Mustelinae are among the most diverse and taxonomically complex subfamilies within the Mustelidae, yet their evolutionary history and genetic diversity remain largely unexplored at the whole-genome level. Here, we present the first comprehensive comparative and phylogenomic study of this lineage, integrating nuclear and mitochondrial genomes from 10 species across the Holarctic and Indomalayan realms. Our dataset includes two novel genome assemblies (Mustela strigidorsa, M. sibirica) and an improved genome for M. nivalis, enabling robust cross-species analyses of genome size, chromosomal evolution, genetic diversity, and demographic history. We uncover striking inter- and intraspecific variation in genome-wide heterozygosity and genome size, with evidence of marked homozygosity in some Asian lineages (M. eversmanii, M. sibirica, M. strigidorsa) and remarkable genetic diversity in widespread species such as M. nivalis and M. erminea. Phylogenomic results support the previously suggested split of M. richardsonii from M. erminea, but we found no evidence for speciation within M. nivalis. Ancestral reconstruction of chromosomal rearrangements revealed key chromosomal fissions that shaped the Mustelinae radiation, including early events predating the divergence of modern Mustela species. The results confirmed the suggested ancestral karyotypes of Mustela (2n = 44) and Mustelinae (2n = 42). Finally, demographic reconstructions exposed species-specific responses to Quaternary climatic cycles, ranging from long-term resilience in M. nivalis to repeated population bottlenecks in M. putorius and M. sibirica. Collectively, our findings establish a genomic foundation for future evolutionary and conservation genomic research on this emblematic Mustelidae lineage.

The sand martin (Riparia riparia), a widely distributed migratory songbird, is a promising model for evolutionary and population genetics due to its unique life-history traits. It also provides a valuable system for studying germline-restricted chromosome (GRC) inheritance and evolution. However, the absence of a high-quality genomic resource has limited in-depth investigation of these phenomena. Here, we present a chromosome-level somatic genome assembly for a R. riparia male generated using PacBio HiFi long-read sequencing and Hi-C scaffolding. The pseudohaploid assembly spans 1.19 Gb across 40 chromosome models and shows high completeness (97.6% BUSCO score). Repetitive elements make up 20.2% of the assembled chromosomes. A total of 19,624 protein-coding genes were annotated by integrating transcriptome evidence, ab initio gene prediction, and homology-based approaches. This high-quality reference genome provides a valuable foundation for studying population structure, adaptation, and evolutionary history in R. riparia. It serves as a critical resource for future assembly and investigation of the GRC, and contributes to a broader understanding of genome evolution in birds.

Our study contributes to the characterization of the phylogeography, genetic diversity, range, time of extinction, demographic history of the Ovodov horses (Equus ovodovi) from Southern Siberia in comparison with previously studied Ovodov horses from China. Phylogeographic and haplotype analysis based on the mitogenome sequences we have obtained through targeted enrichment and previously published mitogenome sequences showed that some of the Ovodov horses of Krasnoyarsk Krai (Siberia) examined turned out to be the closest to one of the most ancient mitotypes, related to the Altai Ovodov horse. The remaining Ovodov horses from Southern Siberia that we studied showed the closest maternal relationship with the Holocene horses of Northeast China (Heilongjiang Province). Nucleotide diversity and FST analyses indicated a greater maternal genetic closeness between the Pleistocene population of Ovodov horses in Southern Siberia and the Holocene population of Ovodov horses in Northeast China than between the Pleistocene populations of Ovodov horses in Siberia and China, which may indicate the migration of Ovodov horses from Siberia to the south. Our sample also included the northernmost Late Pleistocene dated Ovodov horses of Siberia, which extended the boundary of its range up to 56 degrees north latitude and the time of its extinction in Siberia to 15,000-11,000 years ago. The constructed population curves showed several sharp declines in the number of Ovodov horses in the Late Pleistocene and Holocene, one of which corresponded to the great human expansion into Asia, and the second - to the rapid climate changes at the beginning of the Holocene.

This study presents, for the first time, a detailed cytogenetic description and comparative analysis of the karyotypes of the Manchurian white-toothed shrew Crocidura shantungensis Miller, 1901 and Ussuri white-toothed shrew Crocidura lasiura Dobson, 1890 from the Russian Far East. These sympatric species represent the different monophyletic groups of 40-chromosome white-toothed shrews. The GTG-banded karyotypes of C. shantungensis and C. lasiura are homologous to the previously described karyotypes of their groups, C. suaveolens and C. dsinezumi respectively. Six apomorphic chromosomes accompanied the formation of the C. dsinezumi – C. lasiura group, while species of the C. suaveolens group are characterized by nine chromosomal markers. A comparative analysis of the karyotypes of white-toothed shrews and Suncus murinus from the genus Suncus, closely related to Crocidura, revealed the presence of 10 pairs of plesiomorphic chromosomes. Seven of these have been conserved since the divergence of these genera approximately 6.8 million years ago (MYA), and 3 pairs of chromosomes since the divergence of both groups approximately 5.4 MYA. The larger number of ancestral chromosomes and fewer chromosomal rearrangements observed in the karyotypes of the C. dsinezumi - C. lasiura group indicate a lower rate of chromosomal evolution compared to the C. suaveolens group.

The stone marten (Martes foina) is an important species for cytogenetic studies in the order Carnivora. ZooFISH probes created from its chromosomes provided a strong and clean signal in chromosome painting experiments and were valuable for studying the evolution of carnivoran genome architecture. The research revealed that the stone marten chromosome set is similar to the presumed ancestral karyotype of the Carnivora, which added an additional value for the species. Using linked-read and Hi-C sequencing, we generated a chromosome-length genome assembly of a male stone marten (Gansu province, China) from a primary cell line. The stone marten assembly had a length of 2.42 Gbp, scaffold N50 of 144 Mbp, and a 96.2% BUSCO completeness score. We identified 19 chromosomal scaffolds (2n = 38) and assigned them chromosome ids based on chromosome painting data. Annotation identified 20,087 protein-coding gene models, of which 18,283 were assigned common names. Comparison of the stone marten assembly with the cat, dog, and human genomes revealed several small syntenic blocks absent on the published painting maps. Finally, we assessed the heterozygosity and its distribution over the chromosomes. The detected low heterozygosity level (0.4 hetSNPs/kbp) and the presence of long runs of homozygosity require further research and a new evaluation of the conservation status of the stone marten in China. Combined with available carnivoran genomes in large-scale synteny analysis, the stone marten genome will highlight new features and events in carnivoran evolution, hidden from cytogenetic approaches.

Karyotypic data on the world’s smallest mammal—the Etruscan shrew Suncus etruscus—and an endemic of the Siculo-Maltese archipelago—the Sicilian shrew Crocidura sicula—have so far been limited to a few conventional and differentially stained karyograms, respectively. We present the first detailed characterization of karyotypes of these species using several differential staining (G- and C-banding) and advanced molecular cytogenetic techniques (CMA3-DAPI and FISH of telomeric and 5.8S/18S/28S ribosomal-DNA probes). The S. etruscus female karyotype was found to have 2n = 42, NF = 78; differential staining was applied for the first time. C-positive heterochromatic blocks were detected in centromeric regions of all autosomes (except for six C-negative pairs) and terminally on autosome pair 14. X chromosomes are C-negative. Karyotypes of C. sicula were found to have 2n = 36, NF = 56. G-banding was applied for the first time to specimens originating from Sicily Island and appeared very similar to the only available G-karyogram from Malta Island (where the species is considered extinct). The examined C. sicula karyotypes differ from some previously published ones in chromosome morphology and the number and localization of C-blocks. By CMA3-DAPI after G-banding, we showed that the S. etruscus karyotype contains less GC-rich heterochromatin as compared to the C. sicula karyotype. In both examined species, FISH signals of telomeric DNA were detectable at terminal loci of all chromosomes; interstitial signals were absent. Clusters of ribosomal DNA were observed at a terminal position in two and six autosome pairs in S. etruscus and C. sicula karyotypes, respectively.

INTRODUCTION:Satellite DNA is an important component of the eukaryotic genome. Some satellite DNAs plays an important role in various biological processes. The red-eared slider (Trachemys scripta elegans, 2n = 50, C = 1.43 pg) belongs to the American freshwater turtle family and is recognized as one of the world's most invasive species. In the T. s. elegans chromosome-level genome assembly, which has been recently published, satellite DNAs comprise only 0.1%. From the repetitive repertoire of the T. elegans genome, only ribosomal DNA genes and telomeric repeats have been localized on the species' chromosomes. METHODS:Using publicly available short-read sequencing data, we conducted de novo identification of the most abundant satellite DNAs in T. s. elegans using the TAREAN pipeline. We combined bioinformatics (using blastn) and chromosome mapping by fluorescence in situ hybridization to describe the distribution of major tandem repetitive DNAs. The diversity and distribution of satDNA in the assembled genome of T. s. elegans were explored using the SatXplor pipeline. RESULTS:Six major satellite sequences occupying approximately 0.8% of the genome were identified in the genome data, all of which were successfully localized both in situ and in silico on T. s. elegans chromosomes and in silico on chromosomal scaffolds. We revealed a complex structural organization of these sequences: monomers may be moderately or highly variable and they may contain regions homologous to retrotransposons. Cytogenetic mapping showed the accumulation of satellite DNAs in the pericentromeric regions of most chromosomes and in the distal regions of the short arms of submetacentric chromosomes. Comparisons between cytogenetic maps and genome assembly data revealed discrepancies in the number and chromosomal locations of the identified satellite DNA clusters. CONCLUSION:The red-eared slider genome has a greater proportion of satellite DNA than was previously reported. These satellites demonstrate no specificity for either macrochromosomes or microchromosomes. Differences between in situ and in silico results indicate the challenges of repetitive sequence assembly, as well as discrepancies between chromosome numbering in the current chromosome-level genome assembly and the physical chromosome map.

Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth’s death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.

The subgenus Stenocranius contains two cryptic species: Lasiopodomys gregalis (subdivided into three allopatrically distributed and genetically well-isolated lineages A, B, and C) and Lasiopodomys raddei. To identify karyotype characteristics of this poorly studied cryptic species complex, we used comparative cytogenetic analysis of 138 individuals from 41 localities in South Siberia and Mongolia. A detailed description of the L. raddei karyotype and of the L. gregalis lineage С karyotype is presented for the first time. The A chromosome complement of all examined narrow-headed voles consisted of 2n = 36 and a fundamental number of autosomal arms (FNa) of 50. Between species, patterns of differential staining were similar, though additional C-heterochromatic blocks were found in L. gregalis lineages; Ag-positive nucleolar organizers and ribosomal DNA (rDNA) clusters are located on eight and nine acrocentric pairs, respectively. No B chromosomes (Bs) were found in the Early Pleistocene relic L. raddei, while one to five small heterochromatic acrocentric Bs were detected in all L. gregalis lineages; the number and frequency of Bs varied considerably within lineages, but no intraindividual variation was observed. In both species, telomeric repeats were visualized at termini of all chromosomes, including Bs. The number and localization of rDNA clusters on Bs varied among B-carriers. Immunodetection of several meiotic proteins indicated that meio-Bs are transcriptionally inactive and have a pattern of meiotic behavior similar to that of sex chromosomes (some homology of Bs to sex chromosomes is supposed). The nature, mechanisms of inheritance and stability of Bs in L. gregalis require further investigation.

Constitutive-heterochromatin placement in the genome affects chromosome structure by occupying centromeric areas and forming large blocks. To investigate the basis for heterochromatin variation in the genome, we chose a group of species with a conserved euchromatin part: the genus Martes [stone marten (M. foina, 2n = 38), sable (M. zibellina, 2n = 38), pine marten (M. martes, 2n = 38), and yellow-throated marten (M. flavigula, 2n = 40)]. We mined the stone marten genome for the most abundant tandem repeats and selected the top 11 macrosatellite repetitive sequences. Fluorescent in situ hybridization revealed distributions of the tandemly repeated sequences (macrosatellites, telomeric repeats, and ribosomal DNA). We next characterized the AT/GC content of constitutive heterochromatin by CDAG (Chromomycin A3-DAPI-after G-banding). The euchromatin conservatism was shown by comparative chromosome painting with stone marten probes in newly built maps of the sable and pine marten. Thus, for the four Martes species, we mapped three different types of tandemly repeated sequences critical for chromosome structure. Most macrosatellites are shared by the four species with individual patterns of amplification. Some macrosatellites are specific to a species, autosomes, or the X chromosome. The variation of core macrosatellites and their prevalence in a genome are responsible for the species-specific variation of the heterochromatic blocks.

In recent years, the number of mole species with species status confirmed by genetic methods has been continuously increasing. Unfortunately, cytogenetic data are not yet available for all species. Here, for the first time, a GTG-banded karyotype of the small-toothed mole from Vietnam, Euroscaptor parvidens, a representative of the Eastern clade of the genus Euroscaptor, has been described. Through comparative analysis of available Euroscaptor (Euroscaptor parvidens, Euroscaptor klossi, and Euroscaptor malayana) and Oreoscaptor (Oreoscaptor mizura) karyotypes, we found cytogenetic signatures for each of the studied species. Zoo-FISH with sorted chromosomes of the Siberian mole (Talpa altaica) on chromosome sets of the small-toothed mole (E. parvidens), the small Japanese mole (Mogera imaizumii) from the closely related genus, and the Japanese shrew mole (Urotrichus talpoides) from the tribe Urotrichini made it possible to identify syntenic regions between these species. We propose a possible ancestral karyotype of the tribe and, based on it, traced the features of chromosomal rearrangements accompanying the divergence of moles. The low rates of chromosomal evolution within the species of the genus Talpa—T. altaica and T. europaea—and the high rates of karyotypic reshuffling within the Asian genera of the tribe were confirmed. The karyotype of the Japanese mountain mole O. mizura seems to be the most conserved among the Asian moles. The most frequently occurring types of chromosomal rearrangements in moles are the pericentric inversions and amplification of heterochromatin. The pericentric inversions on four pairs of autosomes are shared between the closely related genera Euroscaptor, Oreoscaptor, and Mogera, while many more apomorphic rearrangements have occurred in each lineage additionally. The highest rate of chromosomal changes, with five rearrangements occurring over approximately 7 million years, was recorded in the lineage of the small-toothed mole.

Pusa sibirica, the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat—the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of this species, we generated a de novo chromosome-length assembly, and compared it with three closely related marine pinniped species. Multiple whole genome alignment of the four species compared with their karyotypes showed high conservation of chromosomal features, except for three large inversions on chromosome VI. We found the mean heterozygosity of the studied Baikal seal individuals was relatively low (0.61 SNPs/kbp), but comparable to other analyzed pinniped samples. Demographic reconstruction of seals revealed differing trajectories, yet remarkable variations in Ne occurred during approximately the same time periods. The Baikal seal showed a significantly more severe decline relative to other species. This could be due to the difference in environmental conditions encountered by the earlier populations of Baikal seals, as ice sheets changed during glacial–interglacial cycles. We connect this period to the time of migration to Lake Baikal, which occurred ~3–0.3 Mya, after which the population stabilized, indicating balanced habitat conditions.

In modern molecular and cellular biology, CRISPR/Cas9 technology has been widely used for targeted modification of human and animal genomes. In this work, using molecular-cytogenetics methods, we have analyzed the karyotype in 18 mouse fibroblast cell lines (MFs), whose genome had a Cntn6 gene edited with CRISPR/Cas9. The modifications of Cntn6 gene were 2374-kb duplications, 1137-kb deletions, and inversions of similar size. In addition, cytogenetic analysis was performed for five control lines of mouse embryonic fibroblasts (MEFs) carrying an intact Cntn6 gene allele. The study showed the presence of a high level of polyploidy for MF lines that were heterozygous for Cntn6 gene inversions and homozygous and heterozygous for Cntn6 gene duplications (20–46

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. Comparative chromosome maps obtained by FISH with chromosome-specific probes link genomic scaffolds to individual chromosomes and orient them relative to centromeres and heterochromatic blocks. Hi-C assembly made it possible to close all gaps on the comparative maps and to reveal additional rearrangements that distinguish the karyotypes of the three species. As a result, we integrated the bioinformatic and cytogenetic data and adjusted the previous comparative maps and genome assemblies of the guinea pig, naked mole-rat, and human. Syntenic associations in the two hystricomorphs indicate features of their putative ancestral karyotype. We postulate that the two approaches applied in this study complement one another and provide complete information about the organization of these genomes at the chromosome level.

CRISPR/Cas9 technology has been widely used for targeted modification of the mammalian genomes. We have analyzed the karyotype of 18 mouse fibroblast cell lines with Cntn6 gene rearrangements introduced by CRISPR/Cas9. We have produced cell lines with 2374 kb Cntn6 gene duplications, 1137 kb deletions and inversions of similar size. In addition, we have performed cytogenetic analysis for five control mouse embryonic fibroblasts with the intact Cntn6 gene alleles. The cell lines heterozygous for Cntn6 gene inversion and homozygous and heterozygous for Cntn6 gene duplication had a high level of polyploidy (20–46%), as well as chromosome 6 monosomy (1–9%) and trisomy (1–8%). No trisomy was detected in the four cell lines with the deletion and duplication of the Cntn6 gene in the compound, and the proportion of polyploid cells was minimal (1.5–5.7%). Thus, we have shown the karyotype destabilization in the cell lines that have undergone genome editing using CRISPR/Cas9 system.

Comparative whole-genome analyses hold great power to illuminate commonalities and differences in the evolution of related species that share similar ecologies. The mustelid subfamily Lutrinae includes 13 currently recognized extant species of otters,1-5 a semiaquatic group whose evolutionary history is incompletely understood. We assembled a dataset comprising 24 genomes from all living otter species, 14 of which were newly sequenced. We used this dataset to infer phylogenetic relationships and divergence times, to characterize patterns of genome-wide genealogical discordance, and to investigate demographic history and current genomic diversity. We found that genera Lutra, Aonyx, Amblonyx, and Lutrogale form a coherent clade that should be synonymized under Lutra, simplifying the taxonomic structure of the subfamily. The poorly known tropical African Aonyx congicus and the more widespread Aonyx capensis were found to be reciprocally monophyletic (having diverged 440,000 years ago), supporting the validity of the former as a distinct species. We observed variable changes in effective population sizes over time among otters within and among continents, although several species showed similar trends of expansions and declines during the last 100,000 years. This has led to different levels of genomic diversity assessed by overall heterozygosity, genome-wide SNV density, and run of homozygosity burden. Interestingly, there were cases in which diversity metrics were consistent with the current threat status (mostly based on census size), highlighting the potential of genomic data for conservation assessment. Overall, our results shed light on otter evolutionary history and provide a framework for further in-depth comparative genomic studies targeting this group.

Whole-genome analyses of complete clades hold great power to illuminate their evolutionary history, current levels of diversity and species-specific responses to environmental changes. The mustelid subfamily Lutrinae includes 13 currently recognized extant species of otters, a semiaquatic group whose evolutionary history is incompletely understood. We assembled a dataset comprising 21 genomes from all living otter species, 14 of which were newly sequenced. We used this dataset to infer phylogenetic relationships and divergence times, to characterize patterns of genome-wide genealogical discordance and to investigate the demographic history and current genomic diversity of these species. We found that genera Lutra, Aonyx, Amblonyx, and Lutrogale form a coherent clade that we propose should be synonymized under Lutra, thus simplifying the taxonomic structure of the subfamily. We found that the poorly known, tropical African Aonyx congicus and the more widespread Aonyx capensis are reciprocally monophyletic (having diverged 440,000 years ago), supporting the validity of the former as a distinct species. We observed disparate demographic histories among otters, including pairs of sympatric species, indicating that they responded very differently to environmental shifts in the past. This has led to disparate levels of current genomic diversity assessed by overall heterozygosity, genome-wide SNV density and Run of Homozygosity burden. Interestingly, there were cases in which diversity metrics matched the current threat status for the respective species, highlighting the potential of genomic data for conservation assessment. Overall, our results shed light on otter evolutionary history and provide a genomic platform for in-depth comparative studies targeting this group.

The Puma lineage within the family Felidae consists of 3 species that last shared a common ancestor around 4.9 million years ago. Whole-genome sequences of 2 species from the lineage were previously reported: the cheetah (Acinonyx jubatus) and the mountain lion (Puma concolor). The present report describes a whole-genome assembly of the remaining species, the jaguarundi (Puma yagouaroundi). We sequenced the genome of a male jaguarundi with 10X Genomics linked reads and assembled the whole-genome sequence. The assembled genome contains a series of scaffolds that reach the length of chromosome arms and is similar in scaffold contiguity to the genome assemblies of cheetah and puma, with a contig N50 = 100.2 kbp and a scaffold N50 = 49.27 Mbp. We assessed the assembled sequence of the jaguarundi genome using BUSCO, aligned reads of the sequenced individual and another published female jaguarundi to the assembled genome, annotated protein-coding genes, repeats, genomic variants and their effects with respect to the protein-coding genes, and analyzed differences of the 2 jaguarundis from the reference mitochondrial genome. The jaguarundi genome assembly and its annotation were compared in quality, variants, and features to the previously reported genome assemblies of puma and cheetah. Computational analyzes used in the study were implemented in transparent and reproducible way to allow their further reuse and modification.

The taxonomy of the genus Calomyscus remains controversial. According to the latest systematics the genus includes eight species with great karyotypic variation. Here, we studied karyotypes of 14 Calomyscus individuals from different regions of Iran and Turkmenistan using a new set of chromosome painting probes from a Calomyscus sp. male (2n = 46, XY; Shahr-e-Kord-Soreshjan-Cheshme Maiak Province). We showed the retention of large syntenic blocks in karyotypes of individuals with identical chromosome numbers. The only rearrangement (fusion 2/21) differentiated Calomyscus elburzensis, Calomyscus mystax mystax, and Calomyscus sp. from Isfahan Province with 2n = 44 from karyotypes of C. bailwardi, Calomyscus sp. from Shahr-e-Kord, Chahar Mahal and Bakhtiari-Aloni, and Khuzestan-Izeh Provinces with 2n = 46. The individuals from Shahdad tunnel, Kerman Province with 2n = 51–52 demonstrated non-centric fissions of chromosomes 4, 5, and 6 of the 46-chromosomal form with the formation of separate small acrocentrics. A heteromorphic pair of chromosomes in a specimen with 2n = 51 resulted from a fusion of two autosomes. C-banding and chromomycin A3-DAPI staining after G-banding showed extensive heterochromatin variation between individuals.

The genus status of Urocricetus was defined recently based on morphological and molecular data. Even though the amount of evidence for a separate phylogenetic position of this genus among Cricetinae continues to increase, there is still no consensus on its relationship to other groups. Here we give the first comprehensive description of the U. kamensis karyotype (2 n = 30, NF a = 50) including results of comparative cytogenetic analysis and detailed examination of its phylogenetic position by means of numerous molecular markers. The molecular data strongly indicated that Urocricetus is a distant sister group to Phodopus . Comparative cytogenetic data showed significant reorganization of the U. kamensis karyotype compared to karyotypes of all other hamsters investigated earlier. The totality of findings undoubtedly means that Urocricetus belongs to a separate divergent lineage of Cricetinae.