Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic
Abstract Background Phylogenetic gaps of public databases of reference sequences are a major obstacle for comparative genomics and management of marine resources, particularly in the Global South, where economically important fisheries and conservation flagship species often lack closely-related ref...
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| Format: | Article |
| Language: | English |
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BMC
2024-02-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-024-10035-5 |
| _version_ | 1827328489883172864 |
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| author | Marcela Alvarenga Ananda Krishna Pereira D’Elia Graciane Rocha Clara Alvarez Arantes Frederico Henning Ana Tereza Ribeiro de Vasconcelos Antonio Mateo Solé-Cava |
| author_facet | Marcela Alvarenga Ananda Krishna Pereira D’Elia Graciane Rocha Clara Alvarez Arantes Frederico Henning Ana Tereza Ribeiro de Vasconcelos Antonio Mateo Solé-Cava |
| author_sort | Marcela Alvarenga |
| collection | DOAJ |
| description | Abstract Background Phylogenetic gaps of public databases of reference sequences are a major obstacle for comparative genomics and management of marine resources, particularly in the Global South, where economically important fisheries and conservation flagship species often lack closely-related references. We applied target-enrichment to obtain complete mitochondrial genomes of marine ichthyofauna from the Brazilian coast selected based on economic significance, conservation status and lack of phylogenetically-close references. These included sardines (Dorosomatidae, Alosidae), mackerels (Scombridae) croakers (Sciaenidae), groupers (Epinephelidae) and snappers (Lutjanidae). Results Custom baits were designed to enrich mitochondrial DNA across a broad phylogenetic range of fishes. Sequencing generated approximately 100k reads per sample, which were assembled in a total of 70 complete mitochondrial genomes and include fifty-two new additions to GenBank, including five species with no previous mitochondrial data. Departures from the typical gene content and order occurred in only three taxa and mostly involved tRNA gene duplications. Start-codons for all genes, except Cytochrome C Oxidase subunit I (COI), were consistently ATG, whilst a wide range of stop-codons deviated from the prevailing TAA. Phylogenetic analysis confirmed assembly accuracy and revealed signs of cryptic diversification within the Mullus genus. Lineage delimitation methods using Sardinella aurita and S. brasiliensis mitochondrial genomes support a single Operational Taxonomic Unit. Conclusions Target enrichment was highly efficient, providing complete novel mitochondrial genomes with little sequencing effort. These sequences are deposited in public databases to enable subsequent studies in population genetics and adaptation of Latin American fish species and serve as a vital resource for conservation and management programs that rely on molecular data for species and genus-level identification. |
| first_indexed | 2024-03-07T15:18:39Z |
| format | Article |
| id | doaj.art-0f4526a3417642f1be487949876d348e |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-07T15:18:39Z |
| publishDate | 2024-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-0f4526a3417642f1be487949876d348e2024-03-05T17:46:38ZengBMCBMC Genomics1471-21642024-02-0125111310.1186/s12864-024-10035-5Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South AtlanticMarcela Alvarenga0Ananda Krishna Pereira D’Elia1Graciane Rocha2Clara Alvarez Arantes3Frederico Henning4Ana Tereza Ribeiro de Vasconcelos5Antonio Mateo Solé-Cava6CENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ)CENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ)CENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ)CENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ)CENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ)LNCC, Laboratório Nacional de Computação CientíficaCENIMP, Centro Nacional para a Identificação Molecular do Pescado, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ)Abstract Background Phylogenetic gaps of public databases of reference sequences are a major obstacle for comparative genomics and management of marine resources, particularly in the Global South, where economically important fisheries and conservation flagship species often lack closely-related references. We applied target-enrichment to obtain complete mitochondrial genomes of marine ichthyofauna from the Brazilian coast selected based on economic significance, conservation status and lack of phylogenetically-close references. These included sardines (Dorosomatidae, Alosidae), mackerels (Scombridae) croakers (Sciaenidae), groupers (Epinephelidae) and snappers (Lutjanidae). Results Custom baits were designed to enrich mitochondrial DNA across a broad phylogenetic range of fishes. Sequencing generated approximately 100k reads per sample, which were assembled in a total of 70 complete mitochondrial genomes and include fifty-two new additions to GenBank, including five species with no previous mitochondrial data. Departures from the typical gene content and order occurred in only three taxa and mostly involved tRNA gene duplications. Start-codons for all genes, except Cytochrome C Oxidase subunit I (COI), were consistently ATG, whilst a wide range of stop-codons deviated from the prevailing TAA. Phylogenetic analysis confirmed assembly accuracy and revealed signs of cryptic diversification within the Mullus genus. Lineage delimitation methods using Sardinella aurita and S. brasiliensis mitochondrial genomes support a single Operational Taxonomic Unit. Conclusions Target enrichment was highly efficient, providing complete novel mitochondrial genomes with little sequencing effort. These sequences are deposited in public databases to enable subsequent studies in population genetics and adaptation of Latin American fish species and serve as a vital resource for conservation and management programs that rely on molecular data for species and genus-level identification.https://doi.org/10.1186/s12864-024-10035-5Target-enrichment sequencingMitochondrial genomeComparative genomicsGenome structureConservation genomicsFisheries management |
| spellingShingle | Marcela Alvarenga Ananda Krishna Pereira D’Elia Graciane Rocha Clara Alvarez Arantes Frederico Henning Ana Tereza Ribeiro de Vasconcelos Antonio Mateo Solé-Cava Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic BMC Genomics Target-enrichment sequencing Mitochondrial genome Comparative genomics Genome structure Conservation genomics Fisheries management |
| title | Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic |
| title_full | Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic |
| title_fullStr | Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic |
| title_full_unstemmed | Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic |
| title_short | Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic |
| title_sort | mitochondrial genome structure and composition in 70 fishes a key resource for fisheries management in the south atlantic |
| topic | Target-enrichment sequencing Mitochondrial genome Comparative genomics Genome structure Conservation genomics Fisheries management |
| url | https://doi.org/10.1186/s12864-024-10035-5 |
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