In fishes, as in other vertebrate species, the DNA component of the telomeres consists of the tandemly repeated TTAGGG motif. The length of the telomeric arrays in fishes ranges from 2 to 25 kb and shortens with age in some of the species. To date, chromosomal distribution of the telomeric DNA sequences has been examined in approximately 80 fish species of which about 42% show additional telomeric hybridization signals far from the chromosomal termini. Based on the chromosomal location, such internally located telomeric repeats may be classified into 4 categories: (1) telomeric DNA sequences located at the pericentromeric regions, (2) interstitial telomeric sites observed between centromeres and the bona fide telomeres, (3) telomeric DNA sequences that scatter along the nucleolus organizer regions, and (4) telomeric DNA repeats interspersed with the entire chromosomes. Most of the pericentromeric and interstitial telomeric sequences in fish are possible relicts of chromosome fusion events. The origin of the telomeric sequences co- localizing with the major rDNA sequences or scattered along the whole chromosomes is not clear. Internally located telomeric repeats are considered as ‘hot spots' for recombination and thus may potentially increase the rates of chromosome breaks and rearrangements leading to the various chromosomal polymorphisms in fishes. FISH with telomeric probe applied to metaphase spreads of androgenetic specimens that hatched from eggs exposed to ionizing radiation before insemination enabled the detection of small radiation-induced fragments of maternal chromosomes. Remnants of the irradiated chromosomes were found to be ring chromosomes with the interstitial telomeric signals, telomerless rings, fragments with fused sister chromatids, and linear fragments with telomeres detected at both of their ends. The increasing availability of techniques enabling the study of fish telomeres and telomerase and the easy access to numerous fish species strongly confirm that these animals are promising models in research concerning the role of telomeres and telomerase in vertebrate aging, repair of ionizing radiation-induced DNA double strand breaks, and chromosomal rearrangements.

The understanding of the evolution of variable sex determination mechanisms across taxa requires comparative studies among closely related species. Following the fate of a known master sex-determining gene, we traced the evolution of sex determination in an entire teleost order (Esociformes). We discovered that the northern pike (Esox lucius) master sex-determining gene originated from a 65 to 90 million-year-old gene duplication event and that it remained sex-linked on undifferentiated sex chromosomes for at least 56 million years in multiple species. We identified several independent species- or population-specific sex determination transitions, including a recent loss of a Y-chromosome. These findings highlight the diversity of evolutionary fates of master sex-determining genes and the importance of population demographic history in sex determination studies. We hypothesize that occasional sex reversals and genetic bottlenecks provide a non-adaptive explanation for sex determination transitions.

BackgroundPikes represent an important genus (Esox) harbouring a pre-duplication karyotype (2n = 2x = 50) of economically important salmonid pseudopolyploids. Here, we have characterized the 5S ribosomal RNA genes (rDNA) in Esox lucius and its closely related E. cisalpinus using cytogenetic, molecular and genomic approaches. Intragenomic homogeneity and copy number estimation was carried out using Illumina reads. The higher-order structure of rDNA arrays was investigated by the analysis of long PacBio reads. Position of loci on chromosomes was determined by FISH. DNA methylation was analysed by methylation-sensitive restriction enzymes.ResultsThe 5S rDNA loci occupy exclusively (peri)centromeric regions on 30–38 acrocentric chromosomes in both E. lucius and E. cisalpinus. The large number of loci is accompanied by extreme amplification of genes (>20,000 copies), which is to the best of our knowledge one of the highest copy number of rRNA genes in animals ever reported. Conserved secondary structures of predicted 5S rRNAs indicate that most of the amplified genes are potentially functional. Only few SNPs were found in genic regions indicating their high homogeneity while intergenic spacers were more heterogeneous and several families were identified. Analysis of 10–30 kb-long molecules sequenced by the PacBio technology (containing about 40% of total 5S rDNA) revealed that the vast majority (96%) of genes are organised in large several kilobase-long blocks. Dispersed genes or short tandems were less common (4%). The adjacent 5S blocks were directly linked, separated by intervening DNA and even inverted. The 5S units differing in the intergenic spacers formed both homogeneous and heterogeneous (mixed) blocks indicating variable degree of homogenisation between the loci. Both E. lucius and E. cisalpinus 5S rDNA was heavily methylated at CG dinucleotides.ConclusionsExtreme amplification of 5S rRNA genes in the Esox genome occurred in the absence of significant pseudogenisation suggesting its recent origin and/or intensive homogenisation processes. The dense methylation of units indicates that powerful epigenetic mechanisms have evolved in this group of fish to silence amplified genes. We discuss how the higher-order repeat structures impact on homogenisation of 5S rDNA in the genome.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3774-7) contains supplementary material, which is available to authorized users.

SUMMARY The study provides new data on the stability of gamma radiation-induced chromosome fragments of a putative maternal nuclear genome in an androgenetic vertebrate, rainbow trout (Oncorhynchus mykiss Walbaum). The fragments were found in five of 16 examined individuals and they were mostly centromeric parts of metacentric or subtelocentric chromosomes. Chromosome fragments were identical in all cells of a given androgenetic individual,indicating that segregation of chromosome fragments is active from the early cell divisions. Most of the fragments were telomereless, i.e. they had no telomeric sequences on their ends. This shows that telomeres are not necessary for stability of chromosomal structures in a vertebrate genome. In one individual, the interstitial telomeric sites were found in chromosomes, which could be the effect of joining chromosome fragments.

The purpose of this work was to quantify the impact of spontaneous and X-radiation-induced chromosome rearrangements on survival rate of androgenetic rainbow trout (Oncorhynchus mykiss). Various doses of X irradiation (50, 150, 250, 350 Gy) were used for inactivation of nuclear DNA in oocytes. After the irradiation, eggs were inseminated with normal sperm from 4 males derived from a strain characterized by Robertsonian rearrangements and length polymorphism of the Y chromosome. The haploid zygotes were exposed to a high hydrostatic pressure (7000 psi) to duplicate the paternal DNA. Neither Robertsonian chromosome polymorphism nor the Y chromosome morphology impaired the viability of the androgenetic embryos and alevins. Moreover, survival of eyed embryos of the androgenetic rainbow trout increased significantly with increasing doses of oocyte X irradiation. After 6 months of rearing, only specimens from the 250 and 350 Gy variants survived. The number of fingerlings with remnants of the maternal genome in the forms of chromosome fragments was higher in the 250 Gy group. Intraindividual variation of chromosome fragment number was observed, and some individuals exhibited haploid/diploid mosaicism and body malformations. Individuals irradiated with less than 250 Gy died, presumably because of the conflict between intact paternally derived chromosomes and the residues of maternal genome in the form of chromosome fragments.

The chromosomal characteristics, locations and variations of the C-band positive heterochromatin and telomeric DNA sequences were studied in the European grayling karyotype (Thymallus thymallus, Salmonidae) using conventional C-banding, endonucleases digestion banding, silver nitrate (AgNO3), chromomycin A3 and 4′,6-diamidino-2-phenylindole staining techniques as well as fluorescence in situ hybridization (FISH) and primed in situ labelling. Original data on the chromosomal distribution of segments resistant to AluI restriction endonuclease and identification of the C-banded heterochromatin presented here have been used to characterize the grayling karyotype polymorphism. Structural and length polymorphism of the chromosome 21 showing a conspicuous heterochromatin block adjacent to the centromere seems to be the result of the deletion and inversion. Two pairs of nuclear organizer regions (NOR)-bearing chromosomes were found to be polymorphic in size and displaying several distinct forms. FISH with telomeric peptide nucleic acid probe enabled recognition of the conservative telomeric DNA sequences. The karyotype of the thymallid fish is thought to experienced numerous pericentric inversions and internal telomeric sites (ITSs) observed at the pericentromeric regions of the six European grayling metacentric chromosomes are likely relics of the these rearrangements. None of the ITS sites matched either chromosome 21 or NOR bearing chromosomes.

Highly polymorphic Arctic charr ( Salvelinus alpinus Linnaeus, 1758) chromosomes were studied using conventional and molecular methods. The diploid chromosome number in the studied individuals was 2n = 81 or 2n = 82, with a fundamental arm number (NF) = 100. These differences are due to Robertsonian fusions. Interindividual variation in the number and size of DAPI and CMA(3) positively stained chromatin sites was observed in studied specimens. In the case of two individuals, the subtelomeric region of the long arm (q) of the largest acrocentric chromosome (chromosome number 10) was positively stained by CMA(3) fluorochrome. Both primed in situ labelling (PRINS) and fluorescence in situ hybridization (FISH) revealed that this CMA(3)-positive region was flanked by telomeric sequences. Previously, the subterminal position of interstitial telomeric sequences located in the vicinity of the CMA(3)-positive guanine-rich chromatin have been described in two other Salvelinus species, brook trout ( Salvelinus fontinalis ) and lake trout ( Salvelinus namaycush ). Moreover, multichromosomal location and variation in size of CMA(3) bands have been observed in various Salvelinus taxa, including fishes with internally located telomeric sequences. These results suggest that relocation of CMA(3)-positive chromatin segments in these species may be facilitated by flanking interstitial telomeric sequences (ITSs).

Bivalent 1 of the synaptonemal complex (SC) in XY male Oreochromis niloticusshows an unpaired terminal region in early pachytene. This appears to be related to recombination suppression around a sex determination locus. To allow more detailed analysis of this, and unpaired regions in the karyotype of other Oreochromis species, we developed techniques for FISH on SC preparations, combined with DAPI staining. DAPI staining identified presumptive centromeres in SC bivalents, which appeared to correspond to the positions observed in the mitotic karyotype (the kinetochores could only be identified sporadically in silver stained EM SC images). Furthermore, two BAC clones containing Dmo (dmrt4) and OniY227 markers that hybridize to known positions in chromosome pair 1 in mitotic spreads (near the centromere, FLpter 0.25, and the putative sex determination locus, FLpter 0.57, respectively) were used as FISH probes on SCs to verify that the presumptive centromere identified by DAPI staining was located in the expected position. Visualization of both the centromere and FISH signals on bivalent 1 allowed the unpaired region to be positioned at Flpter 0.80 to 1.00, demonstrating that the unpaired region is located in the distal part of the long arm(s). Finally, differences between mitotic and meiotic measurements are discussed. (Foresti et al., 1993; Carrasco et al., 1999; Campos-Ramos et al., 2001;Griffin et al., 2002;Campos-Ramos et al., 2003). The exact relationship between these unpaired regions and sex determining loci in this genus is not clear: for example, a terminal region of the largest bivalent shows delayed pairing in XY O. niloticus but not in XX or YY genotypes (Carrasco et al., 1999), however sex-linked LG1 markers in this species have been mapped by FISH onto a small pair of chromosomes (Lee et al., 2003; Mota-Velasco, unpublished observations; Cnaani et al., 2008). Unpairing in both the largest bivalent and a small bivalent have been observed in WZ O. aureus at pachytene (Campos-Ramos et al., 2001), and linkage studies suggest two unlinked genes affect sex determination in this species, with the dominant one (WZ/ZZ, in LG3) mapping to the largest pair of chromosomes (Lee et al., 2004; Cnaani et al., 2008).The kinetochore (centromere) has been visualised in some TEM synaptonemal complex preparations in O. niloticus (Carrasco et al., 1999), allowing orientation of the unpaired region with respect to the chromosome, but this has not been achieved consistently. In this study, we set out to develop a technique that would allow both identification of the centromere and FISH on pachytene stage chromosomes, using male O. niloticus, with the objective of being able to simultaneously visualise unpaired 4 regions, centromeres and FISH markers at pachytene, to further the study of the role of delayed meiotic pairing in the evolution of sex determination in this genus. 5 Materials and Methods Experimental fishPhenotypic male and female O. niloticus (originating from Lake Manzallah, Egypt) used in this experi...