Integration of Maps Enables a Cytogenomics Analysis of the Complete Karyotype in Solea senegalensis

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.

Genomic Characterization of hox Genes in Senegalese Sole (Solea senegalensis, Kaup 1858): Clues to Evolutionary Path in Pleuronectiformes

“…The BAC clones 6D19, 39L15, and 51K20 were localized in acrocentric chromosome pairs, and the 29F20 was localized in a submetacentric chromosome pair. In order to ascertain the specific chromosome, each hox -bearing BAC clone was hybridized with chromosome markers selected from the cytogenetic map of S. senegalensis described by [ 17 ] ( Figure S5 , Figure 4 g). Thus, marker BAC 54E18 allows BAC 6D19 ( hoxab cluster) to be localized in the acrocentric pair number 16, close to the centromere.…”

“…In addition to the localization of the above-mentioned clusters, genomic data also allowed the other three clusters to be localized. The numbering of the chromosomes follows the pattern adopted for the cytogenetic map by [ 17 ], in which we established the equivalence of the chromosome numbering between the cytogenetic map and the genome assembly IFAPA_SoseM_1. Thus, the hoxaa cluster is localized in chromosome 10, the hoxba cluster in chromosome 15, and hoxdb in chromosome 18.…”

“…The recent advances achieved in the structural genomics of S. senegalensis [ 5 , 17 , 59 ] allow strategic research to be undertaken to resolve the most critical points for the culture of this species, i.e., those related to growth and development, including the metamorphosis process. In a previous study, 11 genes related to the metamorphosis in S. senegalensis were isolated from 11 BAC clones, showing a non-chromosome-specific localization [ 12 ], but hox genes were not included in such study.…”

“…Bioinformatics tools have allowed the characterization of genes and sequences of interest, such as those related to sexual differentiation, metamorphosis, immune response, histones, repetitive sequences, and transposable elements, among others [ 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 ]. In addition, these techniques have allowed evolutionary hypotheses to be inferred as well as the development of a high-density cytogenomic map [ 16 , 17 ].…”

Cytomolecular Organisation of the Nuclear Genome

“…In the following article, Ramirez et al [ 18 ] analyse the karyotype of Solea senegalensis (Senegalese sole), one of the aquaculturally most important flatfish species. Using BAC-FISH, the authors constructed a detailed cytogenetic map that they then integrated with already published linkage and physical maps.…”