Integration of fluorescence in situ hybridization and chromosome-length genome assemblies revealed synteny map for guinea pig, naked mole-rat, and human.

Descriptions of karyotypes of many animal species are currently available. In addition, there has been a significant increase in the number of sequenced genomes and an ever-improving quality of genome assembly. To close the gap between genomic and cytogenetic data we applied fluorescent in situ hybridization (FISH) and Hi-C technology to make the first full chromosome-level genome comparison of the guinea pig (Cavia porcellus), naked mole-rat (Heterocephalus glaber), and human.

Chromosome evolution in Iberolacerta, a genus that deviates from the standard karyotype formula of Lacertidae.

This paper describes the preparation of flow-sorted chromosome paints from the Iberian Rock lizard Iberolacerta monticola, exemplifying their subsequent use in cross-species comparisons of chromosome painting. We carried out comparative analyses of chromosome evolution in the congeneric species I. galani and I.

Estimating sequence diversity of prion protein gene () in Portuguese populations of two cervid species: red deer and fallow deer.

Among the transmissible spongiform encephalopathies (TSEs), chronic wasting disease (CWD) in cervids is now a rising concern in wildlife within Europe, after the detection of the first case in Norway in 2016, in a wild reindeer and until June 2022 a total of 34 cases were described in Norway, Sweden and Finland. The definite diagnosis is , performed in target areas of the brain and lymph nodes. Samples are first screened using a rapid test and, if positive, confirmed by immunohistochemistry and Western immunoblotting.

Observations on chromosome-specific sequencing for the construction of cross-species chromosome homology maps and its resolution of human:alpaca homology.

Background: The history of comparative chromosome mapping is briefly reviewed, with discussion about the problem that occurs in chromosome painting when size heteromorphisms between homologues cause contamination in chromosomes sorted by flow cytometry that are used in the preparation of chromosome-specific DNA probes.

Main Body: As an example, we show in the alpaca (Vicagna pacos) that sequencing of contaminated chromosome sorts can reveal chromosome homologies from alignment with human and mouse genome reference sequences. The procedure identifies syntenic blocks of DNA separated in the human karyotype that are associated in the closely related alpaca and dromedary (Camelus dromedarius) karyotypes.

Whole-chromosome fusions in the karyotype evolution of (Iguania, Reptilia) are more frequent in sex chromosomes than autosomes.

Whole-chromosome fusions play a major role in the karyotypic evolution of reptiles. It has been suggested that certain chromosomes tend to fuse with sex chromosomes more frequently than others. However, the comparative genomic synteny data are too scarce to draw strong conclusions.

New Data on Comparative Cytogenetics of the Mouse-Like Hamsters ( Thomas, 1905) from Iran and Turkmenistan.

The taxonomy of the genus remains controversial. According to the latest systematics the genus includes eight species with great karyotypic variation. Here, we studied karyotypes of 14 individuals from different regions of Iran and Turkmenistan using a new set of chromosome painting probes from a sp.

Neuropathology of Animal Prion Diseases.

Transmissible Spongiform Encephalopathies (TSEs) or prion diseases are a fatal group of infectious, inherited and spontaneous neurodegenerative diseases affecting human and animals. They are caused by the conversion of cellular prion protein (PrP) into a misfolded pathological isoform (PrP or prion- proteinaceous infectious particle) that self-propagates by conformational conversion of PrP. Yet by an unknown mechanism, PrP can fold into different PrP conformers that may result in different prion strains that display specific disease phenotype (incubation time, clinical signs and lesion profile).

An 8.22 Mb Assembly and Annotation of the Alpaca () Y Chromosome.

The unique evolutionary dynamics and complex structure make the Y chromosome the most diverse and least understood region in the mammalian genome, despite its undisputable role in sex determination, development, and male fertility. Here we present the first contig-level annotated draft assembly for the alpaca () Y chromosome based on hybrid assembly of short- and long-read sequence data of flow-sorted Y. The latter was also used for cDNA selection providing Y-enriched testis transcriptome for annotation.

Comparative chromosome painting in hummingbirds (Trochilidae).

Hummingbirds (Trochilidae) are one of the most enigmatic avian groups, and also among the most diverse, with approximately 360 recognized species in 106 genera, of which 43 are monotypic. This fact has generated considerable interest in the evolutionary biology of the hummingbirds, which is reflected in a number of DNA-based studies. However, only a few of them explored chromosomal data.

Chromosomal Evolution in the Phylogenetic Context: A Remarkable Karyotype Reorganization in Neotropical Parrot (Psittacidae).

is a small Neotropical parrot (Psittaciformes: Arini Tribe) from subtropical and temperate regions of South America. It has a diploid chromosome number 2 = 48, different from other members of the Arini Tribe that have usually 70 chromosomes. The species has the lowest 2 within the Arini Tribe.

A Comprehensive Cytogenetic Analysis of Several Members of the Family Columbidae (Aves, Columbiformes).

The Columbidae species (Aves, Columbiformes) show considerable variation in their diploid numbers (2n = 68-86), but there is limited understanding of the events that shaped the extant karyotypes. Hence, we performed whole chromosome painting (wcp) for paints GGA1-10 and bacterial artificial chromosome (BAC) probes for chromosomes GGA11-28 for , , , and . was only investigated with paints because BACs for GGA10-28 had been previously analyzed.

Phylogenetic Analysis and Karyotype Evolution in Two Species of Core Gruiformes: and .

Gruiformes is a group with phylogenetic issues. Recent studies based on mitochondrial and genomic DNA have proposed the existence of a core Gruiformes, consisting of five families: Heliornithidae, Aramidae, Gruidae, Psophiidae and Rallidae. Karyotype studies on these species are still scarce, either by conventional staining or molecular cytogenetics.

Novel insights into chromosome evolution of Charadriiformes: extensive genomic reshuffling in the wattled jacana (Jacana jacana, Charadriiformes, Jacanidae).

The order Charadriiformes comprises three major clades: Lari and Scolopaci as sister group to Charadrii. Until now, only three Charadriiformes species have been studied by chromosome painting: Larus argentatus (Lari), Burhinus oedicnemus and Vanellus chilensis (Charadrii). Hence, there is a lack of information concerning the third clade, Scolapaci.

Chromosome Painting Does Not Support a Sex Chromosome Turnover in Lacerta agilis Linnaeus, 1758.

Reptiles show a remarkable diversity of sex determination mechanisms and sex chromosome systems, derived from different autosomal pairs. The origin of the ZW sex chromosomes of Lacerta agilis, a widespread Eurasian lizard species, is a matter of discussion: is it a small macrochromosome from the 11-18 group common to all lacertids, or does this species have a unique ZW pair derived from the large chromosome 5? Using independent molecular cytogenetic methods, we investigated the karyotype of L. agilis exigua from Siberia, Russia, to identify the sex chromosomes.

Hybridization between subterranean tuco-tucos (Rodentia, Ctenomyidae) with contrasting phylogenetic positions.

Reproductive compatibility usually decreases according to increasing genetic difference and the time of divergence between species. However, the amount of modification required to influence hybridization may vary in different species. Thus, it is extremely important to conduct studies that seek to understand what and how variables influence the reproductive isolation of species.

Smart Sampling and Probing: Are You Getting All the Relevant Information?

Background: Sampling (collecting) and probing (testing, measuring) are very common tasks in the analytical field, where we need to characterize a given system and complex samples. In this action, we try to ensemble maximal information related with the system under a given study, and, frequently, we may end an inefficient analytical situation.

Objective: The best way to avoid "oversampling" and "overprobing" is to evaluate the number of factors and objects that may be present in a current data set.

Sexual conflict in action: An antagonistic relationship between maternal and paternal sex allocation in the tammar wallaby, .

Sex ratio biases are often inconsistent, both among and within species and populations. While some of these inconsistencies may be due to experimental design, much of the variation remains inexplicable. Recent research suggests that an exclusive focus on mothers may account for some of the inconsistency, with an increasing number of studies showing variation in sperm sex ratios and seminal fluids.

Identification of two independent X-autosome translocations in closely related mammalian (Proechimys) species.

Multiple sex chromosome systems have been described for several mammalian orders, with different species from the same genus sharing the same system (e.g., XXY or XYY).

Genetic Content of the Neo-Sex Chromosomes in Ctenonotus and Norops (Squamata, Dactyloidae) and Degeneration of the Y Chromosome as Revealed by High-Throughput Sequencing of Individual Chromosomes.

Pleurodont lizards are characterized by an ancient system of sex chromosomes. Along with stability of the central component of the system (homologous to the X chromosome of Anolis carolinensis [Dactyloidae], ACAX), in some genera the ancestral sex chromosomes are fused with microautosomes, forming neo-sex chromosomes. The genus Ctenonotus (Dactyloidae) is characterized by multiple X1X1X2X2/X1X2Y sex chromosomes.

Conserved sex chromosomes and karyotype evolution in monitor lizards (Varanidae).

Despite their long history with the basal split dating back to the Eocene, all species of monitor lizards (family Varanidae) studied so far share the same chromosome number of 2n = 40. However, there are differences in the morphology of the macrochromosome pairs 5-8. Further, sex determination, which revealed ZZ/ZW sex microchromosomes, was studied only in a few varanid species and only with techniques that did not test their homology.

Isolating Chromosomes of the Komodo Dragon: New Tools for Comparative Mapping and Sequence Assembly.

We developed new tools to build a high-quality chromosomal map of the Komodo dragon (Varanus komodoensis) available for cross-species phylogenomic analyses. First, we isolated chromosomes by flow sorting and determined the chromosome content of each flow karyotype peak by FISH. We then isolated additional Komodo dragon chromosomes by microdissection and amplified chromosome-specific DNA pools.

Chromosome Painting in Neotropical Long- and Short-Tailed Parrots (Aves, Psittaciformes): Phylogeny and Proposal for a Putative Ancestral Karyotype for Tribe Arini.

Most Neotropical Psittacidae have a diploid number of 2n = 70, and a dichotomy in chromosome patterns. Long-tailed species have biarmed macrochromosomes, while short-tailed species have telo/acrocentric macrochromosomes. However, the use of chromosome painting has demonstrated that karyotype evolution in Psittacidae includes a high number of inter/intrachromosomal rearrangements.

Marsupial chromosome DNA content and genome size assessed from flow karyotypes: invariable low autosomal GC content.

Extensive chromosome homologies revealed by cross-species chromosome painting between marsupials have suggested a high level of genome conservation during evolution. Surprisingly, it has been reported that marsupial genome sizes vary by more than 1.2 Gb between species.

Comparative chromosome painting in Columbidae (Columbiformes) reinforces divergence in Passerea and Columbea.

Pigeons and doves (Columbiformes) are one of the oldest and most diverse extant lineages of birds. However, the karyotype evolution within Columbiformes remains unclear. To delineate the synteny-conserved segments and karyotypic differences among four Columbidae species, we used chromosome painting from Gallus gallus (GGA, 2n = 78) and Leucopternis albicollis (LAL, 2n = 68).

Toward the Understanding of Micro-TLC Behavior of Various Dyes on Silica and Cellulose Stationary Phases Using A Data Mining Approach.

Planar chromatography and related techniques [micro-planar chromatography, micro-TLC, or paper-based microfluidic devices (μPADs)] present several advantages in analytical applications, such as simplicity, low cost of analysis, and the ability to work with raw complex samples without the involvement of time-consuming prepurification steps. By using commonly applied planar chromatographic systems and μPADs devices, stationary phases (silica and cellulose based), different solvent mixtures (methanol-water and dichloromethane-methanol), and proportions varying from 0 to 100% (v/v), micro-TLC migration profiles of several dyes described in terms of characteristic of chromatographic parameters (retardation factor, peak base width, and asymmetry factor) were investigated. Combining these results with some quantum mechanics calculated properties for each solute (dipole moment, polarizability), and by using the data mining approach, we modeled this overall chromatographic behavior in order to describe experimental data.