Genome and Phylogenetic Analysis of Genes Involved in the Immune System of Solea senegalensis – Potential Applications in Aquaculture

Abstract

Global aquaculture production continues to increase rapidly. One of the most important species of marine fish currently cultivated in Southern Europe is Solea senegalensis , reaching more than 300 Tn in 2017. In the present work, 14 Bacterial Artificial Chromosome (BAC) clones containing candidate genes involved in the immune system ( b2m , il10 , tlr3 , tap1 , tnf α, tlr8 , trim25 , lysg , irf5 , hmgb2 , calr , trim16 , and mx ), were examined and compared with other species using multicolor Fluorescence in situ Hybridization (mFISH), massive sequencing and bioinformatic analysis to determine the genomic surroundings and syntenic chromosomal conservation of the genomic region contained in each BAC clone. The mFISH showed that the groups of genes hmgb2-trim25-irf5-b2m ; tlr3-lysg ; tnfα-tap1 , and il10-mx-trim16 were co-localized on the same chromosomes. Synteny results suggested that the studied BACs are placed in a smaller number of chromosomes in S. senegalensis that in other species. Phylogenetic analyses suggested that the evolutionary rate of immune system genes studied is similar among the taxa studied, given that the clustering obtained was in accordance with the accepted phylogenetic relationships among these species. This study contributes to a better understanding of the structure and function of the immune system of the Senegalese sole, which is essential for the development of new technologies and products to improve fish health and productivity.

Development of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in Senegalese sole

“…Flatfish genome comparisons have demonstrated a high degree of conservation at macrosynteny level 5 , 57 , 58 . Our data confirmed that most of chromosomes matched one-by-one with different chromosomes of C. semilaevis supporting this high conservation observed in other flatfish.…”

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

“…The largest metacentric pair has been proposed as a sex proto-chromosome pair, due to different lines of evidence, such as the accumulation of genes related to sex [ 35 , 37 ], existence of Robertsonian fusion [ 33 , 36 ], evidence of recurrent chromosomal inversions [ 36 , 37 ] and accumulation of repetitive sequences [ 28 , 36 ]. Recently, an analysis of the 24 genes related to the immune system in Senegalese sole showed some tendency to group in a few chromosomes, which could provide an evolutionary advantage [ 6 ].…”

“…Through the FISH-BAC technique, the acquisition of the cytogenetic map of the species has been deepened and integrated with physical maps, by using different genes of interest for the cultivation of the species. Similarly, it has been possible to characterize and locate the BAC clones with other types of sequences of interest, such as miRNAs or transposons [ 6 , 28 , 33 , 34 ]. As a result of these studies, evidence has accumulated that the pair of major metacentric chromosomes of S. senegalensis could be a pair of sex proto-chromosomes, which have followed a specific evolutionary pattern involving, among other events, Robertsonian fusion [ 33 , 35 , 36 , 37 ].…”

“…This has led several studies to deepen the knowledge of the biology of the Senegalese sole in order to translate it into an improvement for production. Thus, studies related to the life cycle, reproduction, physiology, pathology, genetics and genomics have been carried out [3][4][5][6][7]. However, the genomic data of this species are still scarce compared to other similar species and insufficient to be used in breeding programs.…”

Cytogenomics Unveil Possible Transposable Elements Driving Rearrangements in Chromosomes 2 and 4 of Solea senegalensis

“…Comparative genomics of orthologous sequences located in the karyotype has opened new ways to detect karyotype differences because it allows comparisons to be made between species, genera, and even families, providing a more detailed overview of the evolutionary changes in the karyotype. It also allows us to overcome serious limitations of cytological studies such as genetic disruption of meiotic pairing and indistinguishable chromosomes [3,4].…”