More sex chromosomes than autosomes in the Amazonian frog Leptodactylus pentadactylus.

Heteromorphic sex chromosomes are common in eukaryotes and largely ubiquitous in birds and mammals. The largest number of multiple sex chromosomes in vertebrates known today is found in the monotreme platypus (Ornithorhynchus anatinus, 2n = 52) which exhibits precisely 10 sex chromosomes. Interestingly, fish, amphibians, and reptiles have sex determination mechanisms that do or do not involve morphologically differentiated sex chromosomes. Relatively few amphibian species carry heteromorphic sex chromosomes, and when present, they are frequently represented by only one pair, either XX:XY or ZZ:ZW types. Here, in contrast, with several evidences, from classical and molecular cytogenetic analyses, we found 12 sex chromosomes in a Brazilian population of the smoky jungle frog, designated as Leptodactylus pentadactylus Laurenti, 1768 (Leptodactylinae), which has a karyotype with 2n = 22 chromosomes. Males exhibited an astonishing stable ring-shaped meiotic chain composed of six X and six Y chromosomes. The number of sex chromosomes is larger than the number of autosomes found, and these data represent the largest number of multiple sex chromosomes ever found among vertebrate species. Additionally, sequence and karyotype variation data suggest that this species may represent a complex of species, in which the chromosomal rearrangements may possibly have played an important role in the evolution process.

Neo-sex chromosomes of Ronderosia bergi: insight into the evolution of sex chromosomes in grasshoppers.

Sex chromosomes have evolved many times from morphologically identical autosome pairs, most often presenting several recombination suppression events, followed by accumulation of repetitive DNA sequences. In Orthoptera, most species have an X0♂ sex chromosome system. However, in the subfamily Melanoplinae, derived variants of neo-sex chromosomes (neo-XY♂ or neo-X1X2Y♂) emerged several times. Here, we examined the differentiation of neo-sex chromosomes in a Melanoplinae species with a neo-XY♂/XX♀ system, Ronderosia bergi, using several approaches: (i) classical cytogenetic analysis, (ii) mapping via fluorescent in situ hybridization of some selected repetitive DNA sequences and microdissected sex chromosomes, and (iii) immunolocalization of distinct histone modifications. The microdissected sex chromosomes were also used as sources for Polymerase chain reaction (PCR) amplification of RNA-coding multigene families, to study variants related to the sex chromosomes. Our data suggest that the R. bergi neo-Y has become differentiated after its formation by a Robertsonian translocation and inversions, and has accumulated repetitive DNA sequences. Interestingly, the ex autosomes incorporated into the neo-sex chromosomes retain some autosomal post-translational histone modifications, at least in metaphase I, suggesting that the establishment of functional modifications in neo-sex chromosomes is slower than their sequence differentiation.

A step to the gigantic genome of the desert locust: chromosome sizes and repeated DNAs.

The desert locust (Schistocerca gregaria) has been used as material for numerous cytogenetic studies. Its genome size is estimated to be 8.55 Gb of DNA comprised in 11 autosomes and the X chromosome. Its X0/XX sex chromosome determinism therefore results in females having 24 chromosomes whereas males have 23. Surprisingly, little is known about the DNA content of this locust's huge chromosomes. Here, we use the Feulgen Image Analysis Densitometry and C-banding techniques to respectively estimate the DNA quantity and heterochromatin content of each chromosome. We also identify three satellite DNAs using both restriction endonucleases and next-generation sequencing. We then use fluorescent in situ hybridization to determine the chromosomal location of these satellite DNAs as well as that of six tandem repeat DNA gene families. The combination of the results obtained in this work allows distinguishing between the different chromosomes not only by size, but also by the kind of repetitive DNAs that they contain. The recent publication of the draft genome of the migratory locust (Locusta migratoria), the largest animal genome hitherto sequenced, invites for sequencing even larger genomes. S. gregaria is a pest that causes high economic losses. It is thus among the primary candidates for genome sequencing. But this species genome is about 50 % larger than that of L. migratoria, and although next-generation sequencing currently allows sequencing large genomes, sequencing it would mean a greater challenge. The chromosome sizes and markers provided here should not only help planning the sequencing project and guide the assembly but would also facilitate assigning assembled linkage groups to actual chromosomes.

U1 snDNA clusters in grasshoppers: chromosomal dynamics and genomic organization.

The spliceosome, constituted by a protein set associated with small nuclear RNA (snRNA), is responsible for mRNA maturation through intron removal. Among snRNA genes, U1 is generally a conserved repetitive sequence. To unveil the chromosomal/genomic dynamics of this multigene family in grasshoppers, we mapped U1 genes by fluorescence in situ hybridization in 70 species belonging to the families Proscopiidae, Pyrgomorphidae, Ommexechidae, Romaleidae and Acrididae. Evident clusters were observed in all species, indicating that, at least, some U1 repeats are tandemly arrayed. High conservation was observed in the first four families, with most species carrying a single U1 cluster, frequently located in the third or fourth longest autosome. By contrast, extensive variation was observed among Acrididae, from a single chromosome pair carrying U1 to all chromosome pairs carrying it, with occasional occurrence of two or more clusters in the same chromosome. DNA sequence analysis in Eyprepocnemis plorans (species carrying U1 clusters on seven different chromosome pairs) and Locusta migratoria (carrying U1 in a single chromosome pair) supported the coexistence of functional and pseudogenic lineages. One of these pseudogenic lineages was truncated in the same nucleotide position in both species, suggesting that it was present in a common ancestor to both species. At least in E. plorans, this U1 snDNA pseudogenic lineage was associated with 5S rDNA and short interspersed elements (SINE)-like mobile elements. Given that we conclude in grasshoppers that the U1 snDNA had evolved under the birth-and-death model and that its intragenomic spread might be related with mobile elements.

Heterochromatin, sex chromosomes and rRNA gene clusters in Coprophanaeus beetles (Coleoptera, Scarabaeidae).

Repetitive DNA sequences constitute a high fraction of eukaryotic genomes and are considered a key component for the chromosome and karyotype evolution. For a better understanding of their evolutionary role in beetles, we examined the chromosomes of 5 species of the genus Coprophanaeus by C-banding, fluorochrome staining CMA3/DA/DAPI, and fluorescence in situ hybridization (FISH) with probes for 18S and 5S rRNA genes. The Coprophanaeus species have identical chromosome numbers and a conserved chromosome morphology. However, they show different sex chromosome forms, XY, Xy, XY(p), and heterochromatin seems to be involved in the origin and diversification of these forms. C-banding showed primarily the presence of diphasic chromosomes in all species examined. After CMA3/DA/DAPI staining, 1-9 autosomal pairs showed CMA3-positive blocks depending on the species, while DAPI-positive blocks were detected only in Coprophanaeusdardanus. FISH mapping revealed 5S rDNA signals in one autosomal pair in each species, whereas the number of pairs with 18S rDNA signals varied from 1-8 between the Coprophanaeus species. Our results suggest that distinct genetic mechanisms had been involved in the karyotype evolution of Coprophanaeus species, i.e. mechanisms maintaining the conserved number of 5S rDNA clusters and those generating variability in the amount of heterochromatin, sex chromosome forms, and distribution of 18S rDNA clusters.

Genomic organization and comparative chromosome mapping of the U1 snRNA gene in cichlid fish, with an emphasis in Oreochromis niloticus.

To better understand genomic and chromosomal organization and evolutionary patterns of the U1 snRNA gene in cichlid fish, the gene was cytogenetically mapped and comparatively analyzed in 19 species belonging to several clades of the group. Moreover, the distribution and organization of U1 snRNA gene was analyzed in the Oreochromis niloticus genome. The results indicated high conservation of one chromosomal cluster of U1 snRNA in the African, Asian, and South American species, with few variations in the chromosomal position of the clusters in the South American species. The genomic analysis of U1 revealed a distinct scenario from that observed under the cytogenetic mapping. An enrichment of the U1 gene on linkage group (LG) 14 was observed that did not correspond to the same chromosome that harbors the U1 cluster identified by cytogenetic mapping. Moreover, it was revealed that the presence of several distinct transposable elements in the U1 gene flanking regions could be involved in the spreading of this sequence, but the generation of new, large snRNA clusters (detectable by fluorescent in situ hybridization, FISH) is apparently hampered. These results contribute to the understanding of multigene families' evolution and reinforce the utility of integrative analysis and the use of cytogenetic and bioinformatic methods to address the genomic and chromosomal evolutionary patterns of repeated DNAs among vertebrates. Moreover, the U1 gene represents a useful new chromosomal marker for cytogenetic studies.

Comparative cytogenetics of ten species of cichlid fishes (Teleostei, Cichlidae) from the Araguaia River system, Brazil, by conventional cytogenetic methods.

Cichlids represent one of the most species-rich families of fishes and have attracted the attention of evolutionary biologists due to the rapid radiation occurring in some groups and the importance of some species in the world aquaculture. Cytogenetic analysis was conducted in 10 cichlid species from the Araguaia River, Amazon Basin, Brazil. The chromosome number was 2n=48 for all analyzed species except for Laetacara araguaiae Ottoni et Costa, 2009 (2n=44). Chromosomal polymorphism was detected only in Geophagus proximus (Castelnau, 1855), which exhibits an extra large submetacentric and and a dot-like chromosomes. Moreover, the C-banding revealed a general pericentromeric heterochromatic pattern and some additional blocks for some species. The heterochromatic blocks corresponding to AgNOR bearing regions were observed in all species and also corresponded to CMA3 positive blocks, which were observed in terminal regions. Besides the general conserved chromosomal and heterochromatin patterns for South American cichlids, the presence of GC-rich heterochromatin was quite different in the species Biotodoma cupido (Heckel, 1840), Geophagus proximus, Retroculus lapidifer (Castelnau, 1855), Crenicichla strigata Günther, 1862 and Heros efasciatus Heckel, 1840. The results suggest that independent events of heterochromatin modification occurred during chromosome evolution in the group, regardless of the conservation of macro-chromosomal structure.

Phosphorylation of histone H3S10 in animal chromosomes: is there a uniform pattern?

Phosphorylation of serine 10 in histone H3 (H3S10ph) has been extensively analyzed and appears to be a conserved chromatin change associated with chromosome condensation in different eukaryotic organisms. In this work, we report the distribution of H3S10ph during meiosis in monocentric and holokinetic chromosomes of 6 insect species and in mitotic chromosomes of 7 mammalian species, aiming to investigate the labeling patterns in phylogenetically distant groups. The results indicated a very similar phosphorylation timing and distribution pattern among insects. The sex chromosomes of insects analyzed were always undercondensed and hypophosphorylated. Similarly, the micro chromosomes of the bug Pachylis aff pharaonis were also undercondensed and hypophosphorylated. Holokinetic chromosomes of bugs and monocentric chromosomes of grasshoppers and beetles displayed identical phosphorylation pattern in spite of the difference in the centromere type. Among mammals, a uniform chromosome phosphorylation was observed in marsupials, whereas bat chromosomes displayed a longitudinal banding pattern. These data indicate that, in general, the intensity of H3S10 phosphorylation in animal chromosomes is variable among the distinct chromosome types and associated with the degree of chromatin condensation at metaphase, but it may vary between different groups of animals.

Cytogenetic mapping of rRNAs and histone H3 genes in 14 species of Dichotomius (Coleoptera, Scarabaeidae, Scarabaeinae) beetles.

Standard cytogenetic analyses and chromosomal mapping of the genes for 18S and 5S rRNAs and histone H3 were performed in 14 species of beetles of the genus Dichotomius (Coleoptera, Scarabaeidae, Scarabaeinae). Conserved karyotypes with 2n = 18 and biarmed chromosomes were observed in all species. Moreover, the presence of a large metacentric pair (pair 1) was characteristic in the studied species, evidencing a remarkable synapomorphy for this genus, which probably originated by an ancient fusion of 2 autosomes while the ancestral sex-chromosome pair remained conserved. FISH showed that the 5S rRNA and histone H3 genes are located in the proximal region of pair 2, with the 2 genes co-located. However, the major rDNA cluster probed by the 18S rRNA gene mapped to 1-3 bivalents, being exclusively autosomal, associated with sex elements, or both. In most species, the major rDNA cluster was observed in pair 3, and it was frequently (64.3%) located in the distal region regardless of the chromosome. The conserved number and position of the 5S rDNA/H3 histone cluster seems to be an ancient pattern shared by all of the studied species. In contrast, the major rDNA clusters apparently tolerate distinct patterns of diversification in the karyotypes of the species that could be associated with small inversions, ectopic recombination, and transposition. Moreover, we reinforced the association/co-localization between the 5S rRNA and histone H3 genes in this group contributing thus to the knowledge about the chromosomal organization and diversification patterns of multigene families in beetles and insects.

Cytogenetic mapping of 5S and 18S rRNAs and H3 histone genes in 4 ancient Proscopiidae grasshopper species: contribution to understanding the evolutionary dynamics of multigene families.

This paper reports on the chromosomal location of 18S rRNA, 5S rRNA and H3 histone multigene families in 4 species of a relatively ancient and diversified group of grasshoppers belonging to the family Proscopiidae. The 5S rRNA and H3 histone genes were highly conserved in the number of sites and chromosomal position in the 4th chromosome pair in all species analyzed, whereas the 18S rRNA genes showed slightly more variation because they were present on one or 2 chromosome pairs, depending on the species. The 5S and 18S rRNA gene families occurred in different chromosomes; in contrast, H3 histone and 5S rRNA genes co-localized in the same chromosomal position, with an apparently interspersed organization. Considering that the Proscopiidae family is a relatively ancient group compared with the Acrididae family, the association of the H3 histone and 5S rRNA multigene families can represent a basal condition for grasshoppers, although more research is needed on other representatives of this insect group to confirm this statement. The presence of such an association of 5S rDNA and H3 histone in mussels and arthropods (beetles, grasshoppers and crustaceans) suggests that this linked configuration could represent an ancestral pattern for invertebrates. These results provide new insights into the understanding of the genome organization and the evolution of multigene families in grasshoppers and in insects as a whole.

Cytogenetic analysis of two related Deltochilum (Coleoptera, Scarabaeidae) species: Diploid number reduction, extensive heterochromatin addition and differentiation.

Male mitotic and meiotic chromosomes of two species of the genus Deltochilum (Scarabaeidae) were analyzed through conventional staining, C-banding, base-specific fluorochromes, silver nitrate staining (AgNO(3)) and FISH (45S rDNA). The two species possessed karyotypes with 2n=14, neo-XY and meta-submetacentric chromosomes. The analysis of constitutive heterochromatin (CH) revealed mainly diphasic chromosomes in the two species, showing heterochromatic long arms. Silver nitrate staining labeled the blocks corresponding to CH in D. (Deltohyboma) aff morbillosum while in D. (Deltohyboma) calcaratum, AgNO(3) staining revealed only the CH blocks of the diphasic autosomes. The fluorochrome staining revealed in D. (D.) calcaratum the diphasic autosomes and the sex chromosomes with CMA(3)(+) blocks, and in D. (D.) aff morbillosum, the GC-rich sequences were restricted to the terminal regions of the long arms of the pairs 1 and 2 and the X. The FISH revealed 45S rDNA sites in two autosomic pairs and in the X chromosome. The analyses performed allowed for the identification of cytogenetic markers and the discussion of possible chromosome rearrangements that have been involved in the karyotypic differentiation of these species mainly related to the repetitive genome.

Chromosomal mapping of repetitive DNAs in the beetle Dichotomius geminatus provides the first evidence for an association of 5S rRNA and histone H3 genes in insects, and repetitive DNA similarity between the B chromosome and A complement.

Chromosomal banding techniques and repetitive DNA mapping are useful tools in comparative analysis and in the elucidation of genome organization of several groups of eukaryotes. In this study, we contributed to the knowledge of Coleoptera genomes by reporting the chromosomal organization of repetitive DNA sequences, as well as the presence and characteristics of a B chromosome in two natural populations of Dichotomius geminatus (Coleoptera; Scarabaeidae) using classical, chromosomal banding and molecular cytogenetic techniques. As in other coleopteran species, the heterochromatin was mainly concentrated in pericentromeric regions and the B chromosome was composed almost entirely of heterochromatin. Physical mapping using double fluorescent in situ hybridization was performed for the first time in Coleoptera; using DNA probes for 5S and 18S ribosomal RNA (rRNA) and histone H3 genes, we showed that ribosomal 18S rDNAs are located in chromosomes 3 and 4, whereas 5S rRNA and histone H3 genes are colocalized in chromosomal pair 2 and show an apparently interspersed organization. Moreover, these genes are not present in the B chromosome, suggesting that the B chromosome did not originate from chromosomal pairs 2, 3 or 4. On the other hand, mapping of the C(0)t-1 DNA fraction showed that the B chromosome is enriched in repetitive DNA elements, also present in the standard complement, indicating an intraspecific origin of this element in D. geminatus. These results will contribute to our understanding of genome organization and evolution of repetitive elements in Coleoptera and other insects regarding both A and B chromosomes.

Organization of repeated DNA elements in the genome of the cichlid fish Cichla kelberi and its contributions to the knowledge of fish genomes.

Repeated DNA elements have been extensively applied as physical chromosome markers in comparative studies for the identification of chromosomal rearrangements, the identification of sex chromosomes, chromosome evolution analysis and applied genetics. Here, we report the characterization of the transposable elements (TE) Tc1, Rex1, Rex3 and Rex6 and a new element called RCk in the genome of the South American cichlid fish Cichla kelberi using nucleotide sequence analysis and hybridization to metaphase chromosomes. The analysis of the repeated elements demonstrated that they are, in most cases, compartmentalized in heterochromatic regions, as has been observed in several other vertebrates. On the other hand, the elements Rex1 and Rex3 were also observed spanning extensive euchromatic regions on 2 chromosome pairs. The RCk element exhibits a wide distribution among fishes and also in amphibians, and it was spread throughout the chromosomes of C. kelberi. Our results have demonstrated that the compartmentalization of repeated elements is not restricted to heterochromatic segments, which has provided new concepts with regard to the genomic organization of transposons.