A Comprehensive Integrated Genetic Map of the Complete Karyotype of Solea senegalensis (Kaup 1858)

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.

A chromosome-level genome assembly enables the identification of the follicle stimulating hormone receptor as the master sex determining gene in Solea senegalensis

“…The solution was filtered (mesh size 40 to 100 μm), subjected to a hypotonic shock with KCl and fixed in Carnoy solution. Positive BAC clones were isolated following Merlo et al (2021) and labelled either by nick translation (García-Cegarra et al, 2013) or by DOP-PCR (Portela-Bens et al, 2017). Pre-treatment, hybridization, post-hybridization and staining for double-fluorescence in situ hybridization (FISH) followed García-Cegarra et al (2013) and for multiple-FISH Portela-Bens et al (2017).…”

“…BAC clones were sequenced using either a Genome Sequencing FLX System or MiSeq Illumina by the LifesequencingTM Platform (Valencia, Spain). Assembly, functional and structural annotation of BAC sequences was carried out as previously reported (Merlo et al, 2021).…”

Fish Cytogenetics: Present and Future

“…There is also the case of the Senegal sole Solea senegalensis , for which a comprehensive integrated genetic map of the complete karyotype was presented. These data on the genome organization support the existence of a sex proto-chromosome pair and show that Robertsonian fusions and chromosomal inversions drive the evolution of the karyotype of this species, demonstrating the existence of conserved gene linkages shared with other fish model species [ 25 ]. Other examples concern Salmonid species.…”

Chromosome Identification and Cytogenetic Map Construction of Zhikong Scallop (Chlamys farreri) Based on Fluorescence in situ Hybridization

“…Unfortunately, there has been no unambiguous numbering and naming for all the chromosomes of C. farreri due to the lack of accurate chromosomal markers. In some species, such as sorghum (Kim et al, 2002(Kim et al, , 2005, silkworm (Yoshido et al, 2005), alpaca (Mendoza et al, 2020), and Senegalese sole (Merlo et al, 2021), all chromosomes could be identified by simultaneous FISH of a cocktail of landed large-insert DNA clones and/or repetitive DNA probes. In this study, we successfully distinguished all the 19 chromosomes of C. farreri through multiple two-color FISH and numbered them based on the chromosome-specific markers aided by the chromosomal morphology and lengths.…”

“…The development of fluorescence in situ hybridization (FISH) is a significant step toward chromosome identification, and FISH is a well-established approach for determining the location and relative order of DNA sequences in chromosomes (Zhang et al, 2008a;Merlo et al, 2021). The initial probes used as landmarks for chromosome distinguish were repetitive sequences, mainly including satellite sequences (Wang et al, 2001;Zhang et al, 2008a), ribosomal DNA (Zhang et al, 1999;Xu et al, 2001;Huang et al, 2007a,b), and histone genes (Eirín-López et al, 2002Zhang et al, 2007a).…”