Mapping Retrotransposon LINE-1 Sequences into Two Cebidae Species and Genomes and a Short Review on Primates.

This work focuses on the distribution of LINE-1 (a Long Interspersed Nuclear Element) in primates and its role during evolution and as a constituent of the architecture of primate genomes. To pinpoint the LINE-1 repeat distribution and its role among primates, LINE-1 probes were mapped onto chromosomes of (Hominidae, Catarrhini), , and (Cebidae, Platyrrhini) using fluorescence in situ hybridisation (FISH). The choice of platyrrhine species are due to the fact they are taxa characterised by a high level of rearrangements; for this reason, they could be a useful model for the study of LINE-1 and chromosome evolution.

Chromosome Distribution of Highly Conserved Tandemly Arranged Repetitive DNAs in the Siberian Sturgeon ().

Polyploid genomes present a challenge for cytogenetic and genomic studies, due to the high number of similar size chromosomes and the simultaneous presence of hardly distinguishable paralogous elements. The karyotype of the Siberian sturgeon () contains around 250 chromosomes and is remarkable for the presence of paralogs from two rounds of whole-genome duplications (WGD). In this study, we applied the sterlet-derived acipenserid satDNA-based whole chromosome-specific probes to analyze the Siberian sturgeon karyotype.

A combined banding method that allows the reliable identification of chromosomes as well as differentiation of AT- and GC-rich heterochromatin.

Сonstitutive heterochromatin areas are revealed by differential staining as C-positive chromosomal regions. These C-positive bands may greatly vary by location, size, and nucleotide composition. CBG-banding is the most commonly used method to detect structural heterochromatin in animals.

First cytogenetic analysis of lesser gymnures (Mammalia, Galericidae, ) from Vietnam.

Gymnures are an ancient group of small insectivorous mammals and are characterized by a controversial taxonomic status and the lack of a description of karyotypes for certain species. In this study, conventional cytogenetic techniques (Giemsa, CBG- and GTG-banding, Ag-NOR), CMA-DAPI staining, and fluorescent hybridization (FISH) with telomeric DNA probes were used to examine for the first time the karyotypes of lesser gymnures of group Müller, 1840 from northern and southern Vietnam. All studied specimens had karyotypes with 2=48, NF=64.

Next Generation Sequencing of Chromosome-Specific Libraries Sheds Light on Genome Evolution in Paleotetraploid Sterlet (Acipenser ruthenus).

Several whole genome duplication (WGD) events followed by rediploidization took place in the evolutionary history of vertebrates. Acipenserids represent a convenient model group for investigation of the consequences of WGD as their representatives underwent additional WGD events in different lineages resulting in ploidy level variation between species, and these processes are still ongoing. Earlier, we obtained a set of sterlet (Acipenser ruthenus) chromosome-specific libraries by microdissection and revealed that they painted two or four pairs of whole sterlet chromosomes, as well as additional chromosomal regions, depending on rediploidization status and chromosomal rearrangements after genome duplication.

Genomic Organization and Physical Mapping of Tandemly Arranged Repetitive DNAs in Sterlet (Acipenser ruthenus).

Acipenseriformes represent a phylogenetically basal clade of ray-finned fish characterized by unusual genomic traits, including paleopolyploid states of extant genomes with high chromosome numbers and slow rates of molecular evolution. Despite a high interest in this fish group, only a limited number of studies have been accomplished on the isolation and characterization of repetitive DNA, karyotype standardization is not yet complete, and sex chromosomes are still to be identified. Here, we applied next-generation sequencing and cluster analysis to characterize major fractions of sterlet (Acipenser ruthenus) repetitive DNA.

Evolutionary plasticity of acipenseriform genomes.

Acipenseriformes is an order of ray-finned fishes, comprising 27 extant species of sturgeons and paddlefishes inhabiting waters of the Northern Hemisphere. The order has a basal position within Actinopteri (ray-finned fish minus polypterids) and is characterized by many specific morphological and genomic features, including high diploid chromosome numbers, various levels of ploidy between species, unclear sex determination, and propensity to interspecific hybridization. Recent advances in molecular genetics, genomics, and comparative cytogenetics produced novel data on different aspects of acipenseriform biology, including improved phylogenetic reconstructions and better understanding of genome structure.

Segmental paleotetraploidy revealed in sterlet (Acipenser ruthenus) genome by chromosome painting.

Background: Acipenseriformes take a basal position among Actinopteri and demonstrate a striking ploidy variation among species. The sterlet (Acipenser ruthenus, Linnaeus, 1758; ARUT) is a diploid 120-chromosomal sturgeon distributed in Eurasian rivers from Danube to Enisey. Despite a high commercial value and a rapid population decline in the wild, many genomic characteristics of sterlet (as well as many other sturgeon species) have not been studied.

A new case of an inherited reciprocal translocation in cattle: rcp(13;26) (q24;q11).

This study reports on a unique balanced reciprocal chromosome translocation detected in a phenotypically normal cattle dam and her calf. CBG-, GTG-banding and FISH using bovine whole-chromosome and telomere probes were applied. The analyses showed that the breakpoints were located near to the centromere in chromosome 26 (q11) and exceptionally close to the telomere in chromosome 13 (q24).

Reconstruction of karyotype evolution in core Glires. I. The genome homology revealed by comparative chromosome painting.

Glires represent a eutherian clade consisting of rodents and lagomorphs (hares, rabbits, and pikas). Chromosome evolution of Glires is known to have variable rates in different groups: from slowly evolving lagomorphs and squirrels to extremely rapidly evolving muroids. Previous interordinal homology maps between slowly evolving Glires were based on comparison with humans.

Tracking genome organization in rodents by Zoo-FISH.

The number of rodent species examined by modern comparative genomic approaches, particularly chromosome painting, is limited. The use of human whole-chromosome painting probes to detect regions of homology in the karyotypes of the rodent index species, the mouse and rat, has been hindered by the highly rearranged nature of their genomes. In contrast, recent studies have demonstrated that non-murid rodents display more conserved genomes, underscoring their suitability for comparative genomic and higher-order systematic studies.

Cross-species chromosome painting among camel, cattle, pig and human: further insights into the putative Cetartiodactyla ancestral karyotype.

The great karyotypic differences between camel, cattle and pig, three important domestic animals, have been a challenge for comparative cytogenetic studies based on conventional cytogenetic approaches. To construct a genome-wide comparative chromosome map among these artiodactyls, we made a set of chromosome painting probes from the dromedary camel (Camelus dromedarius) by flow sorting and degenerate oligonucleotide primed-PCR. The painting probes were first used to characterize the karyotypes of the dromedary camel (C.

Karyotype evolution and phylogenetic relationships of hamsters (Cricetidae, Muroidea, Rodentia) inferred from chromosomal painting and banding comparison.

The evolutionary success of rodents of the superfamily Muroidea makes this taxon the most interesting for evolution studies, including study at the chromosomal level. Chromosome-specific painting probes from the Chinese hamster and the Syrian (golden) hamster were used to delimit homologous chromosomal segments among 15 hamster species from eight genera: Allocricetulus, Calomyscus, Cricetulus, Cricetus, Mesocricetus, Peromyscus, Phodopus and Tscherskia (Cricetidae, Muroidea, Rodentia). Based on results of chromosome painting and G-banding, comparative maps between 20 rodent species have been established.

Reciprocal chromosome painting between three laboratory rodent species.

The laboratory mouse (Mus musculus, 2n = 40), the Chinese hamster (Cricetulus griseus, 2n = 22), and the golden (Syrian) hamster (Mesocricetus auratus, 2n = 44) are common laboratory animals, extensively used in biomedical research. In contrast with the mouse genome, which was sequenced and well characterized, the hamster species has been set aside. We constructed a chromosome paint set for the golden hamster, which for the first time allowed us to perform multidirectional chromosome painting between the golden hamster and the mouse and between the two species of hamster.

Cross-species chromosome painting unveils cytogenetic signatures for the Eulipotyphla and evidence for the polyphyly of Insectivora.

Insectivore-like animals are traditionally believed among the first eutherian mammals that have appeared on the earth. The modern insectivores are thus crucial for understanding the systematics and phylogeny of eutherian mammals as a whole. Here cross-species chromosome painting, with probes derived from flow-sorted chromosomes of human, was used to delimit the homologous chromosomal segments in two Soricidae species, the common shrew (Sorex araneus, 2n = 20/21), and Asiatic short-tailed shrew (Blarinella griselda, 2n = 44), and one Erinaceidae species, the shrew-hedgehog (Neotetracus sinensis, 2n = 32), and human.

Evolution of genome organizations of squirrels (Sciuridae) revealed by cross-species chromosome painting.

With complete sets of chromosome-specific painting probes derived from flow-sorted chromosomes of human and grey squirrel (Sciurus carolinensis), the whole genome homologies between human and representatives of tree squirrels (Sciurus carolinensis, Callosciurus erythraeus), flying squirrels (Petaurista albiventer) and chipmunks (Tamias sibiricus) have been defined by cross-species chromosome painting. The results show that, unlike the highly rearranged karyotypes of mouse and rat, the karyotypes of squirrels are highly conserved. Two methods have been used to reconstruct the genome phylogeny of squirrels with the laboratory rabbit (Oryctolagus cuniculus) as the out-group: (1) phylogenetic analysis by parsimony using chromosomal characters identified by comparative cytogenetic approaches; (2) mapping the genome rearrangements onto recently published sequence-based molecular trees.