Conserved satellite DNA motif and lack of interstitial telomeric sites in highly rearranged African Nothobranchius killifish karyotypes

Using African annual killifishes of the genus Nothobranchius from temporary savannah pools with rapid karyotype and sex chromosome evolution, we analysed the chromosomal distribution of telomeric (TTAGGG)n repeat and Nfu-SatC satellite DNA (satDNA; isolated from Nothobranchius furzeri) in 15 species across the Nothobranchius killifish phylogeny, and with Fundulosoma thierryi as an out-group. Our fluorescence in situ hybridization experiments revealed that all analysed taxa share the presence of Nfu-SatC repeat but with diverse organization and distribution on chromosomes. Nfu-SatC landscape was similar in conspecific populations of Nothobranchius guentheri and Nothobranchius melanospilus but slightly-to-moderately differed between populations of Nothobranchius pienaari, and between closely related Nothobranchius kuhntae and Nothobranchius orthonotus. Inter-individual variability in Nfu-SatC patterns was found in N. orthonotus and Nothobranchius krysanovi. We revealed mostly no sex-linked patterns of studied repetitive DNA distribution. Only in Nothobranchius brieni, possessing multiple sex chromosomes, Nfu-SatC repeat occupied a substantial portion of the neo-Y chromosome, similarly as formerly found in the XY sex chromosome system of turquoise killifish N. furzeri and its sister species Nothobranchius kadleci-representatives not closely related to N. brieni. All studied species further shared patterns of expected telomeric repeats at the ends of all chromosomes and no additional interstitial telomeric sites. In summary, we revealed (i) the presence of conserved satDNA class in Nothobranchius clades (a rare pattern among ray-finned fishes); (ii) independent trajectories of Nothobranchius sex chromosome differentiation, with recurrent and convergent accumulation of Nfu-SatC on the Y chromosome in some species; and (iii) genus-wide shared tendency to loss of telomeric repeats during interchromosomal rearrangements. Collectively, our findings advance our understanding of genome structure, mechanisms of karyotype reshuffling, and sex chromosome differentiation in Nothobranchius killifishes from the genus-wide perspective.

[Genomic Markers Associated with Cold-Hardiness in Brassica rapa L.]

Brassica rapa L. is a valuable and widespread species, but its cultivation in risk farming areas requires high-quality cold-hardy varieties to be developed. Mechanisms of the cold stress response in plants involve expression of numerous genes, including ribosomal ones, and are related to plant chromosome variability. FISH- and PCR-based methods were used to study intraspecific chromosome variability in the number and localization of 45S and 5S rDNA clusters and also to examine a set of molecular markers associated with cold-hardiness in winter B. rapa cultivars from high-risk farming areas. Several SSR (Na10-CO3 and BrgMS5339-1) and SCAR (BoCCA1-F/BoCCA1-1R1 and BoCCA1-F/BoCCA1-2R1) markers were identified as suitable for diagnosing cold-resistant and cold-susceptible genotypes in B. rapa. Compared with fodder cultivars, oilseed and leaf cultivars were shown to have more molecular markers associated with cold-hardiness and a higher level of polymorphism for the chromosomal distribution of 45S and 5S rDNAs, including chromosome heteromorphism. Thus, the least cold-resistant genotypes were found to display the lowest level of chromosome variability in the distribution of the 45S and 5S rDNA clusters and vice versa. The findings could be useful for the development of new cold-tolerant B. rapa varieties.

Wide dispersion of B chromosomes in Rhammatocerus brasiliensis (Orthoptera, Acrididae)

The grasshopper Rhammatocerus brasiliensis shows polymorphism of B chromosomes, but the magnitude of B-chromosome occurrence and the factors that may contribute to their dispersion in the species remain unknown thus far. The present study analyzed the occurrence and dispersion of B chromosomes in R. brasiliensis individuals from 21 populations widely distributed in the Brazilian Northeast. The genetic connectivity between 10 populations was verified through analysis of ISSR markers from 200 individuals. Of the 21 populations, 19 presented individuals with one B chromosome, three with two, and one with three B chromosomes. The B chromosome is of medium size and constitutive heterochromatin (CH) located in the pericentromeric region. A variant B chromosome was observed in three populations, similar in size to that of chromosome X, gap and CH, and located in the terminal region. B chromosome frequencies in different populations varied from 0% to 18,8%, mean 8,5%. The wide distribution of the B chromosome is likely a consequence of the positive gene flow among the analyzed populations. B-chromosome occurrence in populations of R. brasiliensis possibly follows the population genetic structure of the species and, owing to the existence of a variant, its origin may not be recent.

Cytogenetic markers as a tool for characterization of hybrids of Astyanax Baird & Girard, 1854 and Hyphessobrycon Eigenmann, 1907

Astyanax Baird et Girard, 1854, is one of the largest genera in the family Characidae and comprises 177 valid species. This genus has been the focus of cytogenetic studies primarily owing to the presence of B chromosomes and high karyotypic diversity among different populations. The intense genetic variability in Astyanax is one of the factors responsible for the occurrence of species complexes, which are groups (1) with certain difficulties in establishing common genetic pools or (2) belonging to different cryptic species. To evaluate cytogenetic marker inheritance and the possibility of the identification of these hybrids, this study aimed to describe cytogenetic hybrids from three strains of species of the genera Astyanax and Hyphessobrycon Eigenmann, 1908. A. lacustris Lütken, 1875, A. schubarti Britski, 1964, A. fasciatus Cuvier, 1819, and H. anisitsi Eigenmann, 1907 were used to generate three hybrid lineages. The diploid number, heterochromatin sites, and ribosomal genes (18S and 5S rDNA) of the parental strains and the hybrids were analyzed. The results indicated that the three hybrid lineages had cytogenetic markers of both parents, presenting Mendelian inheritance. However, differences in distribution of heterochromatic blocks were observed between the hybrids and the parent strains. Our results allowed the identification of the hybrid strains based on the cytogenetic markers applied, reinforcing the efficiency of cytogenetic markers as tools for identification and indicating that such events may increase the karyotypic diversity in the genera Astyanax and Hyphessobrycon.

Cytogenetic characterization of Hypostomus soniae Hollanda-Carvalho & Weber, 2004 from the Teles Pires River, southern Amazon basin: evidence of an early stage of an XX/XY sex chromosome system

In the present study, we analyzed individuals of Hypostomus soniae (Loricariidae) collected from the Teles Pires River, southern Amazon basin, Brazil. Hypostomus soniae has a diploid chromosome number of 2n = 64 and a karyotype composed of 12 metacentric (m), 22 submetacentric (sm), 14 subtelocentric (st), and 16 acrocentric (a) chromosomes, with a structural difference between the chromosomes of the two sexes: the presence of a block of heterochromatin in sm pair No. 26, which appears to represent a putative initial stage of the differentiation of an XX/XY sex chromosome system. This chromosome, which had a heterochromatin block, and was designated proto-Y (pY), varied in the length of the long arm (q) in comparison with its homolog, resulting from the addition of constitutive heterochromatin. It is further distinguished by the presence of major ribosomal cistrons in a subterminal position of the long arm (q). The Nucleolus Organizer Region (NOR) had different phenotypes among the H. soniae individuals in terms of the number of Ag-NORs and 18S rDNA sites. The origin, distribution and maintenance of the chromosomal polymorphism found in H. soniae reinforced the hypothesis of the existence of a proto-Y chromosome, demonstrating the rise of an XX/XY sex chromosome system.

Karyotype characteristics, chromosomal polymorphism and gene COI sequences of Chironomus heteropilicornis Wülker, 1996 (Diptera, Chironomidae) from the South Caucasus

The study presents data on the karyotype characteristics, features of chromosomal polymorphism and the gene COI sequences of Chironomus heteropilicornis Wülker, 1996 (Diptera, Chironomidae) from the South Caucasus. We found 8 banding sequences in the Caucasian population. Overall, The Caucasian population of the species can be characterized as having a low level of polymorphism. We found one new banding sequence hpiA2 in the banding sequence pool of Ch. heteropilicornis. We observed inversion polymorphism only in the arm F. The dendrogram of genetic distances by Nei criteria (1972) shows a clear separation of the Caucasian population from populations of Siberia. At the same time, the distance between populations of Siberia and the population of South Caucasus (0.379-0.445) almost reach the mean distance (0.474 ± 0.314) between subspecies (Gunderina 2001). Due to this, we can assume that the population of South Caucasus separated from Siberian populations at the level of subspecies. Constructed on data for COI gene sequences the phylogenetic tree estimated by the Bayesian inference shows that the sequences of Ch. heteropilicornis from the South Caucasus form a separate line in the general branch of Ch. heteropilicornis sequences. At the same time, calculated K2P genetic distances between Ch. heteropilicornis sequences from Norway and Caucasus (2.0-2.2%) do not exceed the 3% threshold for the genus Chironomus.

B Chromosomes in Populations of Mammals Revisited

The study of B chromosomes (Bs) started more than a century ago, while their presence in mammals dates since 1965. As the past two decades have seen huge progress in application of molecular techniques, we decided to throw a glance on new data on Bs in mammals and to review them. We listed 85 mammals with Bs that make 1.94% of karyotypically studied species. Contrary to general view, a typical B chromosome in mammals appears both as sub- or metacentric that is the same size as small chromosomes of standard complement. Both karyotypically stable and unstable species possess Bs. The presence of Bs in certain species influences the cell division, the degree of recombination, the development, a number of quantitative characteristics, the host-parasite interactions and their behaviour. There is at least some data on molecular structure of Bs recorded in nearly a quarter of species. Nevertheless, a more detailed molecular composition of Bs presently known for six mammalian species, confirms the presence of protein coding genes, and the transcriptional activity for some of them. Therefore, the idea that Bs are inert is outdated, but the role of Bs is yet to be determined. The maintenance of Bs is obviously not the same for all species, so the current models must be adapted while bearing in mind that Bs are not inactive as it was once thought.

Karyotype characteristics and chromosomal polymorphism of Chironomus "annularius" sensu Strenzke (1959) (Diptera, Chironomidae) from the Caucasus region

The study presents data on the karyotype characteristics and features of chromosomal polymorphism of Chironomus "annularius" sensu Strenzke (1959) (Diptera, Chironomidae) from three populations of the Caucasus region (South and Central Caucasus, and Eastern Ciscaucasia). We found 17 banding sequences in the Caucasian populations. We observed inversion polymorphism in almost all chromosome arms except for arm G. The genetic distances between all the studied populations of Ch. "annularius" were calculated using Nei criteria (1972). In spite of relative geographic proximity, the genetic distances between populations of the Caucasus are quite large, and they do not form a single cluster of Caucasian populations. The population of the South Caucasus goes to the European cluster, the population of the Central Caucasus goes to the Asian cluster and the population of Eastern Ciscaucasia does not belong to any of the outlined clusters. Principal component analysis (PCA) shows a similar picture. Two of the Caucasian populations do not follow Hardy-Weinberg expectation, there being a marked deficiency of heterozygotes in arms A, B and C, arguably, due to negative selection of heterozygotes or founder effect. All the obtained data are indicative of the complex genetic structure of Caucasian populations of Ch. "annularius" and total complexity microevolution processes occurring in the Caucasus region.

Karyotype characteristics and polymorphism peculiarities of Chironomusbernensis Wülker & Klötzli, 1973 (Diptera, Chironomidae) from the Central Caucasus and Ciscaucasia

Data about the karyotype characteristics, features of chromosomal polymorphism and larval morphology of populations of Chironomusbernensis Wülker & Klötzli, 1973 (Diptera, Chironomidae) from the Central Caucasus (the northern macroslope) and Ciscaucasia are presented. The characteristics of the pericentromeric regions of the long chromosomes of this species from Caucasian populations were very similar to the ones from some European populations (from Poland and Italy), but differed from Swiss and Siberian populations. In the North Caucasian populations 10 banding sequences were found: two in arms A, C, and E, and one in arms B, D, F, and G. Nine of them were already known for this species, and one, berC2, is described for the first time. Cytogenetic distances between all the studied populations of Chironomusbernensis show that close geographical location of all studied populations from the Central Caucasus and Ciscaucasia is reflected in their similar cytogenetic structure, but on the other hand, that they are more closely related to populations from Europe than to populations from Western Siberia. At the same time, all studied larvae from Caucasian populations have a four-bladed premandible, instead of a two-bladed one, as in the description of Chironomusbernensis from Switzerland (Wülker and Klötzli 1973, Polukonova 2005c). These peculiarities may indicate the relative isolation of the Caucasus from the viewpoint of microevolution. Further research on karyological and morphological characteristics of Chironomusbernensis from geographically distant regions is necessary as there is a possibility that the presently known species is actually polytypic and consists of several sibling species.

Genome structure and dynamics of the yeast pathogen Candida glabrata

The yeast pathogen Candida glabrata is the second most frequent cause of Candida infections. However, from the phylogenetic point of view, C. glabrata is much closer to Saccharomyces cerevisiae than to Candida albicans. Apparently, this yeast has relatively recently changed its life style and become a successful opportunistic pathogen. Recently, several C. glabrata sister species, among them clinical and environmental isolates, have had their genomes characterized. Also, hundreds of C. glabrata clinical isolates have been characterized for their genomes. These isolates display enormous genomic plasticity. The number and size of chromosomes vary drastically, as well as intra- and interchromosomal segmental duplications occur frequently. The observed genome alterations could affect phenotypic properties and thus help to adapt to the highly variable and harsh habitats this yeast finds in different human patients and their tissues. Further genome sequencing of pathogenic isolates will provide a valuable tool to understand the mechanisms behind genome dynamics and help to elucidate the genes contributing to the virulence potential.

A hybrid zone of the genus Ctenomys: A case study in southern Brazil

We describe variation at microsatellite loci and the chromosomal polymorphisms of a hybrid population, and hybridizing populations of Ctenomys minutus (the minor tuco-tuco) from the coastal plain of Rio Grande do Sul, southern Brazil. Cytogenetic analysis and a survey of six microsatellite loci included 101 specimens of C. minutus from the parental populations (2n/AN = 42/74 and 48a/76) and their contact zone. Cytogenetic analysis recorded 26 different karyotypes exhibited by 50 individuals from the hybrid population. Of the 26 karyotypes, only 14% presented a parental-like configuration, and none had the combinations of 2n and AN expected for an F1 hybrid. The remaining karyotypes were alternative hybrid forms, with 2n varying from 42 to 46 and AN from 68 to 80. These results suggest chromosomal rearrangements are only of minor significance in the establishment of reproductive barriers for this species.

Karyotype and genome size of Iberochondrostoma almacai (Teleostei, Cyprinidae) and comparison with the sister-species I.lusitanicum

This study aimed to define the karyotype of the recently described Iberian endemic Iberochondrostoma almacai, to revisit the previously documented chromosome polymorphisms of its sister species I.lusitanicum using C-, Ag-/CMA₃ and RE-banding, and to compare the two species genome sizes. A 2n = 50 karyotype (with the exception of a triploid I.lusitanicum specimen) and a corresponding haploid chromosome formula of 7M:15SM:3A (FN = 94) were found. Multiple NORs were observed in both species (in two submetacentric chromosome pairs, one of them clearly homologous) and a higher intra and interpopulational variability was evidenced in I.lusitanicum. Flow cytometry measurements of nuclear DNA content showed some significant differences in genome size both between and within species: the genome of I. almacai was smaller than that of I.lusitanicum (mean values 2.61 and 2.93 pg, respectively), which presented a clear interpopulational variability (mean values ranging from 2.72 to 3.00 pg). These data allowed the distinction of both taxa and confirmed the existence of two well differentiated groups within I. lusitanicum: one that includes the populations from the right bank of the Tejo and Samarra drainages, and another that reunites the southern populations. The peculiar differences between the two species, presently listed as “Critically Endangered”, reinforced the importance of this study for future conservation plans.