Reducing the information gap on loricarioidei (Siluriformes) mitochondrial genomics
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...
| Autor principal: | Moreira, Daniel Andrade |
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| Outros Autores: | Buckup, Paulo Andreas, Furtado, Carolina, Val, Adalberto Luis, Schama, Renata, Parente, Thiago E.M. |
| Grau: | Artigo |
| Idioma: | English |
| Publicado em: |
BMC Genomics
2020
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| Assuntos: | |
| Acesso em linha: |
https://repositorio.inpa.gov.br/handle/1/15736 |
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oai:repositorio:1-15736 |
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oai:repositorio:1-15736 Reducing the information gap on loricarioidei (Siluriformes) mitochondrial genomics Moreira, Daniel Andrade Buckup, Paulo Andreas Furtado, Carolina Val, Adalberto Luis Schama, Renata Parente, Thiago E.M. Rna 12s Rna 16s Dna, Mitochondrial Ribosome Rna Callichthyidae Cladistics Controlled Study Fauna Gene Expression Regulation Gene Replication Genetic Conservation Genetic Parameters Genetic Variation Genomics Genotype-environment Interaction Hemiancistrus High Throughput Sequencing Hypostomini Loricariidae Mitochodrial Genomics Mitochondrial Gene Genome, Mitochondrial Molecular Ecology Evolution, Molecular Nonhuman Pairwise Nucleotide Identity Pareiorhaphis Garbei Peckoltia Phylogenetic Tree Schizolecis Guntheri Sequence Alignment Sequence Analysis Sequence Homology Siluriformes Species Difference Start Codon Stop Codon Structure Activity Relation Transcription Regulation Animals Catfish Dna Sequence Genetics Genomics Genome, Mitochondrial Mitochondrion Molecular Genetics Nucleotide Sequence Phylogeny Animal Base Sequence Catfishes Dna, Mitochondrial Evolution, Molecular Genetic Variation Genome, Mitochondrial Genomics Mitochondria Molecular Sequence Annotation Phylogeny Rna, Ribosomal Sequence Analysis, Dna 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. © 2017 The Author(s). 2020-05-18T18:29:12Z 2020-05-18T18:29:12Z 2017 Artigo https://repositorio.inpa.gov.br/handle/1/15736 10.1186/s12864-017-3709-3 en Volume 18, Número 1 Attribution-NonCommercial-NoDerivs 3.0 Brazil http://creativecommons.org/licenses/by-nc-nd/3.0/br/ application/pdf BMC Genomics |
| institution |
Instituto Nacional de Pesquisas da Amazônia - Repositório Institucional |
| collection |
INPA-RI |
| language |
English |
| topic |
Rna 12s Rna 16s Dna, Mitochondrial Ribosome Rna Callichthyidae Cladistics Controlled Study Fauna Gene Expression Regulation Gene Replication Genetic Conservation Genetic Parameters Genetic Variation Genomics Genotype-environment Interaction Hemiancistrus High Throughput Sequencing Hypostomini Loricariidae Mitochodrial Genomics Mitochondrial Gene Genome, Mitochondrial Molecular Ecology Evolution, Molecular Nonhuman Pairwise Nucleotide Identity Pareiorhaphis Garbei Peckoltia Phylogenetic Tree Schizolecis Guntheri Sequence Alignment Sequence Analysis Sequence Homology Siluriformes Species Difference Start Codon Stop Codon Structure Activity Relation Transcription Regulation Animals Catfish Dna Sequence Genetics Genomics Genome, Mitochondrial Mitochondrion Molecular Genetics Nucleotide Sequence Phylogeny Animal Base Sequence Catfishes Dna, Mitochondrial Evolution, Molecular Genetic Variation Genome, Mitochondrial Genomics Mitochondria Molecular Sequence Annotation Phylogeny Rna, Ribosomal Sequence Analysis, Dna |
| spellingShingle |
Rna 12s Rna 16s Dna, Mitochondrial Ribosome Rna Callichthyidae Cladistics Controlled Study Fauna Gene Expression Regulation Gene Replication Genetic Conservation Genetic Parameters Genetic Variation Genomics Genotype-environment Interaction Hemiancistrus High Throughput Sequencing Hypostomini Loricariidae Mitochodrial Genomics Mitochondrial Gene Genome, Mitochondrial Molecular Ecology Evolution, Molecular Nonhuman Pairwise Nucleotide Identity Pareiorhaphis Garbei Peckoltia Phylogenetic Tree Schizolecis Guntheri Sequence Alignment Sequence Analysis Sequence Homology Siluriformes Species Difference Start Codon Stop Codon Structure Activity Relation Transcription Regulation Animals Catfish Dna Sequence Genetics Genomics Genome, Mitochondrial Mitochondrion Molecular Genetics Nucleotide Sequence Phylogeny Animal Base Sequence Catfishes Dna, Mitochondrial Evolution, Molecular Genetic Variation Genome, Mitochondrial Genomics Mitochondria Molecular Sequence Annotation Phylogeny Rna, Ribosomal Sequence Analysis, Dna Moreira, Daniel Andrade Reducing the information gap on loricarioidei (Siluriformes) mitochondrial genomics |
| topic_facet |
Rna 12s Rna 16s Dna, Mitochondrial Ribosome Rna Callichthyidae Cladistics Controlled Study Fauna Gene Expression Regulation Gene Replication Genetic Conservation Genetic Parameters Genetic Variation Genomics Genotype-environment Interaction Hemiancistrus High Throughput Sequencing Hypostomini Loricariidae Mitochodrial Genomics Mitochondrial Gene Genome, Mitochondrial Molecular Ecology Evolution, Molecular Nonhuman Pairwise Nucleotide Identity Pareiorhaphis Garbei Peckoltia Phylogenetic Tree Schizolecis Guntheri Sequence Alignment Sequence Analysis Sequence Homology Siluriformes Species Difference Start Codon Stop Codon Structure Activity Relation Transcription Regulation Animals Catfish Dna Sequence Genetics Genomics Genome, Mitochondrial Mitochondrion Molecular Genetics Nucleotide Sequence Phylogeny Animal Base Sequence Catfishes Dna, Mitochondrial Evolution, Molecular Genetic Variation Genome, Mitochondrial Genomics Mitochondria Molecular Sequence Annotation Phylogeny Rna, Ribosomal Sequence Analysis, Dna |
| description |
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. © 2017 The Author(s). |
| format |
Artigo |
| author |
Moreira, Daniel Andrade |
| author2 |
Buckup, Paulo Andreas Furtado, Carolina Val, Adalberto Luis Schama, Renata Parente, Thiago E.M. |
| author2Str |
Buckup, Paulo Andreas Furtado, Carolina Val, Adalberto Luis Schama, Renata Parente, Thiago E.M. |
| title |
Reducing the information gap on loricarioidei (Siluriformes) mitochondrial genomics |
| title_short |
Reducing the information gap on loricarioidei (Siluriformes) mitochondrial genomics |
| title_full |
Reducing the information gap on loricarioidei (Siluriformes) mitochondrial genomics |
| title_fullStr |
Reducing the information gap on loricarioidei (Siluriformes) mitochondrial genomics |
| title_full_unstemmed |
Reducing the information gap on loricarioidei (Siluriformes) mitochondrial genomics |
| title_sort |
reducing the information gap on loricarioidei (siluriformes) mitochondrial genomics |
| publisher |
BMC Genomics |
| publishDate |
2020 |
| url |
https://repositorio.inpa.gov.br/handle/1/15736 |
| _version_ |
1787143174081216512 |
| score |
11.755432 |