Research Article |
Corresponding author: Renyi Zhang ( zhangrenyi@gznu.edu.cn ) Academic editor: Tihomir Stefanov
© 2022 Renyi Zhang, Lei Deng, Xiaomei Lv, Qian Tang.
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:
Zhang R, Deng L, Lv X, Tang Q (2022) Complete mitochondrial genomes of two catfishes (Siluriformes, Bagridae) and their phylogenetic implications. ZooKeys 1115: 103-116. https://doi.org/10.3897/zookeys.1115.85249
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The mitochondrial genome (mitogenome) has been widely used as a molecular marker to investigate phylogenetic analysis and evolutionary history in fish. However, the study of mitogenomes is still scarce in the family Bagridae. In this study, the mitogenomes of Tachysurus brachyrhabdion and T. gracilis were sequenced, annotated, and analyzed. The mitogenomes were found to be 16,532 bp and 16,533 bp, respectively, and each contained 37 typical mitochondrial genes, which are 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. All PCGs begin with the codon ATG, except for the cytochrome c oxidase subunit 1 (COI) gene, while seven PCGs end with an incomplete termination codon. All tRNA genes can fold into their typical cloverleaf secondary structures, except for tRNASer(AGY), which lacks the dihydrouracil arm. The Ka/Ks ratios for all PCGs are far lower than one. Phylogenetic analyses based on Bayesian inference (BI) and maximum likelihood (ML) showed that the two clades in Bagridae excluded Rita rita. The monophyly of Tachysurus supports previous research and the traditional classification that Leiocassis, Pseudobagrus, Pelteobagrus, and Tachysurus belong to one genus (Tachysurus). These findings provide a phylogenetic basis for future phylogenetic and taxonomic studies of Bagridae.
bagrid catfish, mitogenome, phylogenetic analysis, Tachysurus brachyrhabdion, Tachysurus gracilis
The family Bagridae, commonly known as bagrid catfish, is widely distributed in Asia and Africa, with about 225 species in 19 genera (
Tachysurus brachyrhabdion Cheng, Ishihara & Zhang, 2008 was firstly named Pseudobagrus brachyrhabdion in 2008 (
Mitochondria are eukaryotic organelles that play essential roles in oxidative phosphorylation and other biochemical functions. Similar to other vertebrates, fish mitochondrial DNA (mtDNA) is a circular double-stranded molecule, and it is independent of the nuclear genome (
In this study, the mitochondrial genomes of two catfishes (T. brachyrhabdion and T. gracilis) were sequenced, assembled, and compared to reveal their evolutionary relationship. These mitochondrial genomes will provide a phylogenetic basis for future phylogenetic and taxonomic studies of Bagridae.
Specimens of T. brachyrhabdion and T. gracilis were collected from Jiangkou County (27°46'12"N, 108°46'56"E) and Liping County (26°17'51"N, 109°7'25"E), Guizhou, China, respectively. The samples were preserved in 95% ethanol and stored at -20 °C until DNA extraction. Specimens were recognized as T. brachyrhabdion and T. gracilis by traditional morphology. The voucher specimens were deposited in the fish specimen room, School of Life Science, Guizhou Normal University under the voucher numbers GZNUSLS201909001~006 and GZNUSLS201907029~030 for T. brachyrhabdion and GZNUSLS202005279 for T. gracilis. Specimens GZNUSLS201907029 and GZNUSLS202005279 were destroyed for the molecular analysis. Total genomic DNA was extracted from muscle tissues using a standard high salt method (
The whole mitogenomes of Tachysurus species were amplified in overlapping PCR fragments using 13 primer pairs designed based on the mitogenome of T. brevicaudatus (GenBank accession number: NC_021393) by Primer Premier 5.0 software (
After sequencing, the sequence fragments were edited and assembled using the SeqMan software of DNAStar (DNASTAR Inc., Madison, WI, USA) to obtain the complete mitogenome sequences. Assembled mitogenome sequences were annotated using the MitoAnnotator on the MitoFish homepage (
For phylogenetic analysis, sequences of 32 bagrid catfishes were downloaded from GenBank. Additionally, Cyprinus carpio (NC_001606.1), Silurus asotus (NC_015806.1), Liobagrus andersoni (NC_032035.1), and L. styani (NC_034647.1) were used as outgroups. The species used in the analysis are listed in Suppl. material
The entire mitogenome sequences of the two catfishes had lengths of 16,532 bp for T. brachyrhabdion and 16,533 bp for T. gracilis (GenBank accessions MW712739 and OM759888, respectively) (Fig.
Organization of mitochondrial genome of T. brachyrhabdion (TB) and T. gracilis (TG). H refers to the majority strand and L refers to the minority strand. Position numbers refer to positions on the majority strand.
Gene | Strand | Nucleotide number | Length (bp) | Intergenic nucleotide | Anticodon | Start/Stop codons | |||
---|---|---|---|---|---|---|---|---|---|
TB | TG | TB | TG | Start | Stop | ||||
tRNAPhe | H | 1–70 | 1–70 | 70 | 0 | 0 | GAA | ||
12S rRNA | H | 71–1023 | 71–1023 | 953 | 0 | 0 | |||
tRNAVal | H | 1024–1095 | 1024–1095 | 72 | 0 | 0 | TAC | ||
16S rRNA | H | 1096–2774 | 1096–2774 | 1679 | 0 | 0 | |||
tRNALeu (UUR) | H | 2775–2849 | 2775–2849 | 75 | 0 | 0 | TAA | ||
ND1 | H | 2850–3824 | 2850–3824 | 975 | 2 | 2 | ATG | TAG | |
tRNAIle | H | 3827–3898 | 3827–3898 | 72 | -1 | -1 | GAT | ||
tRNAGln | L | 3898–3968 | 3898–3968 | 71 | -1 | -1 | TTG | ||
tRNAMet | H | 3968–4037 | 3968–4037 | 70 | 0 | 0 | CAT | ||
ND2 | H | 4038–5082 | 4038–5082 | 1045 | 0 | 0 | ATG | T | |
tRNATrp | H | 5083–5153 | 5083–5153 | 71 | 2 | 2 | TCA | ||
tRNAAla | L | 5156–5224 | 5156–5224 | 69 | 1 | 1 | TGC | ||
tRNAAsn | L | 5226–5298 | 5226–5298 | 73 | 32 | 32 | GTT | ||
tRNACys | L | 5331–5397 | 5331–5397 | 67 | 0 | 0 | GCA | ||
tRNATyr | L | 5398–5468 | 5398–5469 | 71/72 | 1 | 1 | GTA | ||
COI | H | 5470–7020 | 5471–7021 | 1551 | 0 | 0 | GTG | TAA | |
tRNASer (UCN) | L | 7021–7091 | 7022–7092 | 71 | 4 | 4 | TGA | ||
tRNAAsp | H | 7096–7168 | 7097–7169 | 73 | 14 | 14 | GTC | ||
COII | H | 7183–7873 | 7184–7874 | 691 | 0 | 0 | ATG | T | |
tRNALys | H | 7874–7947 | 7875–7948 | 74 | 1 | 1 | TTT | ||
ATPase 8 | H | 7949–8116 | 7950–8117 | 168 | -10 | -10 | ATG | TAA | |
ATPase 6 | H | 8107–8789 | 8108–8790 | 683 | 0 | 0 | ATG | TA | |
COIII | H | 8790–9573 | 8791–9574 | 784 | 0 | 0 | ATG | T | |
tRNAGly | H | 9574–9647 | 9575–9648 | 74 | 0 | 0 | TCC | ||
ND3 | H | 9648–9996 | 9649–9997 | 349 | 0 | 0 | ATG | T | |
tRNAArg | H | 9997–10067 | 9998–10068 | 71 | 0 | 0 | TCG | ||
ND4L | H | 10068–10364 | 10069–10365 | 297 | -7 | -7 | ATG | TAA | |
ND4 | H | 10358–11738 | 10359–11739 | 1381 | 0 | 0 | ATG | T | |
tRNAHis | H | 11739–11808 | 11740–11809 | 70 | 0 | 0 | GTG | ||
tRNASer (AGY) | H | 11809–11875 | 11810–11876 | 67 | 3 | 3 | GCT | ||
tRNALeu (CUN) | H | 11879–11951 | 11880–11952 | 73 | 0 | 0 | TAG | ||
ND5 | H | 11952–13778 | 11953–13779 | 1827 | -4 | -4 | ATG | TAA | |
ND6 | L | 13775–14290 | 13776–14291 | 516 | 0 | 0 | ATG | TAA | |
tRNAGlu | L | 14291–14359 | 14292–14360 | 69 | 2 | 2 | TTC | ||
Cytb | H | 14362–15499 | 14363–15500 | 1138 | 0 | 0 | ATG | T | |
tRNAThr | H | 15500–15572 | 15501–15573 | 73 | -2 | -2 | TGT | ||
tRNAPro | L | 15571–15640 | 15572–15641 | 70 | 0 | 0 | TGG | ||
D-loop | H | 15641–16532 | 15642–16533 16533 | 892 | 0 | 0 |
The overall base composition for both species was very similar, 31.02% A, 27.05% T, 15.55% G, and 26.38% C for T. brachyrhabdion and 31.03% A, 27.14% T, 15.52% G, and 26.31% C for T. gracilis (Table
Nucleotide composition of the mitochondrial genomes of T. brachyrhabdion (TB) and T. gracilis (TG).
Length(bp) | A% | T% | G% | C% | A+T% | AT-skew | GC-skew | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
TB | TG | TB | TG | TB | TG | TB | TG | TB | TG | TB | TG | TB | TG | TB | TG | |
genome | 16532 | 16533 | 31.02 | 31.03 | 27.05 | 27.14 | 15.55 | 15.52 | 26.38 | 26.31 | 58.07 | 58.17 | 0.0683 | 0.0669 | -0.2585 | -0.2580 |
PCGs | 11405 | 11405 | 28.94 | 28.99 | 29.13 | 29.25 | 15.37 | 15.30 | 26.56 | 26.46 | 58.07 | 58.24 | -0.0032 | -0.0045 | -0.2668 | -0.2673 |
1st codon position | 3806 | 3806 | 27.06 | 27.17 | 21.94 | 21.94 | 25.49 | 25.35 | 25.51 | 25.54 | 49.00 | 49.11 | 0.1046 | 0.1065 | -0.0005 | -0.0036 |
2nd codon position | 3806 | 3806 | 18.61 | 18.63 | 40.87 | 40.95 | 13.55 | 13.53 | 26.97 | 26.89 | 59.47 | 59.58 | -0.3743 | -0.3746 | -0.3312 | -0.3307 |
3rd codon position | 3806 | 3806 | 41.17 | 41.17 | 24.59 | 24.87 | 7.05 | 7.00 | 27.19 | 26.95 | 65.75 | 66.04 | 0.2522 | 0.2467 | -0.5880 | -0.5876 |
rRNA | 2632 | 2632 | 34.77 | 34.65 | 22.38 | 22.34 | 19.64 | 19.72 | 23.21 | 23.29 | 57.14 | 56.99 | 0.2168 | 0.2160 | -0.0833 | -0.0830 |
tRNA | 1566 | 1567 | 29.12 | 29.16 | 28.10 | 28.33 | 22.48 | 22.34 | 20.30 | 20.17 | 57.22 | 57.50 | 0.0179 | 0.0144 | 0.0507 | 0.0511 |
D-loop region | 892 | 892 | 31.28 | 31.17 | 31.39 | 31.17 | 13.79 | 13.90 | 23.54 | 23.77 | 62.67 | 62.33 | -0.0018 | 0.0000 | -0.2613 | -0.2619 |
The mitogenomes of T. brachyrhabdion and T. gracilis had one PCG (ND6) encoded on the L-strand and the remaining PCGs on the H-strand. Both mitogenomes had 11,405 bp coding for PCGs, accounting for 3627/3626 amino acids (Table
To investigate the evolutionary patterns under different selective pressures among 13 PCGs in bagrid catfishes, the value of Ka/Ks was calculated for each PCG, respectively (Fig.
Both the T. brachyrhabdion and T. gracilis mitogenomes contained two rRNA genes: the large ribosomal RNA subunit (16S rRNA) and small ribosomal RNA subunit (12S rRNA). The 16S rRNA was located between tRNAVal and tRNALeu (UUR), and the 12S rRNA was located between tRNAPhe and tRNAVal. The 12S rRNA genes and the 16S rRNA genes of both mitogenomes were 953 bp and 1679 bp, respectively.
Twenty-one tRNA genes produced the typical cloverleaf secondary structure, while tRNASer (AGY) gene lacked the dihydrouracil (DHU) arm (Figs S1 and S2). The sizes of the tRNA genes ranged from 67 bp (tRNACys and tRNASer (AGY)) to 75 bp (tRNALeu (UUR)) in both T. brachyrhabdion and T. gracilis (Table
The putative control regions were located between tRNAPro and tRNAPhe in the two bagrid catfishes. The control regions of T. brachyrhabdion and T. gracilis were 892 bp in size. The average A+T content of the CRs (62.33%–62.67%) was higher than that of the whole genomes, PCGs, rRNAs, or tRNAs (57.14%–58.24%) (Table
To determine the phylogenetic relationship between T. brachyrhabdion and T. gracilis in the Characidae, we selected the concatenated nucleotide sequences of the combined mitochondrial gene set (13 PCGs) from 34 bagrid catfishes. As shown in Fig.
Over the past two to three decades, mitochondrial genes and genomes have been frequently used in fish studies (
Most of the PCGs of these two species had ATG as the start codon except COI that had GTG as the start codon. The COI gene usually uses GTG as the start codon in other fishes, such as Lateolabrax, Sinocyclocheilus multipunctatus, and Microphysogobio elongatus (
Phylogenetic analysis revealed Bagridae was supported as a monophyletic group with Rita rita excluded (Fig.
This study reported the complete mitochondrial genome sequences of two bagrid catfishes. The study showed that mitogenomes of Bagridae were conserved in structure, gene order, and nucleotide composition. Phylogenetic analysis confirmed that Bagridae is monophyletic group with Rita rita excluded and the traditional classification that Leiocassis, Pseudobagrus, Pelteobagrus, and Tachysurus belong to one genus.
This work was supported by the Joint Fund of the National Natural Science Foundation of China and the Karst Science Research Center of Guizhou Province (Grant No. U1812401), Guizhou Provincial Science and Technology Foundation (Qiankehejichu[2018]1113), Natural Science Foundation of Guizhou Educational Committee (QianjiaoheKY[2021]306) and the Undergraduate Research Training Program of Guizhou Normal University (DK2019A023).
Figure S1. Predicted tRNA structures of Tachysurus brachyrhabdion
Data type: image
Figure S2. Predicted tRNA structures of Tachysurus gracilis
Data type: image
Table S1. Primers used for PCR
Data type:molecular data
Tables S2. Species, GenBank accession number and length of mitogenomes used in this study
Data type: molecular data
Table S3. Number of codons in T. brachyrhabdion (TB) and T. gracilis (TG) for mitochondrial PCGs
Data type: molecular data