All histone sequences were found to be associated with TEs. In situ localization revealed that these DNA sequences are dispersed throughout the autosomes of the species, but they are not involved in differentiation of the specific region of the W sex chromosome in C.
We discuss mechanisms of TE invasion into multigene families that lead to microstructural variation in Characidium genomes. The genomes of all studied eukaryotic species primarily consist of repetitive sequences that are dispersed or found in tandem Sumner, Repetitive sequences were identified in fragile sites and evolutionary break point regions, promoting non-B DNA conformations and double-strand breaks, which are involved in chromosomal rearrangements Eichler and Sankoff, ; Szamalek, ; Wells, ; Barros et al.
Repetitive sequences are also responsible for a significant portion of the karyotype variations observed in many groups of organisms Kidwell, Dispersed DNA sequences can move between chromosome sites, with this movement occurring in the presence or absence of RNA as a transposition intermediate Tollis and Boissinot, These mobile segments are called transposable elements TEs and are classified as retrotransposons class I elements, RNA intermediates of the transposition process or transposons class II elements, DNA intermediates of the transposition process Wicker et al.
These mobile elements can drive genetic and genomic evolution and influence eukaryotic gene regulatory systems Feschotte, In addition to consisting of dispersed DNA sequences, eukaryotic genomes are also enriched in tandem repeats of DNA sequences Hardman, and groups of repeated and linked genes located at the same chromosomal region, shaping clustered but not tandemly repeated genes such as multigene families Hentschel and Birnstiel, ; Heintz et al.
A multigene family is described as a group of genes with similar functions and sequences that originate from a common ancestral gene Nei and Rooney, Histone genes do not have introns, and they comprise a multigene family in which the five genes are in the same order but separated by spacer DNA Hentschel and Birnstiel, Concerning genome diversification, fish represent an important group for studies of genetic variability.
The genus Characidium Characiformes: Crenuchidae presents a diversified karyotype microstructure despite its conserved karyotype macrostructure and prevalent diploid number 2n of 50 Centofante et al. The Characidium species studied to date exhibited differences mainly in the number of ribosomal DNA sites and sex chromosomes Pansonato-Alves et al. The primary goal of this study was to perform sequence analyses and chromosome mapping of some repeated sequences isolated from the genome of C.
Retroelement of Xiphophorus Rex TEs were mapped to chromosomes to elucidate their possible involvement in Characidium karyotype evolution and diversification. The multigene families of U2 snRNA and histones H1, H3, and H4 were also investigated through chromosome mapping and sequence analyses.
Our study revealed associations between TEs and the multigene families. The obtained results will improve our understanding of the evolution and diversification of Characidium genomes.
Individuals of the following species were collected at the indicated locations: C. Chromosome preparations were subjected to conventional Giemsa staining to determine 2n and the chromosome formula. The sequences were edited and analyzed using Geneious 7. Finally, the sequences were deposited in GenBank Table S2. Chromosome spreads were subjected to FISH using the constructed probes.
Chromosomes were counterstained with 4'6-diamidinophenylindole 0. Approximately 20 metaphases were analyzed for each species, and karyotypes were determined from the highest-quality images. Chromosomes were classified as metacentric, submetacentric, subtelocentric, or acrocentric according to the arm ratio Levan et al. The studied species presented a 2n of 50, and these chromosomes have been cytogenetically described by Machado et al. No differentiated sex chromosomes were found in the C.
The C. However, Rex1 did not display clear marks in the Z and W chromosomes either C. Rex3 did not hybridize with the Z and W chromosomes of C. The U2 snRNA probe displayed a single cluster of hybridization signals in the pericentromeric region of meta-centric pair 1 in all analyzed species, with no additional dispersed sites detected Figure 3a—c.
The H1 histone gene probe displayed primary clusters of hybridization signals in the pericentromeric region and short arm of one chromosome of metacentric pair 10, whereas only one cluster was found in the pericentromeric region of the other chromosome in pair 10 of C.
An additional cluster was noted in pair 7 of C. In addition, each species exhibited weak additional signals in several other autosomes Figure 3d—f. The H3 gene probe displayed primary clusters of hybridization signals in the pericentromeric region and short arm of one chromosome of metacentric pair 10 and one cluster in the pericentromeric region of the other chromosome in pair 10 of C. One cluster was also found in the short arm of metacentric pair 5 of C. The H4 gene probe revealed primary clusters of hybridization signals in the pericentromeric region and short arm of one chromosome in metacentric pair 10 and one cluster in the pericentromeric region of the other chromosome in pair 10 of C.
Marks were also noted in some autosomes of both populations of C. Rex elements are non-LTR retrotransposons Wicker et al. Rex1 and Rex3 are significant sequences in the organization and evolution of the genomes in most of the aforementioned species, as indicated by evident hybridization signals and prominent amounts of these sequences.
In this analysis, Rex1 and Rex3 elements were dispersed in small clusters throughout the chromosomes, and they did not display significant chromosome reorganization between Characidium species.
Concerning the distribution of Rex1 and Rex3 in the sex chromosomes, no hybridization sites were identified in the Z and W sex chromosomes of Characidium , whereas these elements are involved in sex chromosome evolution in other species. The Rex1 and Rex3 elements analyzed in the Characidium genome emerged in the ancestral species C.
However, these elements did not exhibit high transposition rates, presenting only small clusters in some autosomes in all analyzed species.
Moreover, the Rex3 element was not identified in the genome of C. Natural selection may minimize the transposition rate, promoting vertical inactivation Lohe et al. Another possible explanation for the low transposition rate could be stochastic loss, in which the element is gradually removed from the genome, as observed for mariner- like elements in the Drosophila melanogaster species complex Lohe et al. Chromosome mapping of U2 snRNA revealed localized clusters in the first metacentric pair in all studied species.
The results suggest that both SSRs were distributed throughout the arms of all chromosomes after the divergence of S. The second stage in the evolution of the genus is relatively young, in the Pleistocene, after the geographical separation of the perennial inbreeding species S. Because deletion may be more difficult or may occur less frequently, it seems reasonable to assume that africanum constitutes an isolated branch that was separated from the rest before the amplification of the bp family, the interstialization of the bp family, and the bifurcation of the rest of the species.
After an indefinite period of time they became disjoined and evolved separately. The main events concerning the repetitive families have been the transference of the bp family from the telomeres toward interstitial sites in S. The homologous physical maps for the distribution of all the repetitive families studied in cultivated and weedy forms of S. In the same context, it should be assumed that the subspecies of the complex group strictum are really the result of independent evolution of isolated populations belonging to the single species S.
The remaining arms of S. The restriction fragment length polymorphism RFLP -based genetic map also suggests this multiple translocation Devos et al. Cuadrado and Jouve , using highly repeat families of rye in FISH experiments were unable to identify the chromosomes involved in these structural interchanges.
Comparison of the physical maps reported in the present study allow the identification of additional putative regions involved in translocations differentiating the different taxa. Heemert and Sybenga , using aneuploids and a standard tester set of reciprocal translocations in S. Differences in the pattern of distribution of AAC 5 in the arm 4RL between africanum and the rest of the complex group strictum seem to suggest that the distal region of this arm could be involved in a translocation.
This was previously suggested for the species S. Due to the high degree of polymorphism and the differences found between the Secale species, we cannot confirm that differences in the physical mapping with these repeats will be due to chromosomal rearrangements. Maybe the potential of such an approach will be in the identification of chromosomes involved in pairing figures in meiosis of the partially fertile hybrids, using simultaneous visualization of multiple DNA probes by FISH.
This kind of analysis proved useful in studying the homologies between T. Corresponding Editor: Stephen J. For chromosome identification the distribution pattern of pSc All chromosomes 1R—7R belong to the same metaphase. Arrows indicate B chromosomes found in this species. Schematic drawing of AAC 5 distribution patterns on rye Imperial. Hybridization sites were overlaid onto the standard karyotype of Sybenga Sites that were seen in Imperial are drawn in dark gray.
Asterisks on right indicate sites not observed in other varieties. Sites observed in other varieties but not in Imperial are drawn in light gray.
Nucleolus-organizing regions on the short arm of chromosome 1R are shown as gaps. Schematic phylogenetic tree only at the species level S. For the outbreeding subspecies of S. The main events, which occurred during the speciation process in the genus Secale , are also summaries. Boxes indicate when a repeat DNA sequence is amplified for the first time. Hammer of the Germplasm Bank at Gatersleben Germany kindly supplied wild materials. A molecular description of telomeric heterochromatin in Secale species.
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Identification of different chromatin classes in wheat using in situ hybridization with simple sequence repeat oligonucleotides. Theor Appl Genet. Chromosomal rearrangements in the rye genome relative to wheat. Assignment of linkage groups to pea chromosomes after karyotyping and gene mapping by fluorescent in situ hybridization. Sequence organization of the repeating units in the nucleus of wheat which contain 5S rRNA genes. Nucleic Acids Res. Heemert CV, Sybenga J, Identification of the three chromosomes involved in the translocation which structurally differentiates the genome of Secale cereale L.
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Cytogenet Cell Genet. Oxford University Press is a department of the University of Oxford. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide. Sign In or Create an Account. Sign In. Figure 4. Materials and Methods The gene annotation of D.
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