Research Article |
Corresponding author: Hung-Du Lin ( varicorhinus@hotmail.com ) Corresponding author: Yun-Rong Yan ( tuna_ps@126.com ) Academic editor: Yahui Zhao
© 2022 Mu-Rong Yi, Kui-Ching Hsu, Sui Gu, Xiong-Bo He, Zhi-Sen Luo, Hung-Du Lin, Yun-Rong Yan.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Yi M-R, Hsu K-C, Gu S, He X-B, Luo Z-S, Lin H-D, Yan Y-R (2022) Complete mitogenomes of four Trichiurus species: A taxonomic review of the T. lepturus species complex. ZooKeys 1084: 1-26. https://doi.org/10.3897/zookeys.1084.71576
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Four Trichiurus species, T. japonicus, T. lepturus, T. nanhaiensis, and T. brevis, from the coasts of the China Seas, have been identified and their entire mitochondrial genomes (mitogenomes) have been sequenced by next-generation sequencing technology. A comparative analysis of five mitogenomes was conducted, including the mitogenome of T. gangeticus. The mitogenomes contained 16.568–16.840 bp and encoded 36 typical mitochondrial genes (13 protein-coding, 2 ribosomal RNA-coding, and 21 transfer RNA-coding genes) and two typical noncoding control regions. Although tRNAPro is absent from Trichiurus mitogenomes, when compared with the 22 tRNAs reported in other vertebrates, the gene arrangements in the mitogenomes of the studied species are consistent with those in most teleost mitogenomes. The full-length sequences and protein-coding genes (PCGs) in the mitogenomes of the five species had obvious AT biases and negative GC skew values. Our study indicate that the specimens in the Indian Ocean are neither T. lepturus nor T. nanhaiensis but they are T. gangeticus; the Trichiurus species composition in the Indian Ocean is totally different from that in Pacific and Atlantic oceans; there are at least two Trichiurus species in Indian Ocean; and the worldwide systematics and diversity of the genus Trichiurus need to be reviewed.
Characterization, mitogenome, molecular tool, phylogeny, taxonomy, Trichiurus
The cutlassfishes include ten genera and 47 species in Eschmeyer’s Catalog of Fishes (ECoF,
According to ECoF, these eleven valid species are divided between two species complexes, the T. lepturus complex and the T. russelli complex. The T. lepturus complex is referred to as the large-headed or long-tailed species complex. This species complex, which has the anal opening positioned vertically at the 38th–41st dorsal fin rays, includes seven species: T. lepturus Linnaeus, 1758, T. japonicus, T. auriga Klunzinger, 1884, T. nitens, T. gangeticus Gupta, 1966, T. margarites Li, 1992 and T. nanhaiensis Wang & Xu, 1992. The T. russelli complex is referred to as the short-tailed species complex, and the anal opening is positioned vertically at the 34th and 35th dorsal fin rays (
Many studies have suggested that Clupea haumela Fabricius, 1775 is a synonym of T. lepturus (
The accurate identification of species is important both for scientists and the broader community. However, correctly identifying species remains a major challenge for the general public.
In this study, we completed four tasks. First, COI sequences were used to identify Trichiurus species to determine the number of species found along the coast of China. Second, the complete mitogenomes of four Trichiurus species in the China Seas were sequenced using next-generation sequencing. Third, we obtained the mitogenome sequences of the family Trichiuridae from the NCBI database (https://www.ncbi.nlm.nih.gov) to clarify the systematics of the genus Trichiurus and to facilitate comparison of the molecular evolutionary characteristics between Trichiurus species and other cutlassfishes. Finally, traditional caliper measurements were performed, which identified 14 landmarks that were used to evaluate morphological differences among Trichiurus species. These results provide further insight into the systematics and diversity of the genus Trichiurus.
Our teams sampled Trichiurus specimens from the China Seas, including the Yellow Sea, East China Sea, and South China Sea in October 2017 and August 2019 by longline, gill net, and trawl net with fishermen (Fig.
A Eighteen sampling localities of the genus the Trichiurus along the Chinese coast and the species composition after our surveys. Refer to Suppl. material
A portion of the muscle tissues from 1.311 specimens was stored in 100% ethanol. Total genomic DNA was extracted from muscle tissue using a Genomic DNA Purification Kit (Gentra Systems, Valencia, CA). The COI gene was amplified by polymerase chain reaction (PCR) using the primers Fish-F2 (5´-ACCTCTGTGTGTGGGGCTAC-3´) and Fish-R2 (5´-GTGATGCATTGGCTTGAAA-3´) (
Next-generation sequencing (NGS) was performed to obtain complete mitogenome sequences. Complete mitogenomes were obtained from high-throughput sequencing with a HiSeqX Ten platform (Illumina, San Diego, CA) with a paired-end, 150-bp approach. All the reads were mapped to the full mitogenome reference sequences of other Trichiurus species (Table
Species | Accession no. | Genome size | References |
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Trichiurus japonicus | EU339148 | 16.796 bp |
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MK292708 | 16.798 bp |
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MW719077 | 16.685 bp | This study | |
T. haumela | MH846121 | 16.855 bp |
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T. lepturus | MK333401 | 16.840 bp |
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T. nanhaiensis | MW719078 | 16.568 bp | This study |
JX477078 | 17.060 bp |
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MW719076 | 16.801 bp | This study | |
T. brevis | MW694877 | 16.733 bp | This study |
Benthodesmus tenuis | AP012522 | 16.864 bp |
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Aphanopus carbo | AP012944 | 16.406 bp |
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Evoxymetopon poeyi | AP012509 | 16.475 bp |
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Assurger anzac | AP012508 | 16.510 bp |
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The relative synonymous codon usage (RSCU), nonsynonymous codon usage (Ka) and synonymous codon usage (Ks) of all PCGs were analyzed using DnaSP. Comparison of the rates of Ka/Ks provides insight into changes in selective pressure: Ka/Ks values > 1 indicate positive selection; Ka/Ks = 1 indicates neutral selection; and Ka/Ks < 1 indicates negative or purifying selection. Some mitogenomes of the family Trichiuridae were downloaded from GenBank (NCBI database, Table
Measurements were referred to the truss network (
A total of 1.311 specimens were collected. Species were first identified by morphology. Two species groups were recognized, the T. lepturus complex, which has the anal opening positioned vertically at the 38th–41st dorsal fin rays, and the T. russelli complex, which has the anal opening positioned vertically at the 34th and 35th dorsal fin rays (
Trichiurus japonicas is distributed in the China Sea; T. lepturus, T. nanhaiensis, and T. brevis are distributed in the South China Sea. The results from the morphological and molecular data were the same. However, our study revealed that T. lepturus is very rare in the South China Sea (Fig.
After identifying species by morphology and DNA barcoding, the complete mitochondrial genomes of four Trichiurus species were sequenced (Fig.
The p-distance based on sequences of partial COI (below) and mitogenome (above, excluding d-loop in brackets). Bold indicates the mean COI divergence within groups.
T. japonicus | T. auriga | T. lepturus | T. nanhaiensis | T. gangeticus | T. brevis | |
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T. japonicus | 0.0054 | – | 0.0984 (0.0965) | 0.1160 (0.1127) | 0.1140 (0.1114) | 0.1306 (0.1280) |
T. auriga | 0.0435 | 0.0069 | – | – | – | - |
T. lepturus | 0.1078 | 0.1149 | 0.0333 | 0.1127 (0.1118) | 0.1119 (0.1107) | 0.1310 (0.1288) |
T. nanhaiensis | 0.1277 | 0.1171 | 0.1255 | 0.0037 | 0.0507 (0.0476) | 0.1308 (0.1244) |
T. gangeticus | 0.1251 | 0.1156 | 0.1093 | 0.0750 | 0.0090 | 0.1331 (0.1279) |
T. brevis | 0.1600 | 0.1505 | 0.1475 | 0.1282 | 0.1357 | 0.0013 |
After identifying species by morphological characters and phylogenetic analysis, traditional caliper measurements were performed, which produced 14 landmark sites (a–n, Fig.
Measurement (cm) | Mean ± S.D. | |||
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T. japonicus | T. lepturus | T. nanhaiensis | T. brevis | |
Total length [D(i,n)*] | 74.7 ± 12.8 | 79.8 ± 6.2 | 55.6 ± 9.2 | 50.6 ± 7.3 |
D(i,m) | 23.7 ± 0.6 | 30.5 ± 0.2 | 20.5 ± 0.2 | 28.0 ± 0.3 |
D(i,l) | 8.7 ± 2.6 | 11.4 ± 1.0 | 7.8 ± 0.8 | 6.4 ± 1.2 |
D(m,n) | 50.8 ± 10.5 | 49.7 ± 5.0 | 35.5 ± 5.2 | 32.8 ± 4.6 |
D(i,j) | 3.0 ± 1.1 | 3.8 ± 0.5 | 2.6 ± 0.3 | 2.2 ± 0.4 |
D(j,k) | 1.3 ± 0.4 | 1.9 ± 0.1 | 1.1 ± 0.2 | 1.0 ± 0.1 |
D(k,l) | 4.4 ± 1.0 | 5.7 ± 0.5 | 4.1 ± 0.4 | 3.3 ± 0.6 |
D(a,b) | 5.2 ± 1.6 | 5.6 ± 0.7 | 5.3 ± 0.5 | 3.9 ± 1.0 |
D(a,c) | 8.3 ± 1.8 | 11.0 ± 1.0 | 7.4 ± 0.9 | 6.1 ± 1.0 |
D(a,d) | 6.0 ± 2.0 | 8.1 ± 0.7 | 5.9 ± 0.7 | 4.4 ± 0.7 |
D(b,c) | 3.9 ± 1.5 | 5.8 ± 0.6 | 2.8 ± 0.4 | 2.5 ± 0.7 |
D(b,d) | 3.9 ± 1.2 | 5.1 ± 0.5 | 4.0 ± 0.3 | 3.3 ± 0.5 |
D(b,e) | 28.6 ± 4.8 | 24.5 ± 2.2 | 17.4 ± 1.1 | 13.8 ± 2.8 |
D(b,f) | 19.2 ± 5.0 | 25.1 ± 1.7 | 18.2 ± 1.3 | 14.4 ± 3.0 |
D(c,d) | 3.9 ± 0.8 | 4.6 ± 0.5 | 3.4 ± 0.5 | 3.1 ± 0.5 |
D(d,e) | 18.2 ± 4.6 | 23.1 ± 1.9 | 17.5 ± 1.3 | 14.2 ± 2.6 |
D(d,f) | 17.9 ± 5.8 | 22.7 ± 1.8 | 17.0 ± 1.4 | 13.9 ± 2.6 |
D(d,o) | 3.8 ± 0.3 | 4.1 ± 0.2 | 4.1 ± 0.2 | 3.3 ± 0.3 |
D(e,f) | 4.2 ± 0.1 | 4.8 ± 0.5 | 4.7 ± 0.4 | 3.6 ± 0.6 |
D(g,h) | 1.3 ± 0.4 | 1.7 ± 0.3 | 1.0 ± 0.2 | 0.9 ± 0.1 |
D(i,n)/D(i,m) | 3.08 ± 0.32 | 2.61 ± 0.09 | 2.74 ± 0.18 | 2.86 ± 0.11 |
D(m,n)/D(i,m) | 2.08 ± 0.32 | 1.62 ± 0.09 | 1.74 ± 0.18 | 1.86 ± 0.11 |
D(i,m)/D(e,f) | 5.59 ± 0.57 | 6.29 ± 0.45 | 4.47 ± 0.79 | 4.91 ± 0.43 |
D(m,n)/D(e,f) | 11.60 ± 1.79 | 10.29 ± 0.87 | 7.77 ± 1.38 | 9.13 ± 0.69 |
D(i,l)/D(d,o) | 2.22 ± 0.14 | 2.73 ± 0.13 | 1.92 ± 0.18 | 2.55 ± 0.13 |
D(d,o)/D(g,h) | 3.10 ± 0.42 | 2.42 ± 0.36 | 3.88 ± 0.67 | 3.57 ± 0.56 |
D(d,o)/D(j,k) | 3.00 ± 0.42 | 2.20 ± 0.32 | 3.57 ± 0.44 | 3.31 ± 0.41 |
Sample size | 75 | 27 | 27 | 96 |
The simple regression and the boxplot analysis in T. japonicus (blue), T. lepturus (orange) and T. nanhaiensis (grey) A Total length [D(i,n)] and Preanal length [D(i,m)] B Caudal length [D(m,n)] and Body depth at anus [D(e,f)] C Head depth [D(d,o)] and Orbital length [D(j,k)] and D Head length [D(i,l)] and Head depth [D(d,o)]. The landmarks are illustrated in Fig.
The mitogenomes of all four Trichiurus species contain 36 mitochondrial genes (13 PCGs, 21 tRNA-coding genes and 2 rRNA-coding genes) and two noncoding regions (OL and d-loop, control region) (Table
Gene | Position | Codons | anticodon | Strand | Intergenic nucleotides | ||
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From | To | Start | Stop | ||||
tRNAPhe | 1/1/1/1 | 69/69/69/70 | GAA | H | 0/0/0/-1 | ||
12S rRNA | 70/70/70/70 | 1027/1027/1026/1028 | H | 0/0/0/0 | |||
tRNAVal | 1028/1028/1027/1029 | 1098/1098/1097/1099 | TAC | H | 0/0/0/0 | ||
16S rRNA | 1099/1099/1098/1100 | 2836/2840/2824/2830 | H | 0/0/0/0 | |||
tRNALeu | 2837/2841/2825/2831 | 2910/2914/2898/2904 | TAA | H | 0/0/0/0 | ||
ND1 | 2921/2923/2910/2916 | 3899/3894/3884/3890 | TTA | TAA | H | 10/9/11/11 | |
tRNAIle | 3900/3900/3890/3895 | 3969/3969/3959/3965 | GAT | H | 0/5/5/5 | ||
tRNAGln | 3968/3969/3959/3965 | 4038/4039/4029/4035 | TTG | L | -2/-1/-1/-1 | ||
tRNAMet | 4038/4039/4029/4035 | 4108/4109/4099/4105 | CAT | H | -1/-1/-1/-1 | ||
ND2 | 4110/4111/4101/4107 | 5156/5157/5147/5153 | ATG | TAA | H | 1/1/1/1 | |
tRNATrp | 5156/5157/5147/5153 | 5228/5229/5220/5226 | TCA | H | -1/-1/-1/-1 | ||
tRNAAla | 5229/5231/5222/5229 | 5297/5299/5290/5297 | TGC | L | 0/1/1/2 | ||
tRNAAsn | 5299/5301/5292/5299 | 5371/5373/5364/5371 | GTT | L | 1/1/1/1 | ||
OL | 5374/5376/5367/5374 | 5403/5405/5396/5403 | L | 2/2/2/2 | |||
tRNACys | 5403/5405/5396/5403 | 5468/5470/5461/5468 | GCA | L | -1/-1/-1/-1 | ||
tRNATyr | 5469/5471/5462/5469 | 5535/5537/5528/5535 | GTA | L | 0/0/0/0 | ||
COI | 5537/5539/5530/5537 | 7087/7089/7080/7087 | GTG | TAA | H | 1/1/1/1 | |
tRNASer | 7088/7090/7081/7088 | 7158/7160/7151/7158 | TGA | L | 0/0/0/0 | ||
tRNAAsp | 7162/7164/7154/7162 | 7234/7236/7226/7230 | GTC | H | 3/3/2/3 | ||
COII | 7236/7240/7229/7235 | 7926/7930/7919/7925 | ATG | TAA | H | 1/3/2/4 | |
tRNALys | 7927/7931/7920/7926 | 7998/8003/7992/7998 | TTT | H | 0/0/0/0 | ||
ATP8 | 7999/8005/7995/8000 | 8166/8172/8162/8167 | ATG | TAA | H | 0/1/2/1 | |
ATP6 | 8157/8163/8153/8158 | 8840/8846/8836/8841 | ATG | TAA | H | -10/-10/-10/-10 | |
COIII | 8840/8846/8836/8841 | 9625/9631/9621/9626 | ATG | TAA | H | -1/-1/-1/-1 | |
tRNAGly | 9625/9631/9621/9626 | 9693/9699/9689/9694 | TCC | H | -1/-1/-1/-1 | ||
ND3 | 9694/9700/9690/9695 | 10044/10050/10040/10045 | ATT | TAA | H | 0/0/0/0 | |
tRNAArg | 10043/10049/10039/10044 | 10111/10117/10107/10112 | TCG | H | -2/-2/-2/-2 | ||
ND4L | 10112/10118/10108/10113 | 10408/10414/10404/10409 | ATG | TAA | H | 0/0/0/0 | |
ND4 | 10402/10408/10398/10403 | 11772/11778/11768/11773 | ATG | AGA | H | -7/-7/-7/-7 | |
tRNAHis | 11781/11787/11776/11781 | 11849/11856/11844/11849 | GTG | H | 8/8/7/8 | ||
tRNASer | 11850/11857/11845/11850 | 11920/11927/11915/11920 | GCT | H | 0/0/0/0 | ||
tRNALeu | 11923/11930/11918/11923 | 11994/12001/11989/11994 | TAG | H | 2/2/2/2 | ||
ND5 | 11997/12004/11992/11997 | 13877/13884/13872/13877 | ATG | TAA | H | 2/2/2/2 | |
ND6 | 13874/13881/13869/13874 | 14395/14402/14390/14395 | ATG | TAG | L | -4/-4/-4/-4 | |
tRNAGlu | 14396/14403/14391/14396 | 14464/14471/14459/14464 | TTC | L | 0/0/0/0 | ||
Cyt b | 14469/14476/14464/14469 | 15609/15616/15604/15609 | ATG | TAA | H | 4/4/4/4 | |
tRNAThr | 15610/15617/15605/15610 | 15683/15692/15678/15683 | TGT | H | 0/0/0/0 | ||
d-loop | 15684/15693/15679/15684 | 16685/16568/16801/16733 | H |
Nucleotide compositions of T. japonicus, T. lepturus, T. nanhaiensis, T. brevis, and T. gangeticus.
Whole genome | Protein-coding genes | Light tRNAs1 | Heavy tRNAs2 | 2 rRNA | d-loop | ||
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AT% | T. japonicus | 55.0 | 53.4 | 56.9 | 53.4 | 52.4 | 66.3 |
T. lepturus | 55.1 | 54.0 | 56.4 | 54.1 | 52.3 | 64.4 | |
T. nanhaiensis | 54.4 | 53.3 | 55.0 | 54.1 | 52.5 | 66.7 | |
T. gangeticus 3 | 54.3 | 53.5 | 54.5 | 54.5 | 52.3 | 67.1 | |
T. brevis | 54.6 | 54.1 | 55.3 | 53.5 | 52.6 | 63.5 | |
AT-skew | T. japonicus | 0.06006 | -0.05230 | 0.11991 | 0.11993 | 0.20156 | 0.04072 |
T. lepturus | 0.04465 | -0.06827 | 0.09293 | 0.11745 | 0.21332 | 0.00621 | |
T. nanhaiensis | 0.05775 | -0.05444 | 0.11080 | 0.11620 | 0.21268 | -0.01349 | |
T. gangeticus 3 | 0.04891 | -0.05679 | 0.10329 | 0.10850 | 0.21337 | -0.03428 | |
T. brevis | 0.06789 | -0.04365 | 0.11892 | 0.13515 | 0.23956 | 0.02992 | |
GC-skew | T. japonicus | -0.17695 | -0.29641 | -0.05917 | -0.20854 | -0.16176 | -0.11573 |
T. lepturus | -0.17258 | -0.29303 | -0.03277 | -0.23999 | -0.15737 | -0.15169 | |
T. nanhaiensis | -0.18480 | -0.30426 | -0.04978 | -0.25498 | -0.17127 | -0.09910 | |
T. gangeticus 3 | -0.18396 | -0.30589 | -0.05000 | -0.23819 | -0.16780 | -0.11246 | |
T. brevis | -0.19633 | -0.30975 | -0.07410 | -0.24391 | -0.19198 | -0.16164 |
The total lengths of PCGs in the five Trichiurus species ranged from 11.530 to 11538 bp, accounting for 68.47%–69.59% of the entire mitogenome. The mitogenomes could be translated into 3.809–3.810 amino acid-coding codons, excluding stop codons. ND5 and ATP8 were the largest and smallest genes, respectively. The majority of PCGs start with an NTN (ATG/GTG/ATT) start codon and are terminated with the stop codons TAA, TAG, and AGA (Table
To better understand the role of selection in the evolution of the PCGs, the Ka/Ks value of each PCG was calculated (Fig.
A Mean evolutionary rates for each protein coding gene in mitogenomes of five Trichiurus species B Evolutionary rates of ND6 gene of five Trichiurus species. C Evolutionary rates of Ka/Ks in ATP8 gene of five Trichiurus species. Indicated the rates of non-synonymous substitutions to the rate of synonymous substitutions (ka/ks). T. japonicus (TJ), T. lepturus (TL), T. nanhaiensis (TN), T. gangeticus (TG) and T. brevis (TB).
The lengths of 16S rRNA genes ranged from 1.725 (T. gangeticus) to 1.742 (T. lepturus), whereas those of 12S rRNAs ranged from 957 (T. gangeticus and T. nanhaiensis) to 959 (T. brevius). These rRNA genes are located between tRNAPhe and tRNALeu and are separated by tRNAVal. The AT content of the rRNA genes ranged from 52.3% to 52.6% (Table
To determine molecular markers that could be used to examine the phylogeny and identify species, the overall interspecific and intergeneric p-distance was used to describe the evolutionary rate of two rRNA-coding genes, 13 PCGs and the mitogenome, excluding the d-loop region (Fig.
The p-distance (*10-2) between Trichiurus species (interspecific) and between genera within Trichiuridae (intergeneric) in each gene and mitogenome (excluding d-loop). T. japonicus (TJ), Trichiurus lepturus (TL), Trichiurus nanhaiensis (TN), T. gangeticus (TG), Trichiurus brevis (TB), Trichiurus (T), Benthodesmus (B), Aphanopus (C), Evoxymetopon (E), and Assurger (A).
12S | 16S | atp6 | atp8 | COI | COII | COIII | cytb | ND1 | ND2 | ND3 | ND4 | ND4L | ND5 | ND6 | genome | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
TG/TB | 9.4 | 3.9 | 17.0 | 17.3 | 12.4 | 14.6 | 8.3 | 14.1 | 13.6 | 15.0 | 15.5 | 17.7 | 13.8 | 16.4 | 23.0 | 12.8 |
TG/TJ | 6.2 | 6.2 | 12.4 | 11.9 | 10.5 | 8.8 | 8.0 | 11.4 | 14.3 | 14.5 | 13.2 | 14.6 | 12.8 | 13.0 | 20.3 | 11.1 |
TG/TL | 6.5 | 6.6 | 14.5 | 13.1 | 9.4 | 7.7 | 8.4 | 12.6 | 14.9 | 14.8 | 14.6 | 14.0 | 12.1 | 11.8 | 20.7 | 11.1 |
TG/TN | 1.4 | 1.5 | 7.2 | 4.2 | 5.4 | 3.6 | 3.4 | 7.2 | 5.4 | 7.0 | 6.3 | 6.9 | 3.7 | 5.7 | 7.3 | 4.8 |
TB/TJ | 7.6 | 7.4 | 14.8 | 15.5 | 13.2 | 13.9 | 10.3 | 13.2 | 16.8 | 14.9 | 16.5 | 15.7 | 16.8 | 15.3 | 17.8 | 12.8 |
TB/TL | 8.3 | 7.7 | 19.2 | 19.6 | 12.8 | 15.3 | 10.7 | 13.2 | 15.7 | 15.6 | 15.1 | 15.2 | 14.8 | 14.1 | 19.7 | 12.9 |
TB/TN | 9.4 | 2.8 | 16.7 | 18.5 | 11.5 | 14.3 | 9.5 | 14.3 | 13.0 | 13.5 | 17.4 | 16.8 | 15.5 | 16.1 | 24.1 | 12.4 |
TJ/TL | 4.6 | 4.9 | 12.1 | 10.7 | 9.4 | 9.0 | 9.7 | 10.3 | 15.1 | 11.1 | 10.8 | 12.0 | 10.4 | 12.2 | 14.2 | 9.7 |
TJ/TN | 6.4 | 6.4 | 11.1 | 13.1 | 9.7 | 8.3 | 8.9 | 11.9 | 14.3 | 16.0 | 14.5 | 13.9 | 14.8 | 13.7 | 21.1 | 11.3 |
TL/TN | 6.5 | 6.9 | 14.5 | 15.5 | 9.6 | 7.5 | 9.4 | 12.5 | 14.7 | 15.3 | 15.7 | 13.1 | 13.5 | 11.9 | 20.9 | 11.2 |
T/B | 16.0 | 18.1 | 34.0 | 47.0 | 19. | 24.2 | 19.9 | 22.6 | 23.3 | 25.3 | 26.6 | 26.6 | 22.6 | 34.4 | 31.1 | 24.1 |
T/C | 15.2 | 17.0 | 31.4 | 43.3 | 18.9 | 22.1 | 18.9 | 24.3 | 23.5 | 23.6 | 26.5 | 25.3 | 23.0 | 31.7 | 30.0 | 22.9 |
T/E | 14.0 | 15.4 | 30.7 | 40.6 | 17.5 | 20.4 | 16.3 | 20.4 | 24.3 | 23.8 | 25.2 | 26.0 | 23.0 | 28.8 | 27.3 | 21.5 |
T/A | 14.0 | 16.0 | 31.5 | 44.3 | 18.3 | 20.4 | 17.6 | 21.2 | 23.5 | 24.0 | 23.1 | 27.5 | 22.3 | 29.1 | 26.9 | 21.9 |
B/C | 7.6 | 7.0 | 21.6 | 26.3 | 13.9 | 17.1 | 12.9 | 19.5 | 14.4 | 15.2 | 21.5 | 15.2 | 15.4 | 28.7 | 19.3 | 16.1 |
B/E | 9.7 | 9.1 | 25.1 | 35.7 | 17.0 | 19.9 | 16.8 | 20.9 | 16.9 | 19.6 | 22.6 | 17.7 | 17.1 | 26.4 | 24.3 | 18.2 |
B/A | 11.6 | 10.1 | 24.9 | 37.4 | 16.4 | 20.3 | 15.9 | 20.7 | 17.5 | 18.5 | 26.4 | 20.2 | 19.1 | 27.9 | 25.5 | 18.9 |
C/E | 7.2 | 6.5 | 20.2 | 34.5 | 16.4 | 18.2 | 14.4 | 22.2 | 16.7 | 17.7 | 21.8 | 17.0 | 18.1 | 22.4 | 23.0 | 16.7 |
C/A | 7.7 | 7.3 | 21.8 | 34.5 | 15.9 | 17.2 | 15.3 | 24.2 | 17.5 | 17.4 | 20.6 | 19.5 | 18.8 | 23.3 | 23.4 | 17.0 |
E/A | 5.6 | 5.4 | 15.4 | 25.7 | 14.2 | 15.1 | 13.5 | 15.4 | 16.2 | 15.1 | 20.3 | 17.9 | 15.4 | 17.2 | 16.5 | 13.5 |
The mitogenomes of Trichiurus species encode 36 typical mitochondrial genes (13 protein-coding, 2 ribosomal RNA-coding genes, and 21 transfer RNA-coding genes) and two typical noncoding control regions, the d-loop and origin of the light strand (OL) (Table
In addition, our study found that the tRNAPro gene was absent in the Trichiurus mitogenomes. Previous studies of the complete mitogenomes of Trichiurus species have also obtained similar findings (e.g.,
Because the systematics of many species remain unresolved, many studies have employed molecular, phylogenetics and DNA barcoding approaches (e.g.,
Moreover, variation in the Ka/Ks values was greater for ATP8 than for other genes (Fig.
The taxonomy of the genus Trichiurus remains unresolved because of the high degree of morphological similarity within the genus in terms of bodily appearance and silvery coloration. Our study also showed that identifying Trichiurus species by morphological characters is very difficult (Fig.
In addition, the results suggested that specimens in the Indian Ocean (MK333401 in
Accurate species identification is important for fishery purposes. The current study represents the first comparative mitogenomic and phylogenetic analysis within Trichiurus and provides new insight into the mitogenomic features and evolution of fishes. Our study suggested that (1) it is difficult to identify species of T. lepturus complex by morphology; (2) T. japonicus is a valid species; and (3) the specimens in Indian Ocean are neither T. lepturus nor T. nanhaiensis. Furthermore,
This work was supported by the grants from National Key R&D Program of China (Grant Number: 2018YFD0900905), Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), (Grant Number: ZJW-2019-08), Science and Technology Plan Projects of Guangdong Province, China (Grant Number: 2018B030320006), Guangdong Basic and Applied Basic Research Foundation (Grant Number: 2019B1515120064) and Marine Economy Development Special Foundation of Department of Natural Resources of Guangdong Province (Grant Number: GDNRC [2020]052). We are grateful to the anonymous referees for their constructive comments.
Table S1–S4, Figure S1, S2
Data type: docx file
Explanation note: Table S1. Sample sizes of the genus Trichiurus in 18 sampling locations in Figure