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Mendizábal-Castillero M, Merlo MA, Cross I, Rodríguez ME, Rebordinos L. Genomic Characterization of hox Genes in Senegalese Sole ( Solea senegalensis, Kaup 1858): Clues to Evolutionary Path in Pleuronectiformes. Animals (Basel) 2022; 12:ani12243586. [PMID: 36552509 PMCID: PMC9774920 DOI: 10.3390/ani12243586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
The Senegalese sole (Solea senegalensis, 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 hox gene clusters in S. senegalensis to understand better the developmental and metamorphosis process in this species. Using a BAC library, the clones that contain hox genes were isolated, sequenced by NGS and used as BAC-FISH probes. Subsequently the hox 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 hox cluster. Analysis of structural and repetitive sequences revealed accumulations of polymorphisms mediated by repetitive elements in the hoxba cluster, mainly retroelements. Therefore, a possible loss of the hoxb7a gene can be established in the Pleuronectiformes lineage. This work allows the organization and regulation of hox clusters to be understood, and is a good base for further studies of expression patterns.
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Ramírez D, Rodríguez ME, Cross I, Arias-Pérez A, Merlo MA, Anaya M, Portela-Bens S, Martínez P, Robles F, Ruiz-Rejón C, Rebordinos L. Integration of Maps Enables a Cytogenomics Analysis of the Complete Karyotype in Solea senegalensis. Int J Mol Sci 2022; 23:ijms23105353. [PMID: 35628170 PMCID: PMC9140517 DOI: 10.3390/ijms23105353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/28/2022] [Accepted: 05/09/2022] [Indexed: 02/06/2023] Open
Abstract
The Pleuronectiformes order, which includes several commercially-important species, has undergone extensive chromosome evolution. One of these species is Solea senegalensis, a flatfish with 2n = 42 chromosomes. In this study, a cytogenomics approach and integration with previous maps was applied to characterize the karyotype of the species. Synteny analysis of S. senegalensis was carried out using two flatfish as a reference: Cynoglossus semilaevis and Scophthalmus maximus. Most S. senegalensis chromosomes (or chromosome arms for metacentrics and submetacentrics) showed a one-to-one macrosyntenic pattern with the other two species. In addition, we studied how repetitive sequences could have played a role in the evolution of S. senegalensis bi-armed (3, and 5–9) and acrocentric (11, 12 and 16) chromosomes, which showed the highest rearrangements compared with the reference species. A higher abundance of TEs (Transposable Elements) and other repeated elements was observed adjacent to telomeric regions on chromosomes 3, 7, 9 and 16. However, on chromosome 11, a greater abundance of DNA transposons was detected in interstitial BACs. This chromosome is syntenic with several chromosomes of the other two flatfish species, suggesting rearrangements during its evolution. A similar situation was also found on chromosome 16 (for microsatellites and low complexity sequences), but not for TEs (retroelements and DNA transposons). These differences in the distribution and abundance of repetitive elements in chromosomes that have undergone remodeling processes during the course of evolution also suggest a possible role for simple repeat sequences in rearranged regions.
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Affiliation(s)
- Daniel Ramírez
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510 Cádiz, Spain; (D.R.); (M.E.R.); (I.C.); (A.A.-P.); (M.A.M.); (M.A.); (S.P.-B.)
| | - María Esther Rodríguez
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510 Cádiz, Spain; (D.R.); (M.E.R.); (I.C.); (A.A.-P.); (M.A.M.); (M.A.); (S.P.-B.)
| | - Ismael Cross
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510 Cádiz, Spain; (D.R.); (M.E.R.); (I.C.); (A.A.-P.); (M.A.M.); (M.A.); (S.P.-B.)
| | - Alberto Arias-Pérez
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510 Cádiz, Spain; (D.R.); (M.E.R.); (I.C.); (A.A.-P.); (M.A.M.); (M.A.); (S.P.-B.)
| | - Manuel Alejandro Merlo
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510 Cádiz, Spain; (D.R.); (M.E.R.); (I.C.); (A.A.-P.); (M.A.M.); (M.A.); (S.P.-B.)
| | - Marco Anaya
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510 Cádiz, Spain; (D.R.); (M.E.R.); (I.C.); (A.A.-P.); (M.A.M.); (M.A.); (S.P.-B.)
| | - Silvia Portela-Bens
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510 Cádiz, Spain; (D.R.); (M.E.R.); (I.C.); (A.A.-P.); (M.A.M.); (M.A.); (S.P.-B.)
| | - Paulino Martínez
- Departamento de Zoología, Genética y Antropología Física, Universidad de Santiago de Compostela, 27002 Lugo, Spain;
| | - Francisca Robles
- Departamento de Genética, Universidad de Granada, 18071 Granada, Spain; (F.R.); (C.R.-R.)
| | - Carmelo Ruiz-Rejón
- Departamento de Genética, Universidad de Granada, 18071 Granada, Spain; (F.R.); (C.R.-R.)
| | - Laureana Rebordinos
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, INMAR, Universidad de Cádiz, 11510 Cádiz, Spain; (D.R.); (M.E.R.); (I.C.); (A.A.-P.); (M.A.M.); (M.A.); (S.P.-B.)
- Correspondence: ; Tel.: +34-956-016181
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Merlo MA, Portela-Bens S, Rodríguez ME, García-Angulo A, Cross I, Arias-Pérez A, García E, Rebordinos L. A Comprehensive Integrated Genetic Map of the Complete Karyotype of Solea senegalensis (Kaup 1858). Genes (Basel) 2020; 12:genes12010049. [PMID: 33396249 PMCID: PMC7824234 DOI: 10.3390/genes12010049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 12/23/2022] Open
Abstract
Solea senegalensis aquaculture production has experienced a great increase in the last decade and, consequently, the genome knowledge of the species is gaining attention. In this sense, obtaining a high-density genome mapping of the species could offer clues to the aquaculture improvement in those aspects not resolved so far. In the present article, a review and new processed data have allowed to obtain a high-density BAC-based cytogenetic map of S. senegalensis beside the analysis of the sequences of such BAC clones to achieve integrative data. A total of 93 BAC clones were used to localize the chromosome complement of the species and 588 genes were annotated, thus almost reaching the 2.5% of the S. senegalensis genome sequences. As a result, important data about its genome organization and evolution were obtained, such as the lesser gene density of the large metacentric pair compared with the other metacentric chromosomes, which supports the theory of a sex proto-chromosome pair. In addition, chromosomes with a high number of linked genes that are conserved, even in distant species, were detected. This kind of result widens the knowledge of this species’ chromosome dynamics and evolution.
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