Genomic Characterization of <i>hox</i> Genes in Senegalese Sole (<i>Solea senegalensis</i>, Kaup 1858): Clues to Evolutionary Path in Pleuronectiformes
The Senegalese sole (<i>Solea senegalensis</i>, Kaup 1858), a marine flatfish, belongs to the Pleuronectiformes order. It is a commercially important species for fisheries and aquaculture. However, in aquaculture, several production bottlenecks have still to be resolved, including skelet...
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MDPI AG
2022-12-01
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| author | Marco Mendizábal-Castillero Manuel Alejandro Merlo Ismael Cross María Esther Rodríguez Laureana Rebordinos |
| author_facet | Marco Mendizábal-Castillero Manuel Alejandro Merlo Ismael Cross María Esther Rodríguez Laureana Rebordinos |
| author_sort | Marco Mendizábal-Castillero |
| collection | DOAJ |
| description | The Senegalese sole (<i>Solea senegalensis</i>, Kaup 1858), a marine flatfish, belongs to the Pleuronectiformes order. It is a commercially important species for fisheries and aquaculture. However, in aquaculture, several production bottlenecks have still to be resolved, including skeletal deformities and high mortality during the larval and juvenile phase. The study aims to characterize the <i>hox</i> gene clusters in <i>S. senegalensis</i> to understand better the developmental and metamorphosis process in this species. Using a BAC library, the clones that contain <i>hox</i> genes were isolated, sequenced by NGS and used as BAC-FISH probes. Subsequently the <i>hox</i> clusters were studied by sequence analysis, comparative genomics, and cytogenetic and phylogenetic analysis. Cytogenetic analysis demonstrated the localization of four BAC clones on chromosome pairs 4, 12, 13, and 16 of the Senegalese sole cytogenomic map. Comparative and phylogenetic analysis showed a highly conserved organization in each cluster and different phylogenetic clustering in each <i>hox</i> cluster. Analysis of structural and repetitive sequences revealed accumulations of polymorphisms mediated by repetitive elements in the <i>hoxba</i> cluster, mainly retroelements. Therefore, a possible loss of the <i>hoxb7a</i> gene can be established in the Pleuronectiformes lineage. This work allows the organization and regulation of <i>hox</i> clusters to be understood, and is a good base for further studies of expression patterns. |
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| last_indexed | 2024-03-09T17:23:53Z |
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| spelling | doaj.art-4877dcb6da82457e86eb76ac2f9d53dc2023-11-24T12:52:23ZengMDPI AGAnimals2076-26152022-12-011224358610.3390/ani12243586Genomic Characterization of <i>hox</i> Genes in Senegalese Sole (<i>Solea senegalensis</i>, Kaup 1858): Clues to Evolutionary Path in PleuronectiformesMarco Mendizábal-Castillero0Manuel Alejandro Merlo1Ismael Cross2María Esther Rodríguez3Laureana Rebordinos4Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510 Cádiz, SpainÁrea de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510 Cádiz, SpainÁrea de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510 Cádiz, SpainÁrea de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510 Cádiz, SpainÁrea de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510 Cádiz, SpainThe Senegalese sole (<i>Solea senegalensis</i>, Kaup 1858), a marine flatfish, belongs to the Pleuronectiformes order. It is a commercially important species for fisheries and aquaculture. However, in aquaculture, several production bottlenecks have still to be resolved, including skeletal deformities and high mortality during the larval and juvenile phase. The study aims to characterize the <i>hox</i> gene clusters in <i>S. senegalensis</i> to understand better the developmental and metamorphosis process in this species. Using a BAC library, the clones that contain <i>hox</i> genes were isolated, sequenced by NGS and used as BAC-FISH probes. Subsequently the <i>hox</i> clusters were studied by sequence analysis, comparative genomics, and cytogenetic and phylogenetic analysis. Cytogenetic analysis demonstrated the localization of four BAC clones on chromosome pairs 4, 12, 13, and 16 of the Senegalese sole cytogenomic map. Comparative and phylogenetic analysis showed a highly conserved organization in each cluster and different phylogenetic clustering in each <i>hox</i> cluster. Analysis of structural and repetitive sequences revealed accumulations of polymorphisms mediated by repetitive elements in the <i>hoxba</i> cluster, mainly retroelements. Therefore, a possible loss of the <i>hoxb7a</i> gene can be established in the Pleuronectiformes lineage. This work allows the organization and regulation of <i>hox</i> clusters to be understood, and is a good base for further studies of expression patterns.https://www.mdpi.com/2076-2615/12/24/3586<i>Solea senegalensis</i><i>hox</i> genescytogenomicscomparative genomicsrepetitive sequences |
| spellingShingle | Marco Mendizábal-Castillero Manuel Alejandro Merlo Ismael Cross María Esther Rodríguez Laureana Rebordinos Genomic Characterization of <i>hox</i> Genes in Senegalese Sole (<i>Solea senegalensis</i>, Kaup 1858): Clues to Evolutionary Path in Pleuronectiformes Animals <i>Solea senegalensis</i> <i>hox</i> genes cytogenomics comparative genomics repetitive sequences |
| title | Genomic Characterization of <i>hox</i> Genes in Senegalese Sole (<i>Solea senegalensis</i>, Kaup 1858): Clues to Evolutionary Path in Pleuronectiformes |
| title_full | Genomic Characterization of <i>hox</i> Genes in Senegalese Sole (<i>Solea senegalensis</i>, Kaup 1858): Clues to Evolutionary Path in Pleuronectiformes |
| title_fullStr | Genomic Characterization of <i>hox</i> Genes in Senegalese Sole (<i>Solea senegalensis</i>, Kaup 1858): Clues to Evolutionary Path in Pleuronectiformes |
| title_full_unstemmed | Genomic Characterization of <i>hox</i> Genes in Senegalese Sole (<i>Solea senegalensis</i>, Kaup 1858): Clues to Evolutionary Path in Pleuronectiformes |
| title_short | Genomic Characterization of <i>hox</i> Genes in Senegalese Sole (<i>Solea senegalensis</i>, Kaup 1858): Clues to Evolutionary Path in Pleuronectiformes |
| title_sort | genomic characterization of i hox i genes in senegalese sole i solea senegalensis i kaup 1858 clues to evolutionary path in pleuronectiformes |
| topic | <i>Solea senegalensis</i> <i>hox</i> genes cytogenomics comparative genomics repetitive sequences |
| url | https://www.mdpi.com/2076-2615/12/24/3586 |
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