DNA Barcode and Correct Scientific Name of Golden Pompano, an Important Marine Aquaculture Fish Species in China

Abstract

The golden pompano ranks at the top of production in current China’s marine fish aquaculture; however, there has been long-standing controversy regarding its valid scientific name. Multiple latin names were used simultaneously to refer to golden pompano, such as Trachinotus ovatus, T. blochii, T. mookalee and T. anak. Moreover, two distinct morphological species are regarded as deserving the scientific name T. ovatus. In this study, we employed DNA barcoding to determine which particular species the “golden pompano” represents and to explore the potential synonyms and cryptic species within T. ovatus and its closely related species. We analyzed the DNA barcodes of golden pompano samples from various aquaculture farms in China’s main production regions, as well as most species within the genus Trachinotus. The phylogenetic analyses revealed that all T. ovatus sequences clustered into two divergent clades with a large genetic distance, and the two clades were geographically separated, being from the Indo-west Pacific and the East Atlantic regions, respectively. Based on the type locality information and historical distribution records, we support the validity of the naming of Trachinotus ovatus from the Indo-west Pacific, and the so-called Trachinotus ovatus from the East Atlantic may represent a cryptic species. All the golden pompano samples were clustered into the Indo-west Pacific T. ovatus clade, with a considerably small intragroup genetic distance, which suggests that the golden pompano in China should be identified as the species Trachinotus ovatus. The golden pompano, T. blochii and T. mookalee were completely separated into distinct monophyletic clades in the phylogenetic trees, which indicated that they are different species. The T. anak clustered with the monophyletic clade of Indo-west Pacific T. ovatus and the genetic distance between them was at the intraspecific difference level. This implied that the T. anak might be the junior synonym of T. ovatus. The species delimitations based on the ABGD and bPTP methods are in agreement with the findings from phylogenetic analyses. The above results help to form a consistent viewpoint regarding the naming of the golden pompano and provide new understandings for the taxonomy of the genus Trachinotus.

1. Introduction

The golden pompano, belonging to the family Carangidae genus Trachinotus, is one of the most commercially valuable marine fish in China [1]. The golden pompano is very common in China’s market and most products come from the widely cultured areas along the southern coast of China [2]. According to the statistics, the Chinese aquaculture production of golden pompano has reached 292,263 tons in 2023, ranking first among all marine aquaculture fish in China [3]. However, although the cultured golden pompano in China was considered to be the species of Trachinotus ovatus (Linnaeus, 1758) in most literature [1,2,4], it has also been identified as Trachinotus blochii (Lacepède, 1801) [5], Trachinotus mookalee Cuvier, 1832 [6] or even Trachinotus anak Ogilby, 1909 [7] in some cases. For instance, in “Marine Fishes of Southern Fujian, China” (2014) [5], the common name of T. blochii was described as “Jin Chang”, which is the Chinese pronunciation of golden pompano. In “key to Marine and Estuarial Fishes of China” (2021) [6], the T. mookalee was considered as an economically valuable aquaculture fish widely cultured in China and the T. ovatus was just regarded as the synonym of it. According to Fan et al. (2021) [7], it is believed that almost all of the commercially cultured T. anak in China were misidentified either as T. ovatus or its closely related species, T. blochii. Furthermore, it cannot be avoided that there are two different descriptions about the native distribution of T. ovatus: East Atlantic and Indo-west Pacific. The individuals from the two sea areas present completely different morphological characteristics and the most obvious morphological difference between them is that the T. ovatus from the East Atlantic have 3–5 vertically elongate black spots on the anterior half of the lateral line (also supported by FishBase) but there are not in the T. ovatus from Indo-west Pacific [8,9,10,11,12,13,14,15,16]. The above problems complicate the identification of the golden pompano; however, clarifying species delimitation and scientific names is fundamental to conservation and utilization of golden pompano germplasm resources in China.

In recent years, DNA barcoding has been suggested as an effective technique to complement the traditional taxonomic expertise and provides an important tool for species identification of various sourced organism specimens. In this study, we analyzed the DNA barcodes of 36 golden pompano individuals sourced from five key aquaculture farms, encompassing the primary production regions of this species in China. The broodstock in golden pompano artificial breeding are usually collected from local wild populations and there is artificial exchange of fish seedlings among different aquaculture regions during the aquaculture process. Therefore, we conducted extensive sampling to ensure obtaining diverse genetic information. The DNA barcode sequences from as many species of the genus Trachinotus as possible included all the species related to the names of “golden pompano” and “T. ovatus” were used as reference sequences for comparative analysis and specimen identification. To ensure accuracy, these sequences were strictly selected by prioritizing those which had been documented by published articles or published in both the Barcode of Life Data System (BOLD) (http://www.boldsystems.org/ (accessed on 10 February 2025)) and GenBank (https://www.ncbi.nlm.nih.gov/genbank/ (accessed on 10 February 2025)). Our objective was to clarify which particular species the “golden pompano” represents in the aquaculture of China and provide the correct DNA barcode. Meanwhile, possible synonyms and cryptic species existing alongside T. ovatus and its closely related species were also discussed. The results are expected to establish a consistent understanding of species determination for golden pompano and provide a scientific basis for the diversity conservation and resource development of pompano fish (genus Trachinotus).

2. Materials and Methods

2.1. Sampling

The 36 individual samples, which were called golden pompano, were collected from five aquaculture farms located in Ningde (ND), Zhangzhou (ZZ), Yangjiang (YJ), Lingshui (LS), and Fangchenggang (FCG), respectively, in the south of China in July 2022 (Figure 1). The sampling numbers at each site are as follows: ND: 4 (named as ND1–ND4), ZZ: 7 (named as ZZ1–ZZ7), YJ: 12 (named as YJ1–YJ12), LS: 7 (named as LS1–LS7), FCG: 6 (named as FCG1–FCG6). A piece of pectoral fin tissue was obtained from each individual and then preserved in 95% ethanol. All samples were stored at −20 °C and preserved at the National Marine Genetic Resource Center in Qingdao, China.

2.2. Molecular Identification

DNA barcoding approach was employed for species identification.

Total genomic DNA was extracted from pectoral fin tissue of each golden pompano sample using TIANamp Marine Animals DNA Kit (TIANGEN BIOTECH, Beijing, China). Partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene were amplified polymerase chain reaction (PCR) using primers FishF1, 5′-TCAACCAACCACAAAGACATTGGCAC-3′, and FishR1, 5′-TAGACTTCTGGGTGGCCAAAGAATCA-3′ [17]. Each 25 μL reaction volume contained 17.25 μL of ultrapure water, 2.5 μL of 10 × PCR buffer, 2 μL of dNTPs, 1 μL of each primer (5 μmol/L), 0.25 μL of Taq polymerase, and 1 μL of DNA template (approximately 100 ng). PCR amplification was carried out under the following conditions: initial denaturation at 95 °C for 2 min followed by 35 cycles of denaturation at 94 °C for 30 s, annealing at 54 °C for 30 s, and extension at 72 °C for 1 min, with a final extension at 72 °C for 10 min. PCR products were purified with a Gel Extraction Mini Kit (Watson BioTechnologies Inc., Shanghai, China). The purified PCR products were directly sequenced using an ABI 3730 automated sequencer with the BigDye Terminator v. 2.0 Cycle Sequencing Kit (Applied Biosystems, Foster City, CA, USA). The sequencing reactions were performed on both forward and reverse strands.

Sequences were edited and aligned using DNASTAR 5.01 software (DNASTAR, Madison, WI, USA). Haplotypes were detected using DnaSP v5 (Librado and Rozas 2009) [18]. In order to determine the species for the golden pompano, 46 reference sequences of mitochondrial DNA COI gene from 16 Trachinotus species and their sibling species, Lichia amia (Linnaeus, 1758), were selected and downloaded from the BOLD and GenBank (Table 1). A neighbor-joining (NJ) tree was constructed using MEGA X (Kumar et al., 2018) [19] with 1000 bootstrap replicates based on genetic distances that were calculated using the best selected model K2P. The Bayesian inference (BI) phylogenetic analyses were conducted using MrBayes v3.2.7a (Ronquist et al., 2012) [20] under the best-fit model HKY+G+F, which was selected using ModelFinder v2.2.0 (Kalyaanamoorthy et al., 2017) [21]. The analyses comprised two parallel runs, each consisting of 5,000,000 generations. The initial 25% of the sampled data were discarded as burn-in to ensure convergence of the Markov chain Monte Carlo (MCMC) process. All haplotype sequences of golden pompano and reference sequences were included in the NJ and BI phylogenetic trees.

Distance-based (Automatic Barcode Gap Discovery, ABGD) and tree-based (Bayesian Poisson Tree Processes, bPTP) methods were conducted for further species delimitation: The ABGD analyses (Puillandre et al., 2012) [22] were conducted online (https://bioinfo.mnhn.fr/abi/public/abgd/ (accessed on 10 February 2025)) using the Jukes–Cantor (JC69) model and settings (Pmin = 0.001, Pmax = 0.1, Steps = 100, X = 1.0, Nb bins = 20). The bPTP (Zhang et al., 2013) [23] was performed using the bPTP webtool (https://species.h-its.org (accessed on 10 February 2025)) based on the obtained BI phylogenetic tree in Newick format, with the following parameters: MCMC generations = 200,000, thinning = 100, and burn-in = 0.1.

Table 1. Species, localities, Barcode Index Number (BIN) of BOLD, GenBank accession number and citation information of the reference sequences used in this study.

Species	Locality	Bold Bin	GenBank Accession No.	Citation
Trachinotus africanus Smith, 1967	South Africa	TZMSC062-05	JF494716	Steinke et al., 2016 [24]
	Indonesia, Java	FOAH845-08	N/A	N/A
Trachinotus anak Ogilby, 1909	Australia	FOAC410-05	EF609479	Ward and Holmes, 2007 [25]
	Australia	FOAC409-05	N/A	N/A
Trachinotus baillonii (Lacepède, 1801)	Australia	FOAC407-05	EF609480	Ward and Holmes, 2007 [25]
	China, Zhoushan	GBGCA9146-15	KM245967	Xu et al., 2015 [26]
Trachinotus blochii (Lacepède, 1801)	Australia	FOAC411-05	EF609481	Ward and Holmes, 2007 [25]
	Seychelles	UKFBJ917-08	KF930508	N/A
	China	GBMNA14603-19	KJ184305	Zhang et al., 2016 [27]
	Australia	LIFS650-08	KP194696	Steinke et al., 2017 [28]
Trachinotus botla (Shaw, 1803)	Indonesia	FOAJ894-09	GU673700	N/A
	South Africa	TZMSC524-05	JF494718	Steinke et al., 2016 [24]
	South Africa	TZMSA220-04	JF494722	Steinke et al., 2016 [24]
Trachinotus carolinus (Linnaeus, 1766)	Brazil, Sao Paulo	MFSP926-11	JQ365599	Ribeiro et al., 2012 [29]
	N/A	GBMNA14604-19	KJ556976	Zhang et al., 2016 [30]
	United States, Texas	GBMNE87372-22	ON995519	N/A
Trachinotus coppingeri Günther, 1884	Australia	FOAC406-05	EF609482	Ward and Holmes, 2007 [25]
	Australia	FOAD511-05	N/A	N/A
Trachinotus falcatus (Linnaeus, 1758)	Brazil, Sao Paulo	MFSP394-10	JQ365601	Ribeiro et al., 2012 [29]
	Mexico	N/A	KR086928	N/A
	Mexico	MLIII196-08	N/A	Leyva-Cruz et al., 2016 [31]
Trachinotus goodei Jordan and Evermann, 1896	Brazil, Sao Paulo	MFSP145-09	GU702385	Ribeiro et al., 2012 [29]
Trachinotus goreensis Cuvier, 1832	Nigeria	BAFEN355-10	HM883015	Nwani et al., 2011 [32]
Trachinotus maxillosus Cuvier, 1832	Gambia, Tanji	N/A	KX512710	Damerau et al., 2018 [33]
Trachinotus mookalee Cuvier, 1832	India	GBMIN119993-17	KU296860	N/A
	India	GBMIN130195-17	KU296861	N/A
	India	GBMIN124842-17	KU296862	N/A
Trachinotus ovatus (Linnaeus, 1758)	Turkey	DNATR106-12	JQ624009	N/A
	Turkey	DNATR1776-13	KC501749	Keskin and Atar, 2013 [13]
	Portugal	MLFPI019-09	KJ768314	Landi et al., 2014 [14]
	Israel	BIM405-15	N/A	N/A
Trachinotus ovatus (Linnaeus, 1758)	China, Zhoushan	GBGCA9147-15	KM245969	Xu et al., 2015 [26]
	China, South China Sea	FSCS483-07	EU595325	Zhang and Hanner, 2012 [11]
	China, South China Sea	ANGBF5359-12	JN242717	Zhang and Hanner, 2012 [11]
	China	GBMNA14602-19	KF356397	Xie et al., 2015 [34]
	Central China Market	N/A	KP112476	Shen et al., 2016 [35]
	N/A	ANGBF17718-19	KY802069	Muri et al., 2018 [36]
	Vietnam	ANGBF55875-19	MK227447	N/A
	China, Beibu Gulf	GBMNE78207-22	OP247575	N/A
Trachinotus paitensis Cuvier, 1832	United States, California	ANGBF1237-12	HQ010062	N/A
	Peru	GBMND24296-21	MN880583	Marín et al., 2021 [37]
	Peru	GBMND24300-21	MN880587	Marín et al., 2021 [37]
Trachinotus rhodopus Gill, 1863	Costa Rica	RDFCA397-05	N/A	N/A
Trachinotus stilbe (Jordan and McGregor, 1898)	Ecuador, Galapagos	LIDMA1275-12	N/A	N/A
Lichia amia (Linnaeus, 1758)	Turkey	N/A	KY176514	N/A
	Turkey	N/A	JQ623944	N/A

Table 1. Species, localities, Barcode Index Number (BIN) of BOLD, GenBank accession number and citation information of the reference sequences used in this study.

Species	Locality	Bold Bin	GenBank Accession No.	Citation
Trachinotus africanus Smith, 1967	South Africa	TZMSC062-05	JF494716	Steinke et al., 2016 [24]
	Indonesia, Java	FOAH845-08	N/A	N/A
Trachinotus anak Ogilby, 1909	Australia	FOAC410-05	EF609479	Ward and Holmes, 2007 [25]
	Australia	FOAC409-05	N/A	N/A
Trachinotus baillonii (Lacepède, 1801)	Australia	FOAC407-05	EF609480	Ward and Holmes, 2007 [25]
	China, Zhoushan	GBGCA9146-15	KM245967	Xu et al., 2015 [26]
Trachinotus blochii (Lacepède, 1801)	Australia	FOAC411-05	EF609481	Ward and Holmes, 2007 [25]
	Seychelles	UKFBJ917-08	KF930508	N/A
	China	GBMNA14603-19	KJ184305	Zhang et al., 2016 [27]
	Australia	LIFS650-08	KP194696	Steinke et al., 2017 [28]
Trachinotus botla (Shaw, 1803)	Indonesia	FOAJ894-09	GU673700	N/A
	South Africa	TZMSC524-05	JF494718	Steinke et al., 2016 [24]
	South Africa	TZMSA220-04	JF494722	Steinke et al., 2016 [24]
Trachinotus carolinus (Linnaeus, 1766)	Brazil, Sao Paulo	MFSP926-11	JQ365599	Ribeiro et al., 2012 [29]
	N/A	GBMNA14604-19	KJ556976	Zhang et al., 2016 [30]
	United States, Texas	GBMNE87372-22	ON995519	N/A
Trachinotus coppingeri Günther, 1884	Australia	FOAC406-05	EF609482	Ward and Holmes, 2007 [25]
	Australia	FOAD511-05	N/A	N/A
Trachinotus falcatus (Linnaeus, 1758)	Brazil, Sao Paulo	MFSP394-10	JQ365601	Ribeiro et al., 2012 [29]
	Mexico	N/A	KR086928	N/A
	Mexico	MLIII196-08	N/A	Leyva-Cruz et al., 2016 [31]
Trachinotus goodei Jordan and Evermann, 1896	Brazil, Sao Paulo	MFSP145-09	GU702385	Ribeiro et al., 2012 [29]
Trachinotus goreensis Cuvier, 1832	Nigeria	BAFEN355-10	HM883015	Nwani et al., 2011 [32]
Trachinotus maxillosus Cuvier, 1832	Gambia, Tanji	N/A	KX512710	Damerau et al., 2018 [33]
Trachinotus mookalee Cuvier, 1832	India	GBMIN119993-17	KU296860	N/A
	India	GBMIN130195-17	KU296861	N/A
	India	GBMIN124842-17	KU296862	N/A
Trachinotus ovatus (Linnaeus, 1758)	Turkey	DNATR106-12	JQ624009	N/A
	Turkey	DNATR1776-13	KC501749	Keskin and Atar, 2013 [13]
	Portugal	MLFPI019-09	KJ768314	Landi et al., 2014 [14]
	Israel	BIM405-15	N/A	N/A
Trachinotus ovatus (Linnaeus, 1758)	China, Zhoushan	GBGCA9147-15	KM245969	Xu et al., 2015 [26]
	China, South China Sea	FSCS483-07	EU595325	Zhang and Hanner, 2012 [11]
	China, South China Sea	ANGBF5359-12	JN242717	Zhang and Hanner, 2012 [11]
	China	GBMNA14602-19	KF356397	Xie et al., 2015 [34]
	Central China Market	N/A	KP112476	Shen et al., 2016 [35]
	N/A	ANGBF17718-19	KY802069	Muri et al., 2018 [36]
	Vietnam	ANGBF55875-19	MK227447	N/A
	China, Beibu Gulf	GBMNE78207-22	OP247575	N/A
Trachinotus paitensis Cuvier, 1832	United States, California	ANGBF1237-12	HQ010062	N/A
	Peru	GBMND24296-21	MN880583	Marín et al., 2021 [37]
	Peru	GBMND24300-21	MN880587	Marín et al., 2021 [37]
Trachinotus rhodopus Gill, 1863	Costa Rica	RDFCA397-05	N/A	N/A
Trachinotus stilbe (Jordan and McGregor, 1898)	Ecuador, Galapagos	LIDMA1275-12	N/A	N/A
Lichia amia (Linnaeus, 1758)	Turkey	N/A	KY176514	N/A
	Turkey	N/A	JQ623944	N/A

3. Results and Discussion

We successfully obtained 36 DNA barcode sequences (655 bp in length) of golden pompano from five aquaculture farms. Confined by the homologous lengths of the 46 reference sequences, only the 530 bp fragments shared by all sequences were ultimately taken to construct a phylogenetic tree. Five haplotypes were detected in golden pompano sequences. The first haplotype (hap1) was shared by 27 individuals and the reference sequence of EU595325, JN242717, KF356397, KP112476 and OP247575. The second haplotype (hap2) included one individual and the reference sequence MK227447. The third haplotype (hap3) was only represented by one individual. The fourth haplotype (hap4) consisted of three individuals. Four individuals and the reference sequence KY802069 shared the fifth haplotype (hap5). The five haplotype sequences have been deposited in GenBank, with the accession numbers PV164038-PV164042 (

Table 2. Haplotype distribution of DNA barcode in golden pompano.

Haplotype	Individual No.	GenBank Accession No.
hap1	ZZ2, ZZ4, ZZ5, ZZ6, YJ1, YJ2, YJ3, YJ4, YJ5, YJ6, YJ7, YJ8, YJ9, YJ10, YJ12, LS1, LS3, LS4, LS5, LS6, LS7, ND2, ND4, FCG1, FCG2, FCG3, FCG5, EU595325, JN242717, KF356397, KP112476, OP247575	PV164038
hap2	ZZ1, MK227447	PV164039
hap3	YJ11	PV164040
hap4	ZZ3, LS2, FCG4	PV164041
hap5	FCG6, ZZ7, ND1, ND3, KY802069	PV164042

). The phylogenetic trees constructed in this study included most species (16 species) in the genus Trachinotus (21 species), the species in this genus were covered as many as possible if only there are homologous sequences in public database (Figure 2 and Figure 3). Although only limited information could be provided from comparatively short fragments we used in phylogenetic reconstruction, the sequences from each species could be clustered into independent branches in both the NJ and BI phylogenetic trees (except T. ovatus and T. anak) and the species could be distinguished. For all sequences used in phylogenetic tree construction, the ABGD analysis identified 16 distinct species, while the bPTP analysis delimited 17 species. The difference in the results of the two methods lies in the delimitation of the species T. goodei and T. rhodopus. In the ABGD analysis, the two species were delimited as a single species, indicating a potentially close genetic relationship between them.

All the reference sequences of T. ovatus were clustered into two different branches in the phylogenetic trees with large genetic distance respectively. One group (Group1) consisted of MK227447, KM245969, EU595325, JN242717, KF356397, KP112476, OP247575 and KY802069, which were known to come from Indo-west Pacific except KY802069 (Figure 2 and Figure 3, Table 1). All the golden pompano samples we collected from China were also be included in this group. Another group (Group2) included KC501749, JQ624009, BIM405-15 and KJ768314, which were all from East Atlantic (Figure 2 and Figure 3, Table 1). It could be inferred that the so-called Trachinotus ovatus represents two independent species that are distantly related. In the ABGD and bPTP analyses, the two groups were also delimited into two different species. Linnaeus (1758) [8] named Trachinotus ovatus as Gasterosteus ovatus for the first time in 1758 and documented its habitat is in Asia, while the habitat description is considered by Eschmeyer’s catalog of fishes to be a possible error record for the eastern Atlantic [38]. Kendall and Goldsborough (1911) [9] placed the species in the genus Trachinotus and documented that its type locality is in Tonga (Oceania). This appears to support the validity of the naming of Trachinotus ovatus from the Indo-west Pacific, and the so-called Trachinotus ovatus from the East Atlantic, which have 3–5 vertically elongated black spots on the anterior half of their lateral line, may represent a cryptic Trachinotus species, while its taxonomic status and whether it needs to be renamed requires further research. In Group1, between the golden pompano samples we collected and the reference sequences of T. ovatus, there are three shared haplotypes (hap1, hap2, and hap5) and the mean distance within group is only 0.1%, which is much smaller than the species-level divergence (2%) [39]. The above results support that the golden pompano in China can be provisionally identified as the species Trachinotus ovatus (Linnaeus, 1758).

The reference sequences of the Oyster pompano (Trachinotus anak) clustered with the monophyletic clade of Group1 in the phylogenetic trees (Figure 2 and Figure 3). Although there was no shared haplotype between them, the genetic distance between T. anak and Group1 (0.7%) was smaller than 2%, which revealed an intraspecific difference [39]. The ABGD and bPTP analyses also indicated that they are the same species. These implied that the Trachinotus anak might be the junior synonyms of Trachinotus ovatus (Indo-west Pacific type) considering the principle of priority for naming species. However, the above results only provide limited evidence, and further integrated taxonomic research are needed to solve the problem of the validity of Trachinotus anak.

The sequences of the Trachinotus ovatus and Trachinotus blochii were completely divided into two different monophyletic clades in phylogenetic trees and all the golden pompano samples we collected from China clustered with Trachinotus ovatus (Indo-west Pacific type) (Figure 2 and Figure 3). The ABGD and bPTP analyses also inferred that they are different species. These results showed a relatively far genetic distance between the golden pompano and Trachinotus blochii, while the golden pompano was most often misidentified as Trachinotus blochii in China [5,40]. We infer that it is because the similar body coloration of the two species and there used to be small scale aquaculture production of T. blochii in China [10,40,41].

Due to similar morphological character with Trachinotus ovatus, the Indian pompano (Trachinotus mookalee) with a native distribution from western Indian Ocean to the western Pacific Ocean is considered to be the golden pompano sometimes [6,40]. To clarify the naming of golden pompano, the reference sequences of Trachinotus mookalee that from India, one of the main producing areas of the species, were used in phylogenetic reconstruction. The results showed that the sequences of the Trachinotus mookalee and the cultured golden pompano from China were completely divided into two different monophyletic clades (Figure 2 and Figure 3), which revealed the inconsistency in species division of them. The ABGD and bPTP analyses also showed the same species delimitation.

Based on the above findings, we suggest that the golden pompano should be referring in particular to the species Trachinotus ovatus (Linnaeus, 1758) in order to avoid ambiguity. It should be noted that this study has only examined the DNA barcoding of golden pompano, while the taxonomic status and nomenclature of the so-called Trachinotus ovatus (Indo-west Pacific type and East Atlantic type) and the species Trachinotus anak deserve to be further studied based on type specimens and morphological character analysis. In this study, DNA barcoding approach has been used as an effective solution to identify species. However, what cannot be ignored is that there is a serious limitation to the utility of DNA barcoding as a molecular diagnostics tool for species identification. That is, conflicting identifications made by different labs may cause inadequate priori identification of specimens and can compromise the effectiveness of reference libraries [42,43]. Therefore, we have selected the DNA barcode reference sequences which could present a bibliography of references or provide supporting information and voucher specimens as far as possible to ensure the accuracy of identification in this study. These results are valuable for clarifying what species the golden pompano is referred to as and forming a consistent understanding about the naming of the species, which is of great significance to the protection and sustainable development of pompano germplasm resources.

4. Conclusions

To determine the correct scientific name of golden pompano, a commercially valuable marine cultured fish species in China, the DNA barcoding technique was employed in this study. Through the examination of 36 individuals from five major aquaculture regions, we identified five haplotypes and constructed NJ and BI phylogenetic trees incorporating reference sequences from multiple Trachinotus species. The ABGD and bPTP methods were conducted for further species delimitation: Our results demonstrate that the cultured golden pompano in China can be accurately identified as Trachinotus ovatus (Indo-west Pacific type), distinct from other closely related species such as T. blochii, T. mookalee, and T. anak, and the so-called T. ovatus from the East Atlantic may represent a cryptic species. Additionally, the potential synonymy between T. ovatus and T. anak has been identified, highlighting the need for more integrated taxonomic studies. By selecting well-documented reference sequences and ensuring rigorous validation, we have contributed to a clearer understanding of systematic classification within the genus Trachinotus. The results are expected to clarify the valid scientific naming of golden pompano and benefit diversity conservation and resource development of pompano fish.