The complete mitochondrial genome of Poropuntius huangchuchieni (Cyprinidae)

Abstract

We sequenced the mitogenome of Poropuntius huangchuchieni from Yunnan Plateau. The mitogenome was 16,554 bp in length and comprised 13 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs. The base composition included 32.3% for A, 25.8% for T, 15.6% for G, and 26.3% for C, respectively. The gene order was identical to other published Cyprinidae species. The phylogenetic analysis showed that P. huangchuchieni was close to Puntius tetrazona, a Puntigrus fish in Cyprinidae family.

Poropuntius huangchuchieni is a freshwater fish and belongs to the Poropuntius genus, Cyprinidae family (Ding et al. 2013). It is widely distributed in Mekong and Red Rivers of Yunnan Plateau in China. Examining the phylogeography of this species from different drainages would be applied to evaluating the effects of the geologic movement and climate change on the drainages in Yunnan Plateau (Wu et al. 2013). The mitogenome of P. huangchuchieni would help study the phylogeographic pattern of this fish and determine the taxonomic relationship between this species and other Cyprinidae fish.

Here we report its mitochondrial genome (GenBank accession: MN723896.1). One specimen of P. huangchuchieni was collected from the Lancang River, Xishuangbanna, Yunnan Province, China (21°48′ N and 101°57′E) and was stored in the fish specimen room of Center for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences (specimen Accession number: CAAG-2019-1219). Total genomic DNA was extracted with the DNeasy Tissue Kit (Qiagen, Valencia, CA) and then the mitochondrial genome was sequenced and assembled following Xue et al.’s method (Xue et al. 2013), and then annotated using MitoAnnotator (Bernt et al. 2013).

The complete mitogenome of P. huangchuchieni is 16,554 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNAs, and 2 ribosomal RNAs. Among the 13 PCGs, only COX1 uses GTG as the start codon and the rest genes initiate with the start codon ATG. The most common stop codons are TAA (COX1, ATP6, COX3, NAD4L, NAD5, and NAD6) and TAG (NAD1, NAD3, and ATP8). The rest four PCGs (COX2, NAD2, NAD4, and COB) end with the incomplete stop codon T (Boore 1999). The overall nucleotide composition was estimated to be 32.3% of A, 25.8% of T, 15.6% of G, and 26.3% of C, with a slightly higher A + T content (58.1%).

Based on the PCGs encoded in P. huangchuchieni and the other nine Cyprinidae fish, a phylogenetic analysis (Figure 1) was carried out using the MEGA7 package (Kumar et al. 2016) with the parameters of maximum-likelihood (ML) analysis, Jones–Taylor–Thornton model, and 1000 bootstrap replicates. The analysis revealed that P. huangchuchieni was clustered with Puntius tetrazona, a fish in Puntigrus genus, Cyprinidae family. The mitogenome resource will contribute to study the biogeography and diversification of P. huangchuchieni in Yunnan Plateau.

Figure 1.

A phylogenetic tree of P. huangchuchieni and the other nine species. The species used are as follows: Cyprinus carpio (NC_001606.1), Carassius auratus (NC_002079.1), Sinocyclocheilus grahami (NC_013189.1), Puntius tetrazona (NC_010110.1), Tanichthys albonubes (NC_015539.1), Ctenopharyngodon idella (NC_010288.1), Hypophthalmichthys molitrix (NC_010156.1), Megalobrama amblycephala (NC_010341.1), and Danio rerio (NC_002333.2). The number at each branch is the bootstrap value of ML analysis.

Funding Statement

This work was supported by the Special Scientific Research Funds for Central Nonprofit Institutes, Chinese Academy of Fishery Sciences, under Grant [2014A11JC07].

Disclosure statement

No potential conflict of interest was reported by the author(s).