Complete mitochondrial genome of four <i>Scleromystax barbatus</i> (Siluriformes: Callichthyidae) populations

The complete mitogenome of four Scleromystax barbatus populations distributed along the species natural range was reconstructed, comprising the first study with this genus and the second with Corydoradinae specimens sampled from their natural environment and deposited in permanent collections. The mitogenome of S. barbatus is a circular molecule of 16,694 base pairs (bp) comprising 37 genes, 22 of which are tRNA, two are rRNA, 13 are protein-coding genes and one control region (D-loop). An 18-nucleotide insertion sequence was found between the ATPase subunit 6 and COIII genes. Most genes are encoded on the heavy strand, while the ND6 and eight tRNAs are found on the light strand. Phylogenetic analyses using other available Callichthyidae mitogenomes confirmed the monophyly of Callichthyinae and Corydoradinae and indicate that S. barbatus populations form a separate and more closely related branch of Corydoras nattereri + Corydoras paleatus.

Keywords:
Markers; Mitochondrial DNA; Molecular identification; Phylogenetic analysis

Authorship

Roger Henrique Dalcin

Conceptualization

Methodology

Writing-original draft

Programa de Pós-Graduação em Zoologia, Universidade Federal do Paraná, Campus Centro Politécnico, Av. Cel. Francisco H. dos Santos, 100, 81530-000 Curitiba, PR, Brazil. roger_dalcin@hotmail.com (corresponding author). Universidade Federal do ParanáBrazilCuritiba, PR, Brazil Programa de Pós-Graduação em Zoologia, Universidade Federal do Paraná, Campus Centro Politécnico, Av. Cel. Francisco H. dos Santos, 100, 81530-000 Curitiba, PR, Brazil. roger_dalcin@hotmail.com (corresponding author).

http://orcid.org/0000-0001-7896-7404

Luz Elena De La Ossa-Guerra

Conceptualization

Methodology

Writing-original draft

Programa de Pós-Graduação em Genética Evolutiva e Biologia Molecular, Universidade Federal de São Carlos, Rodovia Washington Luis, 13565-905 São Carlos, SP, Brazil. 03ledg@gmail.com Universidade Federal de São CarlosBrazilSão Carlos, SP, Brazil Programa de Pós-Graduação em Genética Evolutiva e Biologia Molecular, Universidade Federal de São Carlos, Rodovia Washington Luis, 13565-905 São Carlos, SP, Brazil. 03ledg@gmail.com

http://orcid.org/0000-0001-7407-9709

Roberto Ferreira Artoni

Conceptualization

Writing-review & editing

Programa de Pós-Graduação em Biologia Evolutiva, Universidade Estadual de Ponta Grossa, Av. Carlos Cavalcanti, 4748, 84030- 900 Ponta Grossa, PR, Brazil. rfartoni@gmail.com Universidade Estadual de Ponta GrossaBrazilPonta Grossa, PR, Brazil Programa de Pós-Graduação em Biologia Evolutiva, Universidade Estadual de Ponta Grossa, Av. Carlos Cavalcanti, 4748, 84030- 900 Ponta Grossa, PR, Brazil. rfartoni@gmail.com

http://orcid.org/0000-0002-2528-9846

Vinícius Abilhoa

Conceptualization

Writing-review & editing

Museu de História Natural Capão da Imbuia, MAPCF/PMC, Rua Prof. Nivaldo Braga, 1369, 82810-080 Curitiba, PR, Brazil. vinicius.abilhoa@gmail.com Museu de História Natural Capão da ImbuiaBrazilAltamira, PA, Brazil Museu de História Natural Capão da Imbuia, MAPCF/PMC, Rua Prof. Nivaldo Braga, 1369, 82810-080 Curitiba, PR, Brazil. vinicius.abilhoa@gmail.com

http://orcid.org/0000-0002-9463-0200

Edited-by

Alexandre Hilsdorf

Correspondence

Roger Henrique Dalcin roger_dalcin@hotmail.com

Competing Interests

The authors declare no competing interests.

Ethical Statement

Experiments were approved by the Ethical Committee for Animal Use from the Biological Sciences Section of the Universidade Federal do Paraná (CEU/BIO-UFPR), process 23075, 066050/2022-03 number 1489.

SCIMAGO INSTITUTIONS RANKINGS

Figures | Tables

Figures (2)
Tables (4)

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FIGURE 1 |
A. Geographic location of the Scleromystax barbatus populations in coastal Atlantic Rainforest rivers. B. Male of S. barbatus. Photo by Caio Feltrin. C. Complete mitochondrial genome of S. barbatus from the AR population. Population codes in Tab. 1.

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FIGURE 2 |
Phylogenetic analysis of 13 Corydoradinae and Hoplosternum littorale (Callichthyinae member) species as the outgroup based on the nucleotide sequences of 13 PCGs from the mitochondrial genome. Bootstrap values are shown next to nodes and the scale bar shows 0.03 changes. Population codes in Tab. 1.

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TABLE 1 |
Code used in the analysis of Scleromystax barbatus populations, locality, river, and coordinates where the collections were carried out.

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TABLE 2 |
Species used from Genbank and the present study and their respective accession and source numbers.

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TABLE 3 |
Annotation of the complete mitochondrial genome of a Scleromystax barbatus individual belonging to the Ariró River (AR) population.

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TABLE 4 |
Nucleotide composition of the four Scleromystax barbatus populations used in this study. %T (thymine percentage), %C (cytosine percentage), %A (adenine percentage), %G (guanine percentage), %GC content (guanine and cytosine percentages). Population codes in Tab. 1.

FIGURE 1 | A. Geographic location of the Scleromystax barbatus populations in coastal Atlantic Rainforest rivers. B. Male of S. barbatus. Photo by Caio Feltrin. C. Complete mitochondrial genome of S. barbatus from the AR population. Population codes in Tab. 1.

FIGURE 2 | Phylogenetic analysis of 13 Corydoradinae and Hoplosternum littorale (Callichthyinae member) species as the outgroup based on the nucleotide sequences of 13 PCGs from the mitochondrial genome. Bootstrap values are shown next to nodes and the scale bar shows 0.03 changes. Population codes in Tab. 1.

TABLE 1 | Code used in the analysis of Scleromystax barbatus populations, locality, river, and coordinates where the collections were carried out.

Code	Locality	River	Latitude/Longitude	Voucher
AE	Itariri, SP	Aerado	24°17’51.31”S 47°08’47.83”W	MHNCI 12734
AR	Angra dos Reis, RJ	Ariró	22°54’7.33”S 44°20’46.56”W	MHNCI 12735
PE	Barra do Sul, SC	Pernambuco	26°23’19.60”S 48°40’55.94”W	MHNCI 12736
PS	Teresópolis, RJ	Vargem Grande	22°24’24.55”S 42°52’27.34”W	MHNCI 12737

TABLE 2 | Species used from Genbank and the present study and their respective accession and source numbers.

Species	Accession number	Author
Scleromystax barbatus (AE)	OQ507208	This study
Scleromystax barbatus (AR)	OQ507209	This study
Scleromystax barbatus (PE)	OQ507210	This study
Scleromystax barbatus (PS)	OQ507211	This study
Corydoras aeneus (Gill, 1858)	MZ571336	Sun et al. (2022)
Corydoras arcuatus Elwin, 1938	NC_049096	*Liu et al. (2019d)*Liu Y, Xu B, Xiao T, Liu Q. Characterization and phylogenetic analysis of Corydoras arcuatus mitochondrial genome. Mitochondrial DNA Part B. 2019d; 4(2):2876–77. https://doi.org/10.1080/23802359.2019.1660251 https://doi.org/10.1080/23802359.2019.16...
Corydoras duplicareus Sands, 1995	NC_049095	*Liu et al.* (2019c)**Liu Q, Xu B, Xiao T. Complete mitochondrial genome of Corydoras duplicareus (Teleostei, Siluriformes, Callichthyidae). Mitochondrial DNA Part B. 2019c; 4(1):1832–33. https://doi.org/10.1080/23802359.2019c.1612714 https://doi.org/10.1080/23802359.2019c.1...
Corydoras nattereri Steindachner, 1876	KT239009	Moreira et al. (2016)
Corydoras paleatus (Jenyns, 1842)	MZ571337	Sun et al. (2022)
Corydoras panda Nijssen & Isbrücker, 1971	NC_049097	Liu et al. (2019a)
Corydoras rabauti LaMonte, 1941	NC_004698	Saitoh et al. (2003)
Corydoras sterbai Knaack, 1962	NC_048967	Liu et al. (2019b)
Corydoras trilineatus Cope, 1872	NC_049098	Chen et al. (2020)
Hoplosternum littorale (Hancock, 1828)	KX087170	Parente et al. (2018)

TABLE 3 | Annotation of the complete mitochondrial genome of a Scleromystax barbatus individual belonging to the Ariró River (AR) population.

Gene	Strand	Position		Length(bp)	Codon
Gene	Strand	Start	End	Length(bp)	Start	Stop
tRNA-Phe	H	1	68	68
12S rRNA	H	69	1016	948
tRNA-Val	H	1017	1088	72
16S rRNA	H	1089	2756	1668
tRNA-Leua	H	2757	2831	75
ND1	H	2832	3803	972	ATG	TAG
tRNA-Ile	H	3812	3883	72
tRNA-Gln	L	3882	3952	71
tRNA-Met	H	3952	4021	70
ND2	H	4022	5066	1045	ATG	T--
tRNA-Trp	H	5067	5137	71
tRNA-Ala	L	5139	5207	69
tRNA-Asn	L	5209	5281	73
tRNA-Cys	L	5312	5378	67
tRNA-Tyr	L	5378	5447	70
COI	H	5449	7008	1560	GTG	AGG
tRNA-Serb	L	6996	7066	71
tRNA-Asp	H	7071	7140	70
COIIc	H	7145	7835	691	ATG	T--
tRNA-Lys	H	7836	7909	74
ATPase 8	H	7911	8078	168	ATG	TAA
ATPase 6c	H	8069	8752	684	ATG	TAA
COIIIc	H	8771	9554	784	ATG	T--
tRNA-Gly	H	9555	9626	72
ND3c	H	9627	9975	349	ATG	T--
tRNA-Arg	H	9976	10045	70
ND4L	H	10046	10342	297	ATG	TAA
ND4c	H	10336	11716	1381	ATG	T--
tRNA-His	H	11717	11786	70
tRNA-Serd	H	11787	11853	67
tRNA-Leue	H	11855	11927	73
ND5	H	11928	13754	1827	ATG	TAA
ND6	L	13751	14266	516	ATG	TAA
tRNA-Glu	L	14267	14335	69
Cyt b	H	14338	15475	1138	ATG	T--
tRNA-Thr	H	15476	15547	72
tRNA-Pro	L	15546	15615	70
D-loop	H	15616	16694	1079

TABLE 4 | Nucleotide composition of the four Scleromystax barbatus populations used in this study. %T (thymine percentage), %C (cytosine percentage), %A (adenine percentage), %G (guanine percentage), %GC content (guanine and cytosine percentages). Population codes in Tab. 1.

Population	Genome size (bp)	%T	%C	%A	%G	%GC
AE	16,651	26.5	26.4	32.0	15.2	41.6
AR	16,694	26.4	26.4	31.2	15.1	41.6
PE	16,614	26.5	26.4	31.9	15.2	41.6
PS	16,693	26.4	26.4	32.0	15.2	41.6

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Sociedade Brasileira de Ictiologia Neotropical Ichthyology, Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura, Universidade Estadual de Maringá., Av. Colombo, 5790, 87020-900, Phone number: +55 44-3011-4632 - Maringá - PR - Brazil
E-mail: neoichth@nupelia.uem.br

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Complete mitochondrial genome of four <i>Scleromystax barbatus</i> (Siluriformes: Callichthyidae) populations

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[1] Edited-by

Alexandre Hilsdorf