Replication banding studies in two cyprinid fishes

GC and Repeats Profiling along Chromosomes-The Future of Fish Compositional Cytogenomics

The study of fish cytogenetics has been impeded by the inability to produce G-bands that could assign chromosomes to their homologous pairs. Thus, the majority of karyotypes published have been estimated based on morphological similarities of chromosomes. The reason why chromosome G-banding does not work in fish remains elusive. However, the recent increase in the number of fish genomes assembled to the chromosome level provides a way to analyse this issue. We have developed a Python tool to visualize and quantify GC percentage (GC%) of both repeats and unique DNA along chromosomes using a non-overlapping sliding window approach. Our tool profiles GC% and simultaneously plots the proportion of repeats (rep%) in a color scale (or vice versa). Hence, it is possible to assess the contribution of repeats to the total GC%. The main differences are the GC% of repeats homogenizing the overall GC% along fish chromosomes and a greater range of GC% scattered along fish chromosomes. This may explain the inability to produce G-banding in fish. We also show an occasional banding pattern along the chromosomes in some fish that probably cannot be detected with traditional qualitative cytogenetic methods.

Paracentric Inversions Differentiate the Conservative Karyotypes in Two Centropomus Species (Teleostei: Centropomidae)

Centropomus is the sole genus of the Centropomidae family (Teleostei), comprising 12 species widely distributed throughout the Western Atlantic and Eastern Pacific, with 6 of them occurring in the Western Atlantic in extensive sympatry. Their life history and phylogenetic relationships are well characterized; however, aspects of chromosomal evolution are still unknown. Here, cytogenetic analyses of 2 Centropomus species of great economic value (C. undecimalis and C. mexicanus) were performed using conventional (Giemsa, Ag-NOR, and fluorochrome staining, C- and replication banding) and molecular (chromosomal mapping of 18S and 5S rDNA, H2A-H2B and H3 hisDNA, and (TTAGGG)n repeats) approaches. The karyotypes of both species were composed of 48 solely acrocentric chromosomes (2n = 48; FN = 48), but the single ribosomal site was located in varying positions in the long arms of the second largest chromosome pair. Replication bands were generally similar, although conspicuous differences were observed in some chromosome regions. In both species, the histone H3 genes were located on 3 apparently homeologous chromosome pairs, but the exact position of these clusters differed slightly. Interspecific hisDNA and rDNA site displacements can indicate the occurrence of multiple paracentric inversions during the evolutionary diversification of the Centropomus genomes. Although the karyotypes remained similar in both species, our data demonstrate an unsuspected microstructural reorganization between them, driven most likely by a series of paracentric inversions.

[FISH analysis of chromosomes of sweet potato(Ipomoea batatas cv.Xushu No.18)]

In order to understand the chromosome structure of sweet potato (Ipomoea batatas cv. Xushu 18), molecular cytogenetic analyses were carried out on I. batatas. by using 45S rDNA fluorescence in situ hybridization (45S rDNA-FISH), self genomic in situ hybridization (self-GISH), and silver staining techniques. Twelve, sixteen, and eighteen regions were silver stained in the interphase nucleus of I. batatas. The results of FISH analysis demonstrated 16 or 18 signals with different intensity on chromosomes of I. batatas. Self-GISH analysis showed that the intensive signals on I. batatas mitotic chromosomes were distributed along the chromosomes. However, the signals located in centromeric, subcentromeric, and telomeric regions were stronger and denser than those in other regions.

Cytogenetics of the bleak (Alburnus alburnus), with special emphasis on the B chromosomes

Some of the largest B chromosomes so far discovered in vertebrates are present in the cyprinid fish Alburnus alburnus. Previous cytogenetic analyses revealed a diploid chromosome number of 2n = 50. In addition, in some individuals one or two unusually large B chromosomes are present. Two morphologically different types of B chromosomes were observed. The frequency of animals bearing a supernumerary chromosome was found to vary considerably between different populations. A more detailed analysis of the A and B chromosomes of A. alburnus by conventional banding techniques, as well as fluorescence in-situ hybridization (FISH) with the telomeric DNA repeats (GGGTTA)7/(TAACCC)7, 18S + 28S rDNA and 5S rDNA were performed in the present study. Furthermore, a B chromosome-specific DNA probe obtained by amplified length polymorphism (AFLP) was hybridized on metaphases of A. alburnus carrying supernumerary B chromosomes. The banding analyses showed that the B chromosomes are completely heterochromatic, consist of GC-rich DNA sequences, replicate their DNA in the very late S-phase of the cell cycle and are composed mainly of a specific retrotransposable DNA element. Finally, blood probes from A. alburnus were collected for DNA-flow cytometric measurements. It could be shown that the huge supernumerary chromosomes represent nearly 10% of the total genome size of A. alburnus.

Chromosome evolution in fish: BrdU replication patterns demonstrate chromosome homeologies in two species of the genus Astyanax

A comparison of R-banding patterns obtained by 5-bromodeoxyuridine incorporation was made between the chromosomes of two fish species of the genus Astyanax (Characiformes: Tetragonopterinae), A. altiparanae with 2n = 50 chromosomes, and A. schubarti with 2n = 36 chromosomes. The two species present the highest and the lowest chromosome numbers found in this fish genus, respectively, for which the modal chromosome number is 50. R-band homeology was detected, involving eleven chromosomes of A. schubarti and seventeen chromosomes of A. altiparanae, indicating a close chromosomal relationship between the two species, in spite of their great difference in chromosome number. A chromosome fusion in the past history of the group was hypothesized as a possible cause of the discrepant chromosome numbers of the two species.

R- and G-band patterns in Astyanax scabripinnis paranae (Pisces, Characiformes, Characidae)

The absence of longitudinal bands in fish chromosomes has been associated with technical problems in chromosome preparations or the absence of a structural compartmentalization in the fish genome. In the present study, a R-banding pattern was obtained using a replication banding technique by in vivo treatment with 5-bromodeoxyuridine (5-BrdU). G-banding patterns were obtained after trypsin treatment and also after chromosome cleavage by in situ treatment with the restriction endonuclease BamHI. A similar G-banding pattern was also obtained after cleavage with the endonuclease HinfI. Presence of a resolute R- and G-banding patterns shows that Astyanax scabripinnis paranae chromosomes could present an isochore-like structure similar to that found in other vertebrates.

Chromosome complement, C-banding, Ag-NOR and replication banding in the zebrafish Danio rerio

The chromosome complement of Danio rerio was investigated by Giemsa staining and C-banding, Ag-NORs and replication banding. The diploid number of this species is 2n = 50 and the arm number (NF) = 100. Constitutive heterochromatin was located at the centromeric position of all chromosome pairs. Nucleolus organizer regions appeared in the terminal position of the long arms of chromosomes 1, 2 and 8. Replication banding pattern allowed the identification of each chromosome pair.

Brdu replication bands in the anguilliform fish Echelus myrus

High-resolution replication banding patterns have been obtained in prometaphase and metaphase chromosomes of the anguilliform fish species Echelus myrus by treating kidney cell cultures with 5-bromodeoxyuridine during the mid-late synthesis phase. The results show the superiority of the in vitro technique in obtaining a higher number of bands which permit an accurate identification of all chromosome pairs. Different replication patterns were compared with C-bands and silver-stained nucleolus organizer regions, providing information on the replication order of different chromatin regions.