochondrial genome of Acheilognathus barbatulus.
CAI |
ENC |
GC |
GC3 |
|
ATP6 |
0.117 |
48.05 |
0.432 |
0.361 |
ATP8 |
0.257 |
44.06 |
0.388 |
0.333 |
COI |
0.177 |
44.77 |
0.446 |
0.374 |
COII |
0.186 |
52.50 |
0.416 |
0.332 |
COIII |
0.196 |
46.88 |
0.454 |
0.380 |
Cytb |
0.160 |
43.52 |
0.415 |
0.363 |
ND1 |
0.121 |
46.39 |
0.440 |
0.361 |
ND2 |
0.139 |
45.89 |
0.464 |
0.399 |
ND3 |
0.126 |
44.61 |
0.445 |
0.400 |
ND4 |
0.125 |
45.72 |
0.422 |
0.343 |
ND4L |
0.116 |
39.00 |
0.443 |
0.365 |
ND5 |
0.152 |
47.11 |
0.418 |
0.394 |
ND6 |
0.141 |
45.53 |
0.470 |
0.442 |
PCGs |
-0.037 |
55.71 |
0.420 |
0.444 |
The animal mitochondrial genome has two types of ribosomal units: the large 16S and small 12S subunits. The 16S subunit is more conserved than the 12S and the secondary structure of both rRNA genes is more conserved than the sequence (
A. barbatulus has 22 tRNA genes (eight in the L-strand and 14 in the H-strand). Their individual gene lengths ranged from 68 bp to 76 bp. Except for Leu and Ser, which both contain two types, the other 18 tRNAs have only one type. Except for tRNASer (GCT) (L strand), which lacks the D-arm resulting in an incomplete secondary structure, all 21 tRNAs can fold into the canonical cloverleaf secondary structure (Fig.
In this study, the ML tree and MrBayes were constructed by tandemly linking 13 PCGs and using Pseudorasbora parva as an outgroup partition to accurately reveal the phylogenetic relationships of A. barbatulus. The best partitioning ML and Bayes models were based on AIC and BIC for 34 PCG tandem sequences and the most suitable nucleotide-substitution models, respectively. The best partitioning models for ML were GTR+F+I+G4: ND1, ND3, ND4, ATP6; GTR+F+I+G4: ND2; GTR+F+I+G4: ND5; GTR+F+I+G4: ND6; HKY+F+I+G4: ATP8; GTR+F+I+G4: COI; GTR+F+I+G4: COII; GTR+F+I+G4: COIII, Cytb, ND4L. The optimal partitioning models of ML and Bayesian were slightly different, with a slight difference in node support. The topological structure was consistent overall, but parts of the support rate or posterior probability of the nodes is inconsistent. This finding may be due to different ML and Bayes algorithms being different, resulting in differences in the subsequent phylogenetic trees. The results support the conclusion that Acheilognathus and Rhodeus constitute monophyletic taxa (
Phylogenetic trees derived from the Bayes approaches, based on concatenation of PCGs. The numbers on the nodes are the bootstrap values of Bayes. The number after the species name is the GenBank accession number. Outgroup taxa are shown, the text is bolded by the Acheilognathus barbatulus.
Phylogenetic trees derived from the Maximum-Likelihood (ML) approaches, based on concatenation of PCGs. The numbers on the nodes are the bootstrap values of ML. The number after the species name is the GenBank accession number. Outgroup taxa are shown, the text is bolded by the Acheilognathus barbatulus.
We successfully obtained and annotated the mitochondrial genome data of A. barbatulus. The length of mitochondrial genome is 16726 bp, which is similar to the length of other fish genomes in Acheilognathinae, such as those of A. signifier (16566 bp) (
By analysing the relative usage frequency (RSCU) of synonymous codons of A. barbatulus mitochondrial genome coding genes, we observed that the RSCU values of 35 codons, such as UCU, AUU and AAA, were greater than 1 (Fig.
The secondary structure of A. barbatulus tRNA is conserved and conforms to the characteristics of fish mitochondrial genome (
The mitochondrial genome of animals is maternally inherited. The nucleic acid sequence and composition are relatively conserved and the gene order is relatively stable and close. Given its structural and evolutionary characteristics, the mitochondrial genome has become an ideal object for studying the origins and evolution of animals and population genetic differentiation. Thus far, phylogenetic analysis still uses single genes as the proxy of species. However, with the continuous development of technology, the inconsistency between gene and species trees has become increasingly prominent. The information sites contained in a single gene are insufficient to reconstruct the phylogenetic relationship of a group with a gene sequence. To date, increasing number of information sites and datasets are being collected, including 13 PCGs in series, to construct phylogenetic trees.
Acheilognathinae have a complicated taxonomic history (
Previous studies have revealed different phylogenetic relationships in A. barbatulus. We first used 13 PCGs in tandem to reconstruct the phylogenetic relationship of A. barbatulus. Phylogenetic results showed topological differences compared with other studies due to variations in outgroups, comparative species, molecular markers and individual gene sequences (
Through the above brief description, the taxonomic status of A. barbatulus in Acheilognathinae has not been well solved. In this paper, the phylogenetic tree was reconstructed by tandem reconstruction of 13 PCGs in the mitochondrial genome. A. barbatulus is most closely related to A. tonkinensis and A. cf. macropterus (
We report the mitochondrial genome sequence and characteristics of Acheilognathus barbatulus. The gene structure, RNA secondary structure, D-loop region and base composition were analysed. The results contribute the mitochondrial genome data of Acheilognathus and provide molecular and genetic information for species conservation, molecular identification and species evolution of Acheilognathinae.
This work was supported by the following funding: the National Natural Science Foundation of China (U2004146, 31872199) and the Science and Technology Innovation team supported the project (CXTD2016043) in Henan Province, China, the training plan of young excellent teachers in colleges and universities of Henan Province (2019GGJS063). This study was supported by the High-Performance Computing Center of Henan Normal University.