Abstract
Pacific sardine Sardinops sagax (Jenyns, 1842), a sardine species that widely distributes in Pacific, is an important commercial species in many areas. In this study, we characterized the complete mitochondrial genome of S. sagax using next generation sequencing technology. The complete mitogenome of S. sagax was 16,883 base pairs (bp) in length and comprised 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA genes (rRNA), and one control region (D-loop). Phylogenetic analysis indicated that sardine species included three clades (I, II and III) and S. sagax clustered with Sardinops melanostictus.
Keywords: Sardinops sagax, mitogenome, sardine species, phylogeny
Pacific sardine Sardinops sagax (Jenyns, 1842) is an important commercial species that supported an important fishery in Pacific waters (www.fishbase.org), which has wide distributions from southern Africa to eastern Pacific. Currently, this species occupies 10%–40% of fishery production in the Northwest Pacific. Empirical data argued that the resources of Pacific sardine had undergone long-term fluctuations in history, which were influenced by climate and current (Yatsu et al. 2005). In this study, we sequenced and characterized the complete mitochondrial genome of S. sagax from the Pacific Northwest. The mitogenome can provide basic genetic information for subsequent population genetic and phylogenetic studies.
A S. sagax individual was sampled from the Northwest Pacific (36.4251 N, 158.6026E) in May 2020. This sample (Voucher number: YDNSD20200501) was stored in the fish collection of East China Sea Fisheries Research Institute. Total genomic DNA was extracted from a bit of tail fin using a Genomic DNA Isolation Kit (QiaGene, Germany). The complete mitochondrial genome was sequenced using the Illumina MiSeq platform (Illumina Inc, San Diego, CA, USA). Finally, we de novo assembled the complete mitochondrial genome using SPAdes 3.9.0 (Bankevich et al. 2012) and annotated Protein-coding genes, rRNA genes and tRNA genes using MITOS (Bernt et al. 2013).
The complete mitochondrial genome of S. sagax was 16,883 base pairs (bp) in length and comprised of 13 protein-coding genes (ND1, ND2, ND3, ND4, ND4L, ND5, ND6, COI, COII, COIII, ATP6, ATP8, Cyt b), 2 rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes and a control region (D-loop) (GenBank nos: MW338734). Its structural organization and gene order were similar with those in other typical teleosts. A total of 17 sardine mitogenomes including 16 published mitogenomes were aligned using MUSCLE (Edgar 2004). We choose 13 protein-coding genes manually and then were combined into a single sequence for phylogenetic analysis. Maximum-likelihood tree was implemented in RAXML-VI-HPC (Stamatakis 2006) using a GTR + I + G model. Nodal support values were estimated from 1000 nonparametric bootstrap replicates.
The maximum-likelihood tree obtained three well supported major clades with high supported values (Clades I, II and III; Figure 1). Clade I contained species from five genera (Clupea, Ethmidium, Nematalosa, Sardinella and Sardinops), Clade II comprised Engraulis species and Clade III consisted of Hyperlophus vittatus. Furthermore, S. sagax was clustered with Sardinops melanostictus (Figure 1), suggesting these two species had a closely related phylogenetic relationship.
Figure 1.
Maximum-likelihood tree showing the phylogenetic relationships among 17 sardine mitogenomes based on 13 protein-coding genes. Values on branches indicate bootstrap values from maximum-likelihood analysis.
Ethical approval
Experiments were performed in accordance with the recommendations of the Ethics Committee of East China Sea Fisheries Research Institute. These policies were enacted according to the Chinese Association for the Laboratory Animal Sciences and the Institutional Animal Care and Use Committee (IACUC) protocols.
Funding Statement
This work was supported by the Open Project of Key Laboratory of Oceanic and Polar Fisheries, Ministry of Agriculture and Rural Affairs [2019HY-XKQ03] and National Key Research and Development Project of China [2019YFD0901405].
Disclosure statement
All authors declare that they have no conflict of interest.
Data accessibility statement
The data that support the findings of this study is openly available in GenBank of NCBI at http://www.ncbi.nlm.nih.gov, reference number MW338734. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA695793, SRR13575827 and SAMN17620116, respectively.
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The data that support the findings of this study is openly available in GenBank of NCBI at http://www.ncbi.nlm.nih.gov, reference number MW338734. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA695793, SRR13575827 and SAMN17620116, respectively.