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Sun CH, Huang Q, Zeng XS, Li S, Zhang XL, Zhang YN, Liao J, Lu CH, Han BP, Zhang Q. Comparative analysis of the mitogenomes of two Corydoras (Siluriformes, Loricarioidei) with nine known Corydoras, and a phylogenetic analysis of Loricarioidei. Zookeys 2022; 1083:89-107. [PMID: 35115873 PMCID: PMC8803743 DOI: 10.3897/zookeys.1083.76887] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/06/2022] [Indexed: 01/04/2023] Open
Abstract
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.
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Rocha-Reis DA, Pasa R, Menegidio FB, Heslop-Harrison JS, Schwarzacher T, Kavalco KF. The Complete Mitochondrial Genome of Two Armored Catfish Populations of the Genus Hypostomus (Siluriformes, Loricariidae, Hypostominae). Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.579965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Gomes-dos-Santos A, Nande M, Espinoza-Ramos LA, Pepe-Victoriano RG, Contreras-Mamani Z, Huanacuni JI, Quispe-Mayta JM, Fernández-Cárdenas CP, Froufe E, Castro LFC. Constructing the mitochondrial genome of the Peruvian grunt Anisotremus scapularis Tschudi, 1846 (Lutjaniformes: Haemulidae) using RNA-seq data. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1754950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- André Gomes-dos-Santos
- CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto, Portugal
| | - Manuel Nande
- CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Luis A. Espinoza-Ramos
- Professional School of Fisheries Engineering, Faculty of Agricultural Sciences, National University of Jorge Basadre Grohmann, Tacna, Peru
| | - Renzo G. Pepe-Victoriano
- Area of Marine Biology and Aquaculture, Faculty of Renewable Natural Resources, University of Arturo Prat, Arica, Chile
| | - Zumilda Contreras-Mamani
- Professional School of Fisheries Engineering, Faculty of Agricultural Sciences, National University of Jorge Basadre Grohmann, Tacna, Peru
| | - Jordan I. Huanacuni
- Professional School of Fisheries Engineering, Faculty of Agricultural Sciences, National University of Jorge Basadre Grohmann, Tacna, Peru
| | - J. Miguel Quispe-Mayta
- Professional School of Fisheries Engineering, Faculty of Agricultural Sciences, National University of Jorge Basadre Grohmann, Tacna, Peru
| | - Cintia P. Fernández-Cárdenas
- Professional School of Fisheries Engineering, Faculty of Agricultural Sciences, National University of Jorge Basadre Grohmann, Tacna, Peru
| | - Elsa Froufe
- CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - L. Filipe C. Castro
- CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto, Portugal
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Moreira DA, Buckup PA, Furtado C, Val AL, Schama R, Parente TE. Reducing the information gap on Loricarioidei (Siluriformes) mitochondrial genomics. BMC Genomics 2017; 18:345. [PMID: 28472937 PMCID: PMC5418769 DOI: 10.1186/s12864-017-3709-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/19/2017] [Indexed: 01/11/2023] Open
Abstract
Background The genetic diversity of Neotropical fish fauna is underrepresented in public databases. This distortion is evident for the order Siluriformes, in which the suborders Siluroidei and Loricarioidei share equivalent proportion of species, although far less is known about the genetics of the latter clade, endemic to the Neotropical Region. Recently, this information gap was evident in a study about the structural diversity of fish mitochondrial genomes, and hampered a precise chronological resolution of Siluriformes. It has also prevented molecular ecology investigations about these catfishes, their interactions with the environment, responses to anthropogenic changes and potential uses. Results Using high-throughput sequencing, we provide the nearly complete mitochondrial genomes for 26 Loricariidae and one Callichthyidae species. Structural features were highly conserved. A notable exception was identified in the monophyletic clade comprising species of the Hemiancistrus, Hypostomini and Peckoltia-clades, a ~60 nucleotide-long deletion encompassing the seven nucleotides at the 3′ end of the Conserved Sequence Block (CSB) D of the control region. The expression of mitochondrial genes followed the usual punctuation pattern. Heteroplasmic sites were identified in most species. The retrieved phylogeny strongly corroborates the currently accepted tree, although bringing to debate the relationship between Schizolecis guntheri and Pareiorhaphis garbei, and highlighting the low genetic variability within the Peckoltia-clade, an eco-morphologically diverse and taxonomically problematic group. Conclusions Herein we have launched the use of high-throughput mitochondrial genomics in the studies of the Loricarioidei species. The new genomic resources reduce the information gap on the molecular diversity of Neotropical fish fauna, impacting the capacity to investigate a variety of aspects of the molecular ecology and evolution of these fishes. Additionally, the species showing the partial CSB-D are candidate models to study the replication and transcription of vertebrate mitochondrial genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3709-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel Andrade Moreira
- Laboratório de Toxicologia Ambiental, Escola Nacional de Saúde Pública (ENSP), Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4036, Rio de Janeiro, Brasil.,Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brasil
| | - Paulo Andreas Buckup
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro (UFRJ), Quinta da Boa Vista, Rio de Janeiro, RJ, Brasil
| | - Carolina Furtado
- Unidade de Genômica, Instituto Nacional do Câncer (INCA), Rua André Cavalcanti, 37, Rio de Janeiro, Brasil
| | - Adalberto Luis Val
- Laboratório de Ecofisiologia e Evolução Molecular, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo, 2936, Manaus, Brasil
| | - Renata Schama
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brasil
| | - Thiago Estevam Parente
- Laboratório de Toxicologia Ambiental, Escola Nacional de Saúde Pública (ENSP), Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4036, Rio de Janeiro, Brasil. .,Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brasil.
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Parente TE, Moreira DA, Magalhães MGP, de Andrade PCC, Furtado C, Haas BJ, Stegeman JJ, Hahn ME. The liver transcriptome of suckermouth armoured catfish (Pterygoplichthys anisitsi, Loricariidae): Identification of expansions in defensome gene families. MARINE POLLUTION BULLETIN 2017; 115:352-361. [PMID: 28062095 PMCID: PMC5310677 DOI: 10.1016/j.marpolbul.2016.12.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/02/2016] [Accepted: 12/05/2016] [Indexed: 06/02/2023]
Abstract
Pterygoplichthys is a genus of related suckermouth armoured catfishes native to South America, which have invaded tropical and subtropical regions worldwide. Physiological features, including an augmented resistance to organic xenobiotics, may have aided their settlement in foreign habitats. The liver transcriptome of Pterygoplichthys anisitsi was sequenced and used to characterize the diversity of mRNAs potentially involved in the responses to natural and anthropogenic chemicals. In total, 66,642 transcripts were assembled. Among the identified defensome genes, cytochromes P450 (CYP) were the most abundant, followed by sulfotransferases (SULT), nuclear receptors (NR) and ATP binding cassette transporters (ABC). A novel expansion in the CYP2Y subfamily was identified, as well as an independent expansion of the CYP2AAs. Two expansions were also observed among SULT1. Thirty-two transcripts were classified into twelve subfamilies of NR, while 21 encoded ABC transporters. The diversity of defensome transcripts sequenced herein could contribute to this species' resistance to organic xenobiotics.
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Affiliation(s)
- Thiago E Parente
- Laboratório de Toxicologia Ambiental, Escola Nacional de Saúde Pública (ENSP), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brasil; Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brasil; Woods Hole Oceanographic Institution (WHOI), Woods Hole, MA 02543, USA.
| | - Daniel A Moreira
- Laboratório de Toxicologia Ambiental, Escola Nacional de Saúde Pública (ENSP), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brasil
| | - Maithê G P Magalhães
- Laboratório de Toxicologia Ambiental, Escola Nacional de Saúde Pública (ENSP), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brasil
| | - Paula C C de Andrade
- Laboratório de Toxicologia Ambiental, Escola Nacional de Saúde Pública (ENSP), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brasil
| | - Carolina Furtado
- Unidade de Genômica, Instituto Nacional do Cancer (INCA), Rio de Janeiro 20230-130, Brasil
| | - Brian J Haas
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - John J Stegeman
- Woods Hole Oceanographic Institution (WHOI), Woods Hole, MA 02543, USA
| | - Mark E Hahn
- Woods Hole Oceanographic Institution (WHOI), Woods Hole, MA 02543, USA
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Magalhães MGP, Moreira DA, Furtado C, Parente TE. The mitochondrial genome of Hypancistrus zebra (Isbrücker & Nijssen, 1991) (Siluriformes: Loricariidae), an endangered ornamental fish from the Brazilian Amazon. CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0645-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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