The complete mitochondrial genome sequence and phylogenetic position of Sinocyclocheilus xiaotunensis (Cypriniformes: Cyprinidae)

Abstract The complete mitochondrial DNA genome of Sinocyclocheilus xiaotunensis was first reported by next-generation sequencing method. The entire length of mitochondrial genome is 16,588 bp and the nucleotide composition was made up of 32.3% A, 25.0% T, 27.2% C, and 15.5% G, indicating an A + T(57.3%) content is greater than C + G(42.7%). The mitogenome is a circular DNA molecule with a D-loop region and contains 22 transfer RNA (tRNA) genes, two ribosomal RNA(rRNA) genes and 13 protein-coding genes.To provide further info on the conserved sequence block observed in the control region of the mitochondrial genome. This info is critical for future application and determination of taxonomic status of this species.

Sinocyclocheilus (Cypriniformes: Cyprinidae) endemic to China and has been listed as endangered species in the IUCN Red List of Threatened Species. However, The fish was collected from Xiaotun Village, Zhenfeng County, Guizhou Province, china (25 50 0 42 00 N; 105 60 0 38 00 E)、 Sancha River, a tributary of Beipanjiang River System and 1165 M above sea level. Through morphological analysis, it is different from Sinocyclocheilus zhenfengensis (Liu et al. 2018); through complete mitochondrial genome analysis, it is different from other species, So we named it Sinocyclocheilus xiaotunensis. In this study, we first reported the complete mitochondrial genome (mitogenome) of S.xiaotunensis, which could provide useful first-hand data for molecular phylogenetics and population genetics studies on this species and its closely related Sinocyclocheilus species. Voucher specimens (gzu20201204) were preserved in 100% ethanol and deposited at zoological museum of the School of Animal Science, Guizhou University.
In terms of morphology, we measured two categories: quantifiable traits and countable traits. In the statistics of the above-mentioned measured growth traits, in order to eliminate the influence on the reliability of the data caused by the size of the fish, we used the head shape measurement value divided by the head length, and the trunk shape measurement value divided by the body Length, the measured value of the tail shape divided by the length of the tail shank.Refer to Table 1 for detailed morphological data. Compared with Liu (2018) (Sinocyclocheilus zhenfengensis) collected in the Shuangrufeng Scenic Spot in Zhexiang Town, Zhenfeng County, among the measurable traits, eye diameter/head length, dorsal fin length/body length, pectoral fin length/ body length, and pectoral fin length/body length all showed significant differences (p < 0.01), and the average values of S.xiaotunensis were 0.133, 0.184, 0.207 and 0.301, The average values of S.zhenfengensis were 0.291, 0.227, 0.247 and 0.337, respectively. In terms of countable traits, the number of dorsal fin spines and gill rakers of S.xiaotunensis was more than S.zhenfengensis. With the deepening of cave life, the eye diameter of the S.xiaotunensis is smaller than the S.zhenfengensis, which is related to the light intensity of the living environment (Langecker et al. 1995;Zhou et al. 2009). Not only that the dorsal and pectoral fins of S.xiaotunensis became shorter and the number of fin spines increased. This is an adaptive change to the living environment, and its balance function has been further adapted to evolve and it showed obvious difference from S.zhenfengensis in morphology.
The complete mitochondrial genome length of S.xiaotunensis was 16,588 bp (GenBank accession number MW574480). It consisted of 13 protein-coding genes, two rRNA genes, 22 tRNA genes and one D-loop region (Table 2; Figure 1). The overall base composition of the mitogenome is 32.3% for A, 27.2% for C, 15.5% for G and 25.0% for T. The percentage of G þ C content is 42.7%.The gene arrangement and nucleotide composition of the mitogenome of S.xiaotunensis were similar to those of other Sinocyclocheilus species (Wu et al. 2010;Chen et al. 2017;Li et al. 2017;Xu et al. 2019). Most mitochondrial genes were encoded on the heavy strand(H-strand), except that the eight tRNA gene and ND6 genes were encoded on the light strand (L-strand). All 13 PCGs except for COI (with a GTG start codon) started with an ATG codon. Six PCGs ended with two types of complete stop codons, TAA(ND1, COI, ND4L, ND5 and ND6)and TAG(ATP8). The remaining PCGs ended with incomplete stop codon, including stop codon T-(ND2, COII, ND3, ND4 and Cytb) and TA-(ATP6 and COIII). The 22 tRNA genes have lengths ranging from 69 to 78 bp. The lengths of 12S and 16S rRNA genes were 955 bp and 1677 bp.The D-loop or control region was located between tRNA-Pro and tRNA-Phe genes with a length of 934 bp. The lengths of COI and Cytb genes were 1551 and 1441 bp, respectively.
To determine the phylogenetic position of S.xiaotunensis, phylogenetic analyses were conducted based on mitogenome sequences of 25 Sinocyclocheilus species and two outgroup species from GenBank by Neighbor-joining tree (NJ) methods (Tamura et al.2013) (Figure 2). The phylogenetic results showed that three clade were observed and S. jii was the most basal species among the Sinocyclocheilus species. Not only that S.xiaotunensis was independent with the bootstrap values 100% and had a close relationship with S.altishoulderus and S.furcodorsalis. In summary, the newly    obtained S.xiaotunensis extranuclear genomic resource would provide valuable molecular information fundamental to conservation and resource restoration studies on this cyprinid species.
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