Identification and phylogenetic analysis of the mitogenome from Acrossocheilus wenchowensis

Abstract

In the present study, the complete mitogenome sequence of Acrossocheilus wenchowensis was obtained using PCR amplification. The complete mitochondrial genome of A. wenchowensis was 16,591 bp in length, it contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one non-coding region. The gene arrangement and organization in the mitogenome of A. wenchowensis were consistent with other Cyprinidae fishes. The phylogenetic analysis was carried out, and the results showed that the mitogenome sequence could be useful data in the field of population genetics and conservation biology for A. wenchowensis and other Cyprinidae fishes.

Keywords:

• Acrossocheilus wenchowensis
• mitochondrial genome
• phylogenetic analysis

Acrossocheilus wenchowensis, a small stream bony fish distributed widely in different area of China (Gao 2011; Lan et al. 2015; Zhou et al. 2016). It was artificially cultured and used as an important commercial fish in recent years (Gao 2011; Yu et al. 2012). However, its wild population declines rapidly because of environment pollution, increasing capture pressure, and irrigation works (Yu et al. 2012). The mitochondrial genes sequence could be useful data in the field of population genetics and conservation biology for different aquatic species (Liu and Cui 2009; Chen et al. 2013; Yang et al. 2014; Wang et al. 2016; Li et al. 2018).

In the present study, an individual of A. wenchowensis was sampled from Hengjiang River (Huangshan city, China), and its complete mitochondrial genome sequence was obtained and identified (designated AW-1). The previously published mitochondrial genome of A. wenchowensis (GenBank accession no. KC495074, designated AW-2) was used to design PCR amplification primers (Han et al. 2015). The specimen and its DNA of AW-1 are now stored in the Shaoxing Aquatic Service Platform.

The complete mitochondrial genome of A. wenchowensis (Cypriniformes: Cyprinidae) is 16,591 bp in length (GenBank accession no. KT985047), it contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one non-coding region (Table 1). The gene arrangement and organization in the mitogenome of A. wenchowensis were consistent with other Cyprinidae fishes (Yang et al. 2014; Jia et al. 2016).

Table 1. Mitochondrial genome characteristics of Acrossocheilus wenchowensis.

Locus	Abbreviations	Position		Size nucleotide (bp)	Codon		Aminoacid	Anti-codon	Intergenicnucleotide	Strand
		From	To		Start	Stop
Cyt b	cytb	1	1141	1141	ATG	T--	380		0	H
tRNA^Thr	T	1142	1213	72				TGT	−1	H
tRNA^Pro	P	1213	1282	70				TGG	0	L
Control region	CR	1283	2219	937					0	–
tRNA^Phe	F	2220	2288	69				GAA	0	H
12S rRNA	12S	2289	3244	956					0	H
tRNA^Val	V	3245	3316	72				TAC	0	H
16S rRNA	16S	3317	4995	1679					0	H
tRNA^Leu(UUR)	L	4996	5071	76				TAA	1	H
ND1	nd1	5073	6047	975	ATG	TAA	324			H
tRNA^Ile	I	6052	6123	72				GAT	−2	H
tRNA^Gln	Q	6121	6191	71				TTG	2	L
tRNA^Met	M	6194	6262	69				CAT	0	H
ND2	nd2	6263	7309	1047	ATG	TAG	348		−2	H
tRNA^Trp	W	7308	7378	71				TCA	2	H
tRNA^Ala	A	7381	7449	69				TGC	1	L
tRNA^Asn	N	7451	7523	73				GTT	0	L
OL		7524	7556	33					0
tRNA^Cys	C	7557	7623	67				GCA	−1	L
tRNA^Tyr	Y	7623	7693	71				GTA	1	L
COX I	cox1	7695	9245	1551	GTG	TAA	516		1	H
tRNA^Ser(UCN)	S	9247	9317	71				TGA	3	L
tRNA^Asp	D	9321	9392	72				GTC	14	H
COX II	cox2	9407	10097	691	ATG	T--	230		0	H
tRNA^Lys	K	10,098	10173	76				TTT	1	H
ATP8	atp8	10,175	10339	165	ATG	TAG	54		−7	H
ATP6	atp6	10,333	11016	684	ATG	TAA	227		−1	H
COX III	cox3	11,016	11801	786	ATG	TAA	261		−1	H
tRNA^Gly	G	11,801	11872	72				TCC	0	H
ND3	nd3	11,873	12223	351	ATG	TAG	116		−2	H
tRNA^Arg	R	12,222	12291	70				TCG	0	H
ND4L	nd4L	12,292	12588	297	ATG	TAA	98		−7	H
ND4	nd4	12,582	13962	1381	ATG	T--	460		0	H
tRNA^His	H	13,963	14031	69				GTG	0	H
tRNA^Ser(AGY)	S	14,032	14100	69					1	H
tRNA^Leu(CUN)	L	14,102	14174	73				TAG	0	H
ND5	nd5	14,175	15998	1824	ATG	TAA	607		−4	H
ND6	nd6	15,995	16516	522	ATG	TAA	173		0	L
tRNA^Glu	E	16,517	16585	69				TTC	6	L

The total length of the protein-coding gene sequences is 10,446 bp, most of these genes are encoded on the light strand (L-strand). The total length of all tRNA genes was 1562 bp varying from 67 bp (tRNA^Cys) to 76 bp (tRNA^Leu and tRNA^Lys). Most of the tRNA genes are encoded on the heavy strand (H-strand). The 12S rRNA gene (956 bp) and 16S rRNA (1679 bp) gene of A. wenchowensis are located between the tRNA^Phe and tRNA^Leu(UUR) gene and are separated by the tRNA^Val gene. The D-loop region is 937 bp in length, which is located between the tRNA^Pro and tRNA^Phe gene. All of the PCD genes except COX I (started with a GTG) are initiate with an ATG. Six PCD genes terminate with TAA (ND1, COXI, ATP6, COXIII, ND4L, and ND5), four PCDs (COX II, ND4, ND6, and Cyt b) ended with (T–), whereas three PCDs (ND2, ND3, and ATP8) ended with TAG (data not shown). The overall nucleotide composition of A. wenchowensis mitogenome is A: 37.85%, G: 13.22%, T: 23.74%, and C: 25.19%, respectively. Which with an A + T rich feature (61.59%) as that of other vertebrate mitochondrial genomes (Tzeng et al. 1992; Jondeung et al. 2007; He et al. 2014).

The phylogenetic analysis showed that two A. wenchowensis individuals (AW-1 and AW-2) are clustered together and showed close relationship with other Acrossocheilus fishes (Figure 1). However, it showed distant kinship with other Cyprinidae fishes. These results showed that the mitogenome sequence could be useful data in the field of population genetics and conservation biology for aquatic species.

Figure 1. The phylogenetic analysis of A. wenchowensis and other Cyprinidae fishes based on the mitogenome sequences.

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.

Additional information

Funding

This work was supported by the Young & Middle-aged Academic Backbone Project of Shaoxing University (2014); the Public Welfare Project of Science Technology Department of Zhejiang Province (2011C22084); the National Mollusc Industry Technology System (KL2015-3).