Research Article |
Corresponding author: Qun Zhang ( tqzhang@jnu.edu.cn ) Academic editor: Tihomir Stefanov
© 2022 Cheng-He Sun, Qi Huang, Xiao-Shu Zeng, Sha Li, Xiao-Li Zhang, Ya-Nan Zhang, Jian Liao, Chang-Hu Lu, Bo-Ping Han, Qun Zhang.
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:
Sun C-H, Huang Q, Zeng X-S, Li S, Zhang X-L, Zhang Y-N, Liao J, Lu C-H, Han B-P, Zhang Q (2022) Comparative analysis of the mitogenomes of two Corydoras (Siluriformes, Loricarioidei) with nine known Corydoras, and a phylogenetic analysis of Loricarioidei. ZooKeys 1083: 89-107. https://doi.org/10.3897/zookeys.1083.76887
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Corydoras is a speciose catfish genus from South America with widely investigated phylogenetic and evolutionary relationships. The complete mitogenomes of C. aeneus and C. paleatus were sequenced, assembled, and annotated using next-generation sequencing. The genome arrangements, gene contents, genome structures, base compositions, evolutionary features, codon usage, and tRNA structures of the two mitogenomes were compared and analyzed with nine published mitogenomes of Corydoras. Phylogenetic analysis was performed using concatenated nucleotide sequences with 13 protein-coding genes and two rRNAs with 44 mitogenomes of Siluriformes. These results provide information on the mitogenomes of eleven Corydoras species and evolutionary relationships within the suborder Loricarioidei, which may be applicable for further phylogenetic and taxonomic studies on Siluriformes and Loricarioidei.
Corydoras aeneus, Corydoras paleatus, genome sequencing, mitochondrial DNA, Phylogenetic tree
Fish mitochondrial DNA shares characteristics with other vertebrate mitochondrial DNA (
Corydoras Lacépède, 1803, belongs to the order Siluriformes, suborder Loricarioidei, family Callichthyidae. Corydoras contains 175 valid species, which makes it the most species-rich genus of the family Callichthyidae (
In this study, the complete mitogenomes of two species of Corydoras (Bronze corydoras C. aeneus Gill, 1858 and peppered corydoras C. paleatus Jenyns, 1842) were sequenced, assembled, and annotated. The genome organization, gene contents, repeat sequences, and tRNA structures of the eleven mitogenomes were compared and analyzed in combination with nine published mitogenomes of Corydoras (
Single specimens of C. aeneus and C. paleatus were collected from the temple of Confucius flower and wood fish market, Nanjing city, Jiangsu province, China (32°0'27.1"N, 118°50'11.5"E) in June 2020 and identified based on their morphological characteristics, according to the latest taxonomic classification of fish (
Next-generation sequencing was performed to determine the complete mitogenome sequence of the two species of Corydoras. The DNA libraries were sequenced on an Illumina sequencing platform by Novogene Co., Ltd. (Beijing, China). Briefly, the total DNA genome was quantified and fragmented into 250-base pair (bp) fragments using a Covaris M220 ultrasonic crushing system (Woburn, MA, USA) followed by whole-genome shotgun sequencing. According to the manufacturer’s instructions, a library was constructed based on two indices using an Illumina TruSeq DNA PCR-Free HT kit (San Diego, CA, USA). An Illumina Novaseq 6000 platform was used for sequencing of 150 paired-end reads approximately 4 Gb in size. Clean reads were generated as previously described, and the remaining high-quality reads were assembled using SPADES V3.15.2 (
The tRNA genes were verified using tRNASCAN-SE V1.3.1 (
Phylogenetic trees for the eleven mitogenomes of Corydoras within the family Callichthyidae and Suborder Loricarioidei were constructed by aligning 13 PCGs and two rRNA sequences with those of 42 species of Loricarioidei, 29 species from Loricariidae, and one species from Trichomycteridae (Table
No. | Suborder | Family | Taxa | GenBank accession no. | Length (bp) | Location/Reference |
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1 | Loricarioidei | Callichthyidae | Corydoras aeneus | MZ571336 | 16604 | This study |
2 | Corydoras agassizii | MN641875.1 | 16538 |
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3 | Corydoras arcuatus | NC_049096.1 | 16177 |
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4 | Corydoras duplicareus | NC_049095.1 | 16632 |
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5 | Corydoras nattereri | KT239008.1 | 16557 |
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6 | Corydoras paleatus | MZ571337 | 16320 | This study | ||
7 | Corydoras panda | NC_049097.1 | 16398 |
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8 | Corydoras rabauti | NC_004698.1 | 16711 |
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9 | Corydoras schwartzi | KT239007.1 | 15671 |
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10 | Corydoras sterbai | NC_048967.1 | 16520 |
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11 | Corydoras trilineatus | NC_049098.1 | 15359 |
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12 | Hoplosternum littorale | KX087170.1 | 16262 |
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13 | Loricariidae | Ancistomus snethlageae | KX087166.1 | 16464 |
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14 | Ancistrus cryptophthalmus | MF804392.1 | 16333 |
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15 | Ancistrus multispinis | KT239006.1 | 16539 |
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16 | Ancistrus temminckii | NC_051963.1 | 16439 |
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17 | Aphanotorulus emarginatus | KT239019.1 | 16597 |
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18 | Baryancistrus xanthellus | KX087167.1 | 16167 |
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19 | Dekeyseria amazonica | KX087168.1 | 16409 |
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20 | Hemipsilichthys nimius | KT239011.1 | 16477 |
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21 | Hisonotus thayeri | KX087173.1 | 16269 |
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22 | Hypancistrus zebra | KX611143.1 | 16202 |
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23 | Hypoptopoma incognitum | NC_028072.1 | 16313 |
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24 | Hypostomus affinis | KT239013.1 | 16330 |
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25 | Hypostomus ancistroides | NC_052710.1 | 16422 |
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26 | Hypostomus francisci | NC_045188.1 | 16916 |
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27 | Hypostomus plecostomus | NC_025584.1 | 16562 |
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28 | Kronichthys heylandi | KT239014.1 | 16632 |
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29 | Loricaria cataphracta | KX087174.1 | 16831 |
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30 | Loricariichthys castaneus | KT239015.1 | 16521 |
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31 | Loricariichthys platymetopon | KT239018.1 | 16521 |
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32 | Neoplecostomus microps | KX087175.1 | 16523 |
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33 | Otocinclus affinis | MT323116.1 | 16501 |
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34 | Pareiorhaphis garbei | KX087178.1 | 16630 |
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35 | Parotocinclus maculicauda | KX087179.1 | 16541 |
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36 | Peckoltia furcata | KX087180.1 | 16497 |
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37 | Pterygoplichthys anisitsi | KT239003.1 | 16636 |
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38 | Pterygoplichthys disjunctivus | NC_015747.1 | 16667 |
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39 | Pterygoplichthys pardalis | KT239016.1 | 16822 |
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40 | Schizolecis guntheri | KT239017.1 | 16611 |
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41 | Sturisomatichthys panamensis | NC_045877.1 | 16526 |
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42 | Trichomycteridae | Trichomycterus areolatus | AP012026.1 | 16657 |
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43 | Siluroidei | Siluridae | Pterocryptis cochinchinensis | NC_027107.1 | 16826 |
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44 | Silurus asotus | NC_015806.1 | 16593 |
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The complete mitogenomes of C. aeneus and C. paleatus comprising 16,604 and 16,593 bp, respectively, were submitted to GenBank (accession nos. MZ571336 and MZ571337, respectively) (Fig.
Characteristic features of Corydoras aeneus and Corydoras paleatus mitogenomes (+ denotes heavy strand; - denotes light strand).
Feature | Position | Length (bp) | Start codons | Stop codons | Anticodon | Strand | Intergenic nucleotides | |||||||
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C. aeneus | C. paleatus | C. aeneus | C. paleatus | C. a | C. p | C. a | C. p | |||||||
From | to | From | to | C. a | C. p | |||||||||
tRNA-Phe | 1 | 68 | 1 | 68 | 68 | 68 | GAA | + | 0 | 0 | ||||
12S rRNA | 69 | 1014 | 69 | 1013 | 946 | 945 | + | 0 | 0 | |||||
tRNA-Val | 1015 | 1086 | 1014 | 1085 | 72 | 72 | TAC | + | 0 | 0 | ||||
16S rRNA | 1087 | 2757 | 1086 | 2753 | 1671 | 1668 | + | 0 | 0 | |||||
tRNA-Leu | 2758 | 2832 | 2754 | 2828 | 75 | 75 | TAA | + | 0 | 0 | ||||
ND1 | 2833 | 3804 | 2829 | 3800 | 972 | 972 | ATG | ATG | TAG | TAG | + | 8 | 8 | |
tRNA-Ile | 3813 | 3884 | 3809 | 3880 | 72 | 72 | GAT | + | -2 | -2 | ||||
tRNA-Gln | 3883 | 3953 | 3879 | 3949 | 71 | 71 | TTG | - | -1 | -1 | ||||
tRNA-Met | 3953 | 4022 | 3949 | 4018 | 70 | 70 | CAT | + | 0 | 0 | ||||
ND2 | 4023 | 5067 | 4019 | 5063 | 1045 | 1045 | ATG | ATG | T | T | + | 0 | 0 | |
tRNA-Trp | 5068 | 5139 | 5064 | 5134 | 72 | 71 | TCA | + | 1 | 1 | ||||
tRNA-Ala | 5141 | 5209 | 5136 | 5204 | 69 | 69 | TGC | - | 1 | 1 | ||||
tRNA-Asn | 5211 | 5283 | 5206 | 5278 | 73 | 73 | GTT | - | 30 | 31 | ||||
tRNA-Cys | 5314 | 5380 | 5310 | 5377 | 67 | 68 | GCA | - | -1 | -1 | ||||
tRNA-Tyr | 5380 | 5449 | 5377 | 5446 | 70 | 70 | GTA | - | 1 | 1 | ||||
COI | 5451 | 7010 | 5448 | 7007 | 1560 | 1560 | GTG | GTG | AGG | AGG | + | -13 | -13 | |
tRNA-Ser | 6998 | 7068 | 6995 | 7065 | 71 | 71 | TGA | - | 4 | 4 | ||||
tRNA-Asp | 7073 | 7141 | 7070 | 7138 | 69 | 69 | GTC | + | 4 | 6 | ||||
COII | 7146 | 7836 | 7145 | 7835 | 691 | 691 | ATG | ATG | T | T | + | 0 | 0 | |
tRNA-Lys | 7837 | 7910 | 7836 | 7909 | 74 | 74 | TTT | + | 1 | 1 | ||||
ATPase 8 | 7912 | 8079 | 7911 | 8078 | 168 | 168 | ATG | ATG | TAA | TAA | + | -10 | -10 | |
ATPase 6 | 8070 | 8753 | 8069 | 8752 | 684 | 684 | ATG | ATG | TAA | TAA | + | 17 | 21 | |
COIII | 8771 | 9554 | 8774 | 9557 | 784 | 784 | ATG | ATG | T | T | + | 0 | 0 | |
tRNA-Gly | 9555 | 9626 | 9558 | 9629 | 72 | 72 | TCC | + | 0 | 0 | ||||
ND3 | 9627 | 9975 | 9630 | 9978 | 349 | 349 | ATG | ATG | T | T | + | 0 | 0 | |
tRNA-Arg | 9976 | 10045 | 9979 | 10048 | 70 | 70 | TCG | + | 0 | 0 | ||||
ND4L | 10046 | 10342 | 10049 | 10345 | 297 | 297 | ATG | ATG | TAA | TAA | + | -7 | -7 | |
ND4 | 10336 | 11716 | 10339 | 11719 | 1381 | 1381 | ATG | ATG | T | T | + | 0 | 0 | |
tRNA-His | 11717 | 11786 | 11720 | 11789 | 70 | 70 | GTG | + | 0 | 0 | ||||
tRNA-Ser | 11787 | 11853 | 11790 | 11856 | 67 | 67 | GCT | + | 1 | 1 | ||||
tRNA-Leu | 11855 | 11927 | 11858 | 11930 | 73 | 73 | TAG | + | 0 | 0 | ||||
ND5 | 11928 | 13754 | 11931 | 13757 | 1827 | 1827 | ATG | ATG | TAA | TAA | + | -4 | -4 | |
ND6 | 13751 | 14266 | 13754 | 14269 | 516 | 516 | ATG | ATG | TAA | TAA | - | 0 | 0 | |
tRNA-Glu | 14267 | 14335 | 14270 | 14337 | 69 | 68 | TTC | - | 2 | 3 | ||||
Cyt b | 14338 | 15475 | 14341 | 15478 | 1138 | 1138 | ATG | ATG | T | T | + | 0 | 0 | |
tRNA-Thr | 15476 | 15548 | 15479 | 15550 | 73 | 72 | TGT | + | -2 | -2 | ||||
tRNA-Pro | 15547 | 15616 | 15549 | 15618 | 70 | 70 | TGG | - | 0 | 0 | ||||
D-loop | 15617 | 16604 | 15619 | 16593 | 988 | 975 | 0 | 0 |
The 13 PCGs of the two new mitogenomes and those of the previously published nine mitogenomes of Corydoras contained COI–COIII, ND1–ND6, ND4L, two ATPases, and one Cyt-b, similar to that in other Siluriformes (
Similar to most previously sequenced members of Loricarioidei, the AT-skews (0.033 to 0.052) and GC-skews (-0.268 to -0.299) of the PCGs were similar among the eleven species of Corydoras (Suppl. material
To reveal the evolutionary pattern of the PCGs, the Ka/Ks, nucleotide diversity, and K2P genetic distance across all mitogenomes of Corydoras were calculated for each aligned PCG. The K2P genetic distances of 13 PCGs were all less than 0.12 (Fig.
The total lengths of the 22 tRNA genes ranged from 1,438 (C. schwartzi) to 1,561 bp (C. arcuatus and C. panda), whereas individual tRNA genes typically ranged from 58 to 75 bp. All tRNA genes displayed the expected cloverleaf secondary structures with normal base pairing, except for tRNA-Ser(GCT), which lacked the DHU stem (Suppl. material
The control region (D-loop), also known as the A+T rich region that contains hypervariable non-coding sequences and regulates the replication and transcription of mitochondrial DNA, is the largest non-coding region and is located between tRNA-Pro and tRNA-Phe in these mitogenomes. Compared with PCGs, the D-loop displayed a higher mutation rate and the highest variation throughout the mitogenome; thus, this region is dominant and can be used to evaluate intraspecies variations. The D-loops in the eleven species of Corydoras were 718‒1,218 bp. Compared with the other four regions (entire genome, PCGs, tRNAs, and rRNAs), the control region showed the highest A+T content, ranging from 66.77% to 71.87%. Like the rRNAs, all AT-skew values were positive, and all GC-skew values were negative.
To determine the phylogenetic relationships within the suborder Loricarioidei and family Callichthyidae, we obtained the concatenated nucleotide sequences of 13 PCGs and two rRNAs from 42 species of Loricarioidei. Phylogenetic analyses based on both ML and BI methods revealed same topologies, which also generally agreed with those presented in previous studies (
Both Callichthyidae and Loricariidae were recovered as monophyletic with very high support values (BI posterior probabilities, PP = 1; ML bootstrap, BS = 100). The 44 species of Siluriformes were divided into four major clades corresponding to the families Siluridae Callichthyidae, Trichomycteridae, and Loricariidae. The target species C. aeneus and C. paleatus were clustered into two clades (C. aeneus + C. rabauti) and (C. paleatus + C. nattereri) with a high nodal support value (PP = 1; BS = 100). The eleven species of the genus Corydoras clustered together quite well [((C. aeneus + C. rabauti) + (C. schwartzi + C. agassizii)) + (C. arcuatus + (C. panda + (C. duplicareus + (C. sterbai + C. trilineatus))))] + [(C. paleatus + C. nattereri)]. Corydoras trilineatus and C. sterbai have short, almost non-existent branch lengths; thus, they are likely the same species. The K2P genetic distances of these two species are 0.000 (Suppl. material
Using next-generation sequencing methods, the complete mitogenomes of the bronze C. aeneus and peppered C. paleatus were analyzed and compared with those of nine members of Corydoras. The complete mitogenomes of C. aeneus and C. paleatus comprised 16,604 and 16,593 bp, respectively. The two mitogenomes had high A+T contents (58.52% in C. aeneus and 58.23% in C. paleatus), a phenomenon that agrees with the typical base bias of ichthyic mitogenomes. Our results indicate that the mitogenome features, including genome size, gene content, and gene arrangement, in Corydoras are highly conserved. Phylogenetic analysis was performed with 42 species of Loricarioidei and two outgroup species. These analyses confirmed the occurrence of the genus Corydoras within the monophyletic family Callichthyidae. The complete mitogenome information, including the gene content, gene orders, genome structure, base compositions, evolutionary features, codon usage, gene arrangement, and phylogenetic analyses, provides a basis for future studies on the population genetic and evolution of Corydoras and related groups.
This work was supported by the National Key R&D Program of China (Grant number 2018YFD0900802); Director’s Fund of the Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, China Three Gorges Corporation (0704157); Outstanding Innovative Talents Cultivation Funded Programs for Doctoral Students of Jinan University (Project No: 2021CXB022) and Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD). We gratefully acknowledge two reviewers for their constructive comments and would like to thank Editage (www.editage.com) for their support with language editing.
COI sequences of Corydoras aeneus and C. paleatus Tables S1–S4, Figs S1–S4
Data type: docx file
Explanation note: COI sequences of Corydoras aeneus and C. paleatus. Table S1. Best substitution models for Bayesian inference (BI) and maximum-likelihood (ML) analyses. Table S2. Summarized mitogenomic characteristics of the eleven Corydoras species investigated in this study. Table S3. The K2P genetic distances of the eleven mitogenomes of Corydoras. Table S4. Start nd stop codons of protein-coding genes in the eleven Corydoras mitogenomes. Figure S1. Gene orders of mitogenomes of the studied species. Figure S2. Relative synonymous codon usage of 13 protein-coding genes in the mitogenomes of eleven Corydoras species. Figure S3. Codon usage patterns of eleven Corydoras mitogenomes. Figure S4. Secondary structures of tRNA-Ser(GCT) in the two newly sequenced Corydoras species.