Cytogenomics Unveil Possible Transposable Elements Driving Rearrangements in Chromosomes 2 and 4 of <i>Solea senegalensis</i>

• Main Authors: María Esther Rodríguez, Ismael Cross, Alberto Arias-Pérez, Silvia Portela-Bens, Manuel Alejandro Merlo, Thomas Liehr, Laureana Rebordinos
• Format: Article
• Language: English
• Published: MDPI AG 2021-02-01
• Series: International Journal of Molecular Sciences
• Subjects: <i>Solea senegalensis</i>; cytogenomics; chromosome evolution; comparative genomic; repetitive sequences; robertsonian fusions
• Online Access: https://www.mdpi.com/1422-0067/22/4/1614
• ISSN: 1661-6596; 1422-0067

Cytogenomics, the integration of cytogenetic and genomic data, has been used here to reconstruct the evolution of chromosomes 2 and 4 of <i>Solea senegalensis</i>. <i>S. senegalensis</i> is a flat fish with a karyotype comprising 2n = 42 chromosomes: 6 metacentric + 4 submetacentric + 8 subtelocentric + 24 telocentric. The Fluorescence <i>in situ</i> Hybridization with Bacterial Artificial Chromosomes (FISH-BAC ) technique was applied to locate BACs in these chromosomes (11 and 10 BACs in chromosomes 2 and 4, respectively) and to generate integrated maps. Synteny analysis, taking eight reference fish species (<i>Cynoglossus semilaevis</i>, <i>Scophthalmus maximus</i>, <i>Sparus aurata</i>, <i>Gasterosteus aculeatus</i>, <i>Xiphophorus maculatus</i>, <i>Oryzias latipes</i>, <i>Danio rerio,</i> and <i>Lepisosteus oculatus</i>) for comparison, showed that the BACs of these two chromosomes of <i>S. senegalensis</i> were mainly distributed in two principal chromosomes in the reference species. Transposable Elements (TE) analysis showed significant differences between the two chromosomes, in terms of number of loci per Mb and coverage, and the class of TE (I or II) present. Analysis of TE divergence in chromosomes 2 and 4 compared to their syntenic regions in four reference fish species (<i>C. semilaevis</i>, <i>S. maximus</i>, <i>O. latipes,</i> and <i>D. rerio</i>) revealed differences in their age of activity compared with those species but less notable differences between the two chromosomes. Differences were also observed in peaks of divergence and coverage of TE families for all reference species even in those close to <i>S. senegalensis, </i>like <i>S. maximus</i> and <i>C. semilaevis</i>. Considered together, chromosomes 2 and 4 have evolved by Robertsonian fusions, pericentric inversions, and other chromosomal rearrangements mediated by TEs.