Conventional and molecular cytogenetics of the pikeperch (Sander luciopercaL.)

Abstract

Pikeperch (Sander lucioperca L.) is a percid fish species of high commercial value and potential for being aquacultured in Europe. As such, pikeperch needs to be karyologically studied with special attention dedicated to arrangement of the homologous chromosomes into pairs and chromosomal location of the chosen DNA sequences. The karyotype of the pikeperch consists of 48 small chromosomes: One pair of metacentric chromosomes, 15 pairs of submetacentric chromosomes and eight pairs of subtelo‐acrocentric chromosomes (FN = 80). Original data on the chromosomal distribution of early and late replication regions, segments resistant to AluI, DdeI, HinfI and HaeIII restriction endonucleases and identification of the C‐banded heterochromatin presented herein have been used to arrange pikeperch chromosomes into the karyotype. After Primed in situ labeling (PRINS) technique with primers enabling amplification of 5S rDNA sequences, hybridization spots observed on the short (p) arms of two the largest pikeperch submetacentric chromosomes (no. 2). Fluorescence in situ hybridization (FISH) with telomeric PNA (Peptide Nucleic Acid) probe enabled recognition of the conservative telomeric DNA sequences on the pikeperch chromosomes. No interstitial signals were observed. The specimens studied did not show any morphologically differentiated sex chromosomes.

An ultra-high density SNP-based linkage map for enhancing the pikeperch (Sander lucioperca) genome assembly to chromosome-scale

“…A range of logarithm of odds (LOD) scores from 5 to 70 incrementing by 5 was tested for linkage grouping. A LOD score of 50 resulted in 24 LGs that were expected to match to the 24 chromosomes observed in karyotype studies in pikeperch 32,33 . In total, 1,023,625 SNPs were uniquely assigned to the 24 LGs and ordered to generate the female, male and sex-averaged linkage maps ( Table 2, Fig.…”

“…Additionally, 7 SNPs were found to be duplicated; they mapped to the same physical position because of collapsing or overlapping contigs in the target assembly. 32,33 . The number of linkage groups for the female, male and sex-averaged maps built in this study was chosen corresponding to the number of chromosome pairs from microscopic observations 32,33 .…”

“…32,33 . The number of linkage groups for the female, male and sex-averaged maps built in this study was chosen corresponding to the number of chromosome pairs from microscopic observations 32,33 . With the aim of identifying the chromosome type and specifying the location of centromeric regions, we applied the centromere mapping method developed by Limborg et al (2015) 42 to all linkage groups of our female map.…”

Telomeres in Fishes

“…Among actinopterygians, chromosomal location of the telomeric DNA repeats has been examined in the Chondrostei species from 2 orders: Acipenseriformes [Fontana et al, 1998[Fontana et al, , 2004[Fontana et al, , 2008 and Polypteriformes [Moreschalchi et al, 2007[Moreschalchi et al, , 2008. Within ray-finned fish of the infraclass Teleostei, the chromosomal distribution of the telomeric DNA sequences has been studied in fish species belonging to 15 orders: Anguilliformes [Salvadori et al, 1995], Batrachoidoformes [Merlo et al, 2007], Characiformes [de Marco Ferro et al, 2003;, Cypriniformes [Meyne et al, 1990;Gornung et al, 1998;Sola et al, 2003a;Ocalewicz et al, 2004a;Gromicho et al, 2006;Schmid et al, 2006], Gasterosteiformes [Ocalewicz et al, 2011], Gymnotiformes [Milhomem et al, 2008;Silva et al, 2009;Felippe and Foresti, 2010;Scacchetti et al, 2011], Mugiliformes [Gornung et al, 2004;Rossi et al, 2005], Osmeriformes , Perciformes [Mandrioli et al, 2000;Sola et al, 2000Sola et al, , 2003bChew et al, 2002;Molina and Galetti, 2002;Mota-Velasco et al, 2010;Wang et al, 2010;Jacobina et al, 2011;Ocalewicz and Sapota, 2011;Jankun et al, 2013], Pleuronectiformes [Cross et al, 2006;Ocalewicz et al, 2008a], Salmoniformes [Reed and Phillips, 1995;Abuin et al, 1996;…”

Hidden Compositional Heterogeneity of Fish Chromosomes in the Era of Polished Genome Assemblies

“…While several attempts have been made to apply G-banding to fish cytogenetics, the results have been largely variable [6][7][8][9] and unsuccessful [8,10,11]. Consequently, to identify homologous pairs, BrdU-labelling to visualise the early and latereplication regions [12][13][14][15] has been applied to fish chromosomes, along with fluorescence in situ hybridisation (FISH) of restriction fragments [12,13,15,16] and ribosomal or bacterial artificial chromosome markers [17]. So far, the only successful application of G-banding to fish chromosomes (proved by bioinformatics) has been with the extant genera Lepisosteus and Atractosteus [18] of ancient ray-fin fishes gars.…”