This was a molecular cytogenetic study of 15 species from nine genera and four ant subfamilies, with data for six genera published for the first time. Colonies were collected from Amazonian and Atlantic rainforest sites in French Guiana and Brazil, including Kourou, Petit Saut, Oiapoque in Amapá State, and Viçosa in Minas Gerais. The investigators prepared mitotic metaphase chromosomes from larval cerebral ganglia, mapped an 18S rDNA probe by FISH and analyzed at least 20 metaphases per species.

The mapping produced varied diploid chromosome numbers, from 2n=12 in Neoponera unidentata to 2n=46 in Megalomyrmex aff. incisus. Most species had rDNA clusters on one chromosome pair in a pericentromeric region. Azteca andreae and Cephalotes minutus instead had sites on chromosome short arms, while two species had clusters on the short arms of several pairs: Camponotus cameroni had four rDNA-bearing pairs, and Solenopsis saevissima had two. The results therefore were not a uniform pattern across every chromosome number or genus.

Data available since the 2021 review expanded the available ant cytogenetic dataset to 103 species or subspecies, 28 genera and six subfamilies. Among the 40 taxa added since that review, the study counted 36 with a single rDNA-bearing chromosome pair, two species with two pairs, and C. cameroni with four pairs. That count concerns the newly added taxa rather than the entire 103-taxon compilation. The single-pair condition was therefore interpreted as ancestral in ants, consistent with the authors’ broader proposal that it may also represent the ancestral condition in Hymenoptera.

The updated data strengthened an association between the position and multiplicity of rDNA sites. Species with multiple sites generally placed them in terminal or short-arm regions, whereas most species with one intrachromosomal site retained a single pair. Under a model proposed by Hirai in 2020, terminal sequences may associate during the meiotic bouquet, potentially allowing ectopic recombination and dispersing rDNA clusters among chromosomes. Intrachromosomal positions would restrict such interactions. The authors also proposed that haploid ant males cannot undergo the same ectopic recombination because recombination in hymenopterans occurs in diploid females; they presented this as a possible reason that repetitive-DNA evolution could be slower in Hymenoptera than in diplodiploid insects.

The findings did not support chromosomal fission as the main explanation for rDNA dispersion. An increase in chromosome number was not consistently accompanied by more rDNA-bearing pairs. For example, S. geminata and S. saevissima both had 2n=32 chromosomes but carried one and two rDNA-bearing pairs, respectively. C. cameroni had 2n=36 and four pairs, whereas studied Camponotus species with 2n=40 had one or two. Mycocepurus smithii sexual and asexual karyomorphs retained one rDNA-bearing pair despite chromosome numbers of 2n=14, 2n=11, and 2n=9. These observations weaken a simple association between higher chromosome number and greater rDNA dispersion, although the authors did not exclude fissions as one possible mechanism in particular lineages.

Patterns also varied substantially among genera. The two newly mapped Brachymyrmex species had rDNA sites in the same pericentromeric region, whereas Strumigenys species with the same 2n=18 count carried sites on different chromosome pairs. In Cyphomyrmex, the mapped sites occupied different chromosome pairs and arms, which the authors considered consistent with possible rearrangements involving rDNA regions. Native Argentine Solenopsis invicta had two rDNA-bearing pairs, while invasive or established populations from Argentina, the United States and Taiwan showed substantial variation: females had between one and 11 rDNA-bearing chromosomes depending on ploidy, and males had haploid through tetraploid karyotypes with one to nine such chromosomes. Hybridization and insecticide exposure were proposed as possible causes, not established mechanisms.

The mapping data also have taxonomic and reproductive significance. Camponotus rufipes has one rDNA-bearing pair and C. renggeri has two, a distinction that accompanied other ecological, molecular and behavioral evidence that they are separate species. Pseudoponera stigma and P. gilberti differ in both karyotype and rDNA location. In M. smithii, rDNA mapping also documented differences in homolog size, particularly in the 2n=11 asexual karyomorph, within the broader pattern of diploid-structure decay in a parthenogenetic lineage.

The analysis has clear limits. Molecular cytogenetic information remains sparse for several large genera, and some genera in this study were represented by only one species, preventing wider comparisons within those groups. FISH detects the mapped rDNA clusters but does not by itself establish the rearrangements or selective processes that produced them. The authors therefore treated ectopic recombination, hybridization, insecticide exposure and lineage-specific fissions as hypotheses to be tested rather than demonstrated universal causes. Even with these constraints, the new maps expand the comparative evidence and support an ancestral single-pair arrangement accompanied by non-random terminal or short-arm positioning in lineages where multiple rDNA sites occur.

Subject of Research: Chromosomal mapping of 18S rDNA in 15 ant species and implications for the evolution of ribosomal gene sites

Article Title: Physical chromosomal mapping of major ribosomal genes in 15 ant species with a review of hypotheses regarding evolution of the number and position of NORs in ants

Article References: Damasceno, M. T. D. S., Teixeira, G. A., Ferreira, P. C., Lod, R. B., Barros, L. A. C., & de Aguiar, H. J. A. C. (2024). Physical chromosomal mapping of major ribosomal genes in 15 ant species with a review of hypotheses regarding evolution of the number and position of NORs in ants. Comparative Cytogenetics, 18, 105-122. https://doi.org/10.3897/compcytogen.18.125235

Image Credits: AI Generated

DOI: 10.3897/compcytogen.18.125235

Keywords: ants, Formicidae, ribosomal DNA, chromosome mapping, fluorescence in situ hybridization, cytogenetics, nucleolar organizer regions, karyotype evolution, Physical, chromosomal, mapping, major

Investigators also reanalysed permanent slides from two Far Eastern populations and two samples collected at Berdsky Pond in Novosibirsk Province in 1985, because the original publication did not provide sufficiently comprehensive data for quantitative analysis. Published data were incorporated for 10 additional populations, bringing the total to 41. Where larvae were collected repeatedly at the same site, the researchers tested for differences in banding-sequence frequencies among sampling years and combined the samples when no significant differences were found.

Species identification was based on larval morphology and polytene chromosomes from the salivary glands. Chromosome arms were mapped using established systems for the Chironomus plumosus species group, and banding sequences were classified as main, alternative, rare or unique. Quantitative analyses used populations represented by at least 10 specimens, and all populations were checked for deviations from Hardy–Weinberg equilibrium.

Only the RAL-MA population showed a deviation, involving more heterozygotes for the arm D combination p’borD1.h’borD2 than expected. Chironomus borokensis has a haploid chromosome number of four, with the arms arranged as AB, CD, EF and G. Chromosomes I and II are metacentric, chromosome III is submetacentric and chromosome IV is telocentric.

Inversion polymorphism occurred in every chromosomal arm, and the study expanded the species’ known banding-sequence pool to 40. The largest number recorded from a single collection date was 18, while one population record contained 23 sequences when observations from multiple years were combined. Six alternative banding sequences across five chromosomal arms met the study’s criteria: h’borA2 and p’borA4 in arm A, h’borB2 in arm B, h’borD2 in arm D, p’borF2 in arm F, and p’borG2 in arm G.

Each was present at high frequency in at least some populations and occurred in both heterozygous and homozygous states. The frequency of p’borG2 reached 100% in many Western Siberian populations. Rare sequences in arms A and F were p’borA5, p’borA8, p’borA9 and h’borF4.

The sequence p’borA5 is a complex inversion that differs from the main arm A sequence by three inversion steps. The authors inferred that it predates the divergence of C. borokensis because an identical sequence occurs in the sibling species C. suwai, while two inversions in C. plumosus can be derived from it through simple inversions. They regarded independent emergence of the same complex inversion in three species as unlikely and presented the common-ancestor interpretation as an inference.

Alongside inversions, the researchers recorded five translocation cases: two involving whole chromosome arms, one with breakpoints inside arms D and E, and a unique larva carrying two reciprocal whole-arm translocations. Rare variation in centromeric heterochromatin size was observed mainly in chromosome II in Western Siberia. B chromosomes occurred in some populations at frequencies of up to 30%.

They commonly lay near or contacted the centromeric heterochromatin of arm G, although the investigators could not determine whether some apparently isolated positions resulted from mechanical disruption of contacts during slide preparation. These observations describe chromosome structure and occurrence frequencies; they do not establish effects on fitness or development. Seven cytogenetic population types were identified.

Populations from Europe, the Urals and Eastern Siberia belonged to type 0, in which all main banding sequences were dominant. Most Western Siberian populations were type G, while others were assigned to types DG, FG and DFG. Far Eastern populations had types ADG and F.

Overall, the sampled Western Siberian populations showed higher chromosomal polymorphism and more varied cytogenetic structures than populations from Europe, Eastern Siberia or the Far East. The authors proposed that alternative sequences in arms D, F and G may have adaptive value in Western Siberia, but this was a hypothesis rather than a tested causal result. Cytogenetic distances among populations ranged from 0.001 to 0.461, with an average of 0.155 ± 0.024.

These within-species values were below the reported average interspecific distance of 2.618 ± 0.400 for seven species in the Chironomus plumosus group. A neighbour-joining analysis broadly grouped populations with similar cytogenetic structures but also placed some geographically distant populations together. The authors noted that water and detritus characteristics may influence chironomid population structure more directly than geography alone, although those environmental variables were not measured in this study.

Based on the greater inversion diversity, higher polymorphism and more varied population structures in Western Siberia, the authors proposed that the region may be the centre of the species’ range and possibly its place of origin; historical ancestry was not directly reconstructed.

Subject of Research: Chromosomal polymorphism across 41 populations of the midge Chironomus borokensis

Article Title: Chromosomal polymorphism in natural populations of Chironomus borokensis Kerkis, Filippova, Shobanov, Gunderina et Kiknadze, 1988 ( Diptera , Chironomidae )

Article References: Golygina, V. V., Broshkov, A. D., & Ermolaeva, O. V. (2025). Chromosomal polymorphism in natural populations of Chironomus borokensis Kerkis, Filippova, Shobanov, Gunderina et Kiknadze, 1988 (Diptera, Chironomidae). Comparative Cytogenetics, 19, 51-74. https://doi.org/10.3897/compcytogen.19.141735

Image Credits: AI Generated

DOI: 10.3897/compcytogen.19.141735

Keywords: Chironomus borokensis, chromosomal polymorphism, polytene chromosomes, inversions, translocations, B chromosomes, cytogenetic distance, Western Siberia, population genetics, Chironomus plumosus group, Chromosomal, polymorphism

The investigation was a cytogenetic study conducted during routine screening of Kangayam bulls before their use for semen collection. The sample comprised 14 bulls from the Buffalo Frozen Semen Station, 16 from the Kangayam Cattle Research Station and 16 field-progeny animals tested in Tamil Nadu. Chromosomes were obtained through a short-term lymphocyte culture technique in the Cytogenetics Laboratory of the Department of Animal Genetics and Breeding at Madras Veterinary College in Chennai.

More than 200 metaphase spreads were screened, and chromosome preparations from the exceptional bull were subjected to further analysis with CBG and GTG banding. Forty-five of the screened bulls had a male chromosome complement consisting of 29 pairs of acrocentric autosomes, one large submetacentric X chromosome and the smallest acrocentric Y chromosome. The exceptional bull had a broadly similar complement, but its Y chromosome was classified as subacrocentric because a small p arm was visible.

This contrasted with the typical acrocentric Y chromosome found in the other animals, in which no prominent short arm could be distinguished. The subacrocentric chromosome was unpaired, and it appeared in every spread screened from this bull, indicating a consistent feature of the sampled metaphases rather than an isolated observation in individual cells. The unusual morphology alone did not establish whether the extra arm represented a structural translocation.

A similar chromosome complement had previously been reported in Chainina cattle and interpreted as a reciprocal translocation between the Y chromosome and chromosome 9. That possibility prompted the investigators to examine the Kangayam bull with CBG banding, which stains constitutive heterochromatin, and GTG banding, which distinguishes chromosome regions through a characteristic pattern of light and dark bands. The purpose was to determine whether the visible p arm belonged to the Y chromosome itself or contained a segment derived from an autosome.

CBG analysis showed characteristically dark centromeric bands on all the acrocentric autosomes, while the X chromosome stained lightly across its length. The exceptional Y chromosome behaved differently: it stained darkly throughout most or all of its length and lacked a clearly delineated centromeric band like that seen on the autosomes. Its small extra p arm was also darkly stained, rather than showing the light appearance characteristic of the autosomes.

These observations identified the additional arm as heterochromatic material associated with the Y chromosome, not a translocated autosomal segment. The GTG-banding results provided a second basis for characterizing the chromosome. The Y chromosome retained a recognizable band pattern, but its distribution differed between the subacrocentric variant in the exceptional bull and the typical acrocentric form.

In the variant, the pattern was divided between two visible arms, designated p and q; in the acrocentric form, the bands were situated together on the q arm. All autosomes retained the typical G-banding pattern expected in cattle. The investigators therefore found no indication of a translocation between the Y chromosome and an autosome, while confirming that the visible short arm was part of the Y-chromosome structure.

The result adds a rare observation to evidence that the Y chromosome of zebu cattle can vary in morphology. Earlier work on the Sahiwal, Sindhi, Brahman, Santa Gertrudis and Belmont Red breeds found differences in the position of the centromere relative to the end of the small p arm. In some bulls, no chromatin was visible beyond the centromere; in others, the p arm was distinct.

Sahiwal bulls were also described as having a visible subtelocentric Y chromosome, although that terminology can be problematic because the definitions of acrocentric and subtelocentric belong to different chromosome-classification systems. For the small Kangayam Y chromosome, the researchers used “subacrocentric” to emphasize the visible short arm relative to the typical acrocentric form seen in other breeding sires. Chromosomal rearrangements, including centric fusions, inversions and changes in the amount of heterochromatin, have been associated with the differentiation of chromosome complements across bovid species.

The chromosome complements of Bos indicus and Bos taurus are otherwise highly similar, but the Y chromosome differs in shape: it is generally acrocentric in Bos indicus and submetacentric or metacentric in Bos taurus. Comparative cytogenetic studies have related this morphological difference to a pericentric inversion, while variation in Y-chromosome size among subspecies has been associated with differences in heterochromatin content. The banding evidence in the Kangayam bull is consistent with heterochromatin variation as the explanation for its unusual p arm.

Because the affected animal was phenotypically healthy and the investigators did not classify the chromosome complement as an abnormality, the study reports a possible chromosomal polymorphism rather than a demonstrated reproductive defect. Its scope remains limited: the variant was detected in one of 46 bulls, and the study did not establish that it affects fertility, productivity or the transmission of the chromosome to offspring. The authors state that the productive and reproductive performance of the bull and its descendants should be studied if the bull is used for breeding.

They also note the possibility of culling an animal after screening, making evaluation relevant when a bull is retained. The central finding is the identification, through CBG and GTG banding, of a stable subacrocentric Y-chromosome variant in Kangayam cattle.

Subject of Research: Cytogenetic identification of a subacrocentric Y-chromosome variant in a Kangayam bull

Article Title: A rare chromosomal polymorphism in a Kangayam bull ( Bos indicus ) of south India

Article References: Harshini, V., Kumarasamy, P., & Karthickeyan, S. M. K. (2021). A rare chromosomal polymorphism in a Kangayam bull (Bos indicus) of south India. Comparative Cytogenetics, 15(4), 459-465. https://doi.org/10.3897/compcytogen.v15.i4.71295

Image Credits: AI Generated

DOI: 10.3897/CompCytogen.v15.i4.71295

Keywords: Kangayam cattle, Bos indicus, Y chromosome, chromosome polymorphism, cytogenetics, heterochromatin, CBG banding, GTG banding, Tamil Nadu India, cattle breeding, rare, chromosomal

Birds are the most diverse class of tetrapod vertebrates, with roughly 11,032 species worldwide, yet they are also among the least studied genetically. According to the IUCN, about 12 percent of bird populations are threatened with potential extinction, and many scientists argue that we are now living through an irreversible sixth mass extinction that could prove more devastating than all previous ones combined. Birds evolved from theropod dinosaurs between 165 and 150 million years ago and separated from crocodiles about 240 million years ago, which makes their genomes a living record of one of the most successful vertebrate radiations. Understanding how their chromosomes are organized, and how they change, is therefore both an evolutionary question and a conservation imperative.

The domestic chicken occupies a special place in this research. Gallus gallus domesticus is considered a model in phylogeny and comparative genomics and represents the only standardized bird karyotype, established in 1999 under the International System of Standardised Avian Karyotypes. Because the chicken shares several features with other avian species, it is regarded as the closest living representative of the common ancestor of birds, and its chromosomes remain the best studied in the class. The team therefore used the chicken as the reference against which the chromosomes of the five other species were compared, focusing on the first eight autosomal pairs and the ZW sex chromosomes.

The technical work behind the study was meticulous. Embryos were collected during the laying period from fertile eggs of Common quail, Japanese quail, Barbary partridge and Chukar partridge obtained from hunting centres in Algeria, while Houbara bustard embryos came from an Emirati bird breeding centre for conservation. Eggs were incubated under controlled conditions of 55 percent humidity and 39.5 degrees Celsius, and primary fibroblast cultures were established from lung, heart, liver, kidney and muscle fragments of embryos aged 6 to 19 days. The cultures were synchronized using a double thymidine block during S phase to increase the yield of metaphase cells, a standard trick that pushes dividing cells into a narrow window of the cell cycle so that more chromosomes can be harvested at their most condensed and analyzable stage.

GTG-banding itself involves treating aged chromosome slides with a brief trypsin exposure followed by Giemsa staining, producing the characteristic striped pattern that reflects the underlying chromatin structure. Because each chromosome carries a reproducible band signature, researchers can compare chromosomes across species by matching the size, morphology and band patterns of each pair. The team classified macrochromosomes in decreasing size according to centromere position and compared the ratio of long-arm to short-arm length, a measure that reveals even subtle shifts in centromere placement. This combination of criteria allowed the researchers to identify homologous chromosomes and to spot rearrangements that occurred during speciation.

The results revealed a striking degree of conservation. Chromosomes 3, 5 and 6 appeared unchanged across all six species, both morphologically and in their GTG banding patterns, and no rearrangement was detected on them. Where differences did appear, they were mostly intrachromosomal, meaning they occurred within a single chromosome rather than between chromosomes. The Japanese quail chromosome 1 and the Houbara bustard chromosome 1 both showed shorter short arms than the chicken homolog, which the authors attribute to the formation of evolutionary neocentromeres, new centromeres that arise de novo in a euchromatic locus while the old centromere is inactivated. This phenomenon, first demonstrated in birds through studies of the red-legged partridge, has since been reported in pheasants, ducks and guineafowl, and it leaves the order of molecular markers along the chromosome essentially undisturbed.

Other chromosomes told more dramatic stories. The Japanese quail chromosome 2 carries a large region with an inverted banding pattern, consistent with a double pericentric inversion previously confirmed by comparative mapping with BAC clones and immunodetection. The Houbara bustard, by contrast, showed the most extensive reorganization of any species in the study. Its chromosome 2 appears to have lost the terminal part of its long arm through a terminal fission, and the researchers detected a similarity between that lost region and the bustard’s microchromosome 10, suggesting that the ancestral chromosome split to give rise to both a macrochromosome and a microchromosome. Even more strikingly, the bustard’s chromosome 4 corresponds only to the distal part of the long arm of chromosome 4 in the other species, with the missing regions apparently redistributed onto the bustard’s microchromosomes 11, 14 and 19. These interchromosomal rearrangements involving microchromosomes are rare events in birds, which makes their detection in the bustard particularly significant.

The sex chromosomes added their own chapter to the story. The Z chromosome showed a terminal inversion in the long arm in both the Barbary partridge and the Houbara bustard, and the bustard’s Z also carried a loss of an interstitial segment in the short arm that potentially corresponds to microchromosome 13. The W chromosome, meanwhile, is submetacentric in the partridges and the bustard but subtelocentric in the quails, a difference the authors explain by an evolutionary new centromere. The Z chromosome in birds contains a high number of breakpoints and is particularly subject to structural changes, broadly represented by paracentric and pericentric inversions, and its evolution has been characterized by a complex process of inversions likely related to the suppression of recombination between Z and W during the early stages of sex chromosome differentiation.

Taken together, the findings confirm a paradox that has emerged from decades of avian cytogenetics: the structure of bird karyotypes is more conserved at the interchromosomal scale, where whole chromosomes retain their identity, than at the intrachromosomal scale, where inversions, deletions, fissions and centromere repositioning accumulate over evolutionary time. The appearance of a small number of inter- and intrachromosomal rearrangements across six species suggests a high degree of conservatism of genome organization, and the team proposed a summary diagram tracing the chronology of these events from the presumed ancestral avian karyotype. The Houbara bustard karyotype carries the highest number of rearrangements, including fissions, compared with the ancestral karyotype, which fits its position in a lineage that diverged early from the Galliformes.

The study also carries practical weight for conservation. Classical cytogenetics can detect chromosomal abnormalities responsible for early embryonic mortality, a crucial capability for breeding programs of endangered species like the Houbara bustard, which is classified as vulnerable by the IUCN and has suffered a significant decline over the past thirty years, particularly due to poaching. The storage of chromosomes and nucleotide sequences is a form of biobanking, and sequence analysis can identify genetically important individuals for breeding. As the authors note, avian genomics and stem cell approaches could offer hope not only for saving endangered species such as the green peafowl but also for other birds threatened with extinction, ensuring that the chromosomal record of this extraordinary lineage survives the extinction crisis now unfolding around it.

Subject of Research: Highlighting chromosomal rearrangements of five species of Galliformes (Domestic fowl, Common and Japanese quail, Barbary and Chukar partridge) and the Houbara bustard, an endangered Otidiformes: banding cytogenetic is a powerful tool

Article Title: Highlighting chromosomal rearrangements of five species of Galliformes (Domestic fowl, Common and Japanese quail, Barbary and Chukar partridge) and the Houbara bustard, an endangered Otidiformes : banding cytogenetic is a powerful tool

Article References: Kartout-Benmessaoud, Y., Ouchia-Benissad, S., Mahiddine-Aoudjit, L., & Ladjali-Mohammedi, K. (2024). Highlighting chromosomal rearrangements of five species of Galliformes (Domestic fowl, Common and Japanese quail, Barbary and Chukar partridge) and the Houbara bustard, an endangered Otidiformes: banding cytogenetic is a powerful tool. Comparative Cytogenetics, 18, 213-237. https://doi.org/10.3897/compcytogen.18.135056

Image Credits: AI Generated

DOI: 10.3897/compcytogen.18.135056

Keywords: Highlighting, chromosomal, rearrangements, five, species, Galliformes, Domestic, fowl, Common, Japanese, quail, Barbary

The study, published in the journal Comparative Cytogenetics, focused on the tribes Bachiini and Cercosaurini, which together contain roughly 204 species. Before this work, only three of them had ever had their karyotypes described. Using standard cytogenetic techniques including Giemsa staining, Ag-NOR staining to locate nucleolus organizer regions, C-banding to reveal constitutive heterochromatin, and RBG-banding for precise chromosome pairing, the researchers characterized seven species: Bachia bresslaui, Bachia dorbignyi, Cercosaura olivacea, Cercosaura schreibersii albostrigatus, Neusticurus bicarinatus, Placosoma cordylinum, and Placosoma glabellum. The specimens came from localities across Brazil, from Goiás and Mato Grosso to Rio de Janeiro, São Paulo, and Amazonas, and were deposited in the Museu de Zoologia da Universidade de São Paulo.

The diploid numbers uncovered ranged dramatically, from 2n = 32 in Bachia dorbignyi to 2n = 58 in Placosoma glabellum. That 26-chromosome spread within a single sample of closely related lizards underscores how dynamically their genomes have evolved. Almost all species displayed karyotypes composed of both macrochromosomes and microchromosomes, a hallmark of the family, but the number, morphology, and relative sizes of these elements varied considerably among species. Within the genus Bachia alone, B. dorbignyi carries 2n = 32 while B. bresslaui carries 2n = 46, a difference that immediately sets these species apart cytogenetically. Similarly, within Placosoma, P. cordylinum has 2n = 44 with a clear macro-microchromosome distinction, while P. glabellum has 2n = 58 with chromosomes decreasing gradually in size, a fundamentally different karyotype architecture.

One of the most intriguing findings concerns sex chromosomes. In Bachia dorbignyi, the researchers observed a dot-like microchromosome exclusively in male specimens, absent from the female. This pattern suggests a putative XX:XY sex determination system, with the dot-like element representing the Y chromosome. It is the first such mechanism with a dot-like Y described in Gymnophthalmidae. The researchers could not obtain meiotic spreads to confirm a heteromorphic bivalent, but they note that such heteromorphism is often undetectable in microchromosomes due to their very small size, as seen in other lizard species. Based on the known phylogenetic distribution of sex determination systems in squamates, the absence of heteromorphic sex chromosomes in the other six species studied may indicate that sex chromosomes in those species are homomorphic, meaning the X and Y are morphologically indistinguishable. Further analyses using cytogenomic techniques will be needed to clarify whether male heterogamety evolved once in the family or independently in different lineages.

Ag-NOR staining revealed notable variability in the number and position of nucleolus organizer regions, the chromosomal sites of ribosomal RNA genes. In Bachia bresslaui, the researchers found between two and six Ag-NORs per metaphase, located at telomeric regions of macrochromosomes and, in the female, also on a single microchromosome in at least 42 percent of cells analyzed. This intra- and interindividual polymorphism may reflect genomic plasticity in rDNA locus activation or positioning, potentially linked to differential gene expression. In contrast, Neusticurus bicarinatus and Placosoma glabellum showed a more conserved pattern, with a single pair of macrochromosomes bearing the NORs. Only in B. bresslaui and C. olivacea were multiple Ag-NORs detected on both macro- and microchromosomes, a pattern also seen in other microteiid species such as Nothobachia ablephara and Micrablepharus atticolus.

C-banding patterns, obtained for four of the seven species, revealed differences in both the amount and distribution of constitutive heterochromatin. Bachia bresslaui displayed conspicuous heterochromatic blocks at pericentromeric regions of all macrochromosomes, a pattern otherwise known only in the distantly related genus Procellosaurinus. Cercosaura olivacea showed small C-bands in both pericentromeric and telomeric regions of its macrochromosomes. In Neusticurus bicarinatus and Placosoma glabellum, heterochromatin was predominantly telomeric, with P. glabellum exhibiting lightly stained telomeric C-bands on most chromosomes, except for the short arm of a subtelocentric pair that was almost completely heterochromatic. These faint telomeric signals are consistent with patterns reported for other gymnophthalmid species, in which heterochromatin frequently serves structural or protective roles at chromosome ends.

RBG-banding, which uses bromodeoxyuridine incorporation to produce replication banding patterns, was successfully applied only to Cercosaura olivacea. The technique allowed the nine pairs of macrochromosomes to be precisely paired, proving its utility as a cytogenetic tool. The researchers note the difficulty in obtaining high-quality metaphase spreads for this technique in microteiids, whose extremely small body size, averaging just 35 millimeters snout-vent length, makes chromosome preparation from intestinal epithelial cells particularly challenging. Meiotic analyses confirmed the karyotypes, revealing 9 macrobivalents and 12 microbivalents in diakinesis cells of C. olivacea, 10 macrobivalents and 12 microbivalents in C. schreibersii albostrigatus, N. bicarinatus, and P. cordylinum, and 29 bivalents in P. glabellum.

Beyond the new karyotypes, the study provides a comprehensive compilation of all chromosomal data available for Gymnophthalmidae, synthesizing decades of scattered cytogenetic literature. The family now shows a diploid number range from 2n = 34 in Gymnophthalmus pleii to 2n = 62 in Nothobachia ablephara, with two distinct karyotype patterns: one with a clear size distinction between macro- and microchromosomes, and another with high diploid numbers and chromosomes decreasing gradually in size. Two forms of male heterogamety have been documented, a standard XX:XY system and an X₁X₁X₂X₂:X₁X₂Y multiple sex chromosome system. Supernumerary chromosomes, or B chromosomes, have also been described in the family, as have diploid and triploid parthenogenetic lineages in Gymnophthalmus and Loxopholis. A recent probabilistic analysis for the superfamily Gymnophthalmoidea, using data from 69 of its 502 species, inferred an ancestral diploid number of 2n = 42, implying that chromosomal fissions and fusions played a significant role in karyotype evolution.

From a taxonomic perspective, the new data highlight the potential utility of chromosomal features as diagnostic characters. The distinct karyotype of Bachia dorbignyi, with its low diploid number and putative sex chromosome system, reinforces the cytogenetic distinctiveness of this species relative to B. bresslaui and may aid in the delimitation of cryptic taxa. Similarly, chromosomal data for Cercosaura schreibersii albostrigatus may contribute to the ongoing debate over the validity of subspecies within C. schreibersii, supporting future integrative taxonomic revisions. The researchers emphasize that, despite the challenges of working with these tiny lizards, the high degree of chromosomal diversity uncovered here corroborates the dynamic nature of genome evolution in this clade and opens new avenues for research on speciation, sex determination, and genomic architecture in Neotropical lizards. Incorporating cytogenomic techniques and broader taxonomic sampling will be essential to fully elucidate the evolutionary mechanisms shaping karyotypes in this enigmatic group.

Subject of Research: Cytogenetics of Neotropical microteiid lizards

Article Title: Seven new karyotypes for subfamily Cercosaurinae ( Squamata , Gymnophthalmidae ) with a synthesis of chromosomal data

Article References: Rachid, L. S. F., Yonenaga-Yassuda, Y., Rodrigues, M. T., & Pellegrino, K. C. M. (2026). Seven new karyotypes for subfamily Cercosaurinae (Squamata, Gymnophthalmidae) with a synthesis of chromosomal data. Comparative Cytogenetics, 20, 21-42. https://doi.org/10.3897/compcytogen.20.170539

Image Credits: AI Generated

DOI: 10.3897/compcytogen.20.170539

Keywords: Gymnophthalmidae, karyotype, cytogenetics, lizards, chromosomes, Cercosaurinae, Seven, karyotypes, subfamily, Squamata, synthesis, chromosomal

Chromosomal instability, commonly abbreviated CIN, is one of the defining hallmarks of cancer. Rather than being a tidy process, it generates a chaotic assortment of copy number variations, structural variants, aneuploidy and, in extreme cases, catastrophic single-event shattering of chromosomes known as chromothripsis. Tumors that accumulate these defects often progress more aggressively, metastasize more readily and respond poorly to immune checkpoint blockade therapies, the blockbuster drugs that have transformed treatment for melanoma, lung cancer and several other malignancies. What has remained less clear is precisely how the individual structural features of unstable genomes relate to the composition and activation state of immune cells infiltrating the tumor. The new study set out to fill that gap by converting messy genomic events into measurable parameters and then testing how each correlates with numerically scored immune status.

The Shizuoka team drew on samples collected through Project HOPE, a multiomics initiative launched by the Shizuoka Cancer Center in 2014 with ethical approval from the center’s Institutional Review Board and informed consent from all participants. For each of the 394 tumors, the researchers performed whole genome sequencing to inventory structural changes and gene expression profiling to capture the transcriptional fingerprint of the tumor and its microenvironment. From the sequencing data they derived a battery of CIN-related metrics: tumor mutation burden, structural variant burden, microsatellite instability score, ploidy, homologous recombination deficiency score, chromothripsis score and whole genome duplication score. Each of these numbers describes a different way a cancer genome can go wrong, from point-level mutational load to wholesale doubling of the entire chromosomal complement.

The analytical centerpiece of the study was TIMMUSCORA, a tumor immune status scoring algorithm the same group had previously developed. Rather than relying on a single marker such as the presence or absence of T cells, the algorithm integrates multiple transcriptional signals to assign each tumor a numerical score that spans the full range of immune states, from robust activation to deep suppression. When the team mapped their CIN-related parameters against these scores, a consistent pattern emerged. Most of the CIN-related parameters were associated with low TIMMUSCORA scores, indicating an immunosuppressive microenvironment. In other words, the more structurally deranged the genome, the colder and less immunologically active the tumor tended to be.

To understand what was happening at the level of individual genes and cell types, the investigators compared differentially expressed genes between tumors that carried whole genome duplication or chromothripsis and tumors that did not. Whole genome duplication, a catastrophic event in which a cell duplicates its entire genome, occurs frequently in solid tumors and is thought to fuel tolerance of aneuploidy. Chromothripsis, meanwhile, pulverizes one or more chromosomes in a single catastrophic episode, scattering fragments that are haphazardly reassembled. The comparison revealed that tumors harboring either event showed down-regulation of B cell markers and down-regulation of myeloid cell markers, suggesting that key populations of adaptive and innate immune cells are depleted or functionally muted in these genomically chaotic tumors. Intriguingly, the same tumors also displayed up-regulation of the NKG2D gene, which encodes a receptor on natural killer cells and cytotoxic T lymphocytes that recognizes stress-induced ligands on malignant cells.

The up-regulation of NKG2D is a particularly interesting signal because it hints at a counter-current within an otherwise immunosuppressive landscape. Natural killer cells represent the innate arm of anti-tumor immunity, and NKG2D is one of their principal activating receptors. Its elevated expression in chromothripsis-positive tumors suggests that the innate immune system may be responding to some danger signal generated by genomic catastrophe, even as other components of the immune response are being suppressed. The researchers also observed up-regulation of cancer-testis antigen genes in chromothripsis-positive tumors, a finding with direct translational implications. Cancer-testis antigens, such as the MAGE family of proteins, are normally silent in adult tissues but become re-expressed in tumors, making them attractive targets for therapeutic vaccines and engineered T cell therapies. If chromothripsis reliably flags tumors that expose these antigens, it could serve as a biomarker to select patients for antigen-directed immunotherapies.

Among the novel observations verified in the study, two stand out. First, the team found that TP53 and EGFR mutation events can be associated with whole genome duplication and with low TIMMUSCORA scores, linking two of the most clinically important driver alterations in cancer to a weakened immune microenvironment. TP53, the so-called guardian of the genome, safeguards chromosomal integrity by halting the cell cycle and triggering apoptosis when DNA damage is detected; its loss is a permissive step toward genome chaos. EGFR, a growth factor receptor frequently mutated in lung and other cancers, drives proliferation through signaling pathways that intersect with cell cycle control. The association of mutations in these genes with both genome doubling and immune suppression provides a mechanistic thread connecting driver genetics to the immune phenotype of tumors. Second, the study tied chromothripsis to natural killer cell activation and cancer-testis antigen up-regulation, a pairing that had not been clearly documented before and that suggests chromosomal shattering may paradoxically create vulnerabilities that immunotherapy could exploit.

The technical achievement of the work lies in its integration of two large, complementary data streams. Whole genome sequencing reveals what has structurally happened to the cancer genome, while gene expression profiling reveals how the tumor and its surrounding immune and stromal cells are behaving at the transcriptomic level. By running both through a single quantitative framework, the researchers converted qualitative descriptions such as hot and cold tumors into continuous, comparable scores. This numerical approach, the authors argue, makes TIMMUSCORA a potentially useful tool for evaluating the immune status of CIN-harboring tumors, which have historically been difficult to stratify because their low mutational burdens and suppressed microenvironments place them outside the population of clear responders to existing checkpoint inhibitors.

The clinical context is significant. Immune checkpoint blockade has produced durable responses in a subset of patients, but the fraction of solid cancer patients who benefit remains limited, and tumors with high chromosomal instability are disproportionately represented among non-responders. Understanding the genomic determinants of immune exclusion and suppression is therefore a priority for expanding the reach of immunotherapy. If parameters such as whole genome duplication, homologous recombination deficiency and chromothripsis can be routinely measured from tumor sequencing, they could join tumor mutation burden and microsatellite instability as part of a standard immunogenomic profile used to predict which patients are likely to respond to treatment and which may need combination strategies, for example pairing checkpoint blockade with agents that license innate immune cells or with vaccines targeting cancer-testis antigens.

The authors caution that the study’s associations do not yet establish the mechanisms by which chromosomal instability actively suppresses immunity, and they identify this as the central question for future work. Possible avenues include exploring how aneuploid cells alter antigen presentation, how genome doubling changes the release of damage-associated molecular patterns, and how chromothriptic tumors recruit or exclude specific myeloid and lymphoid populations. With the full version of the peer-reviewed, open access article now published, the research community has a validated scoring framework and a richly characterized cohort to build upon. The work was supported by a grant from JAMED and involved clinicians and researchers from seventeen clinical divisions across the Shizuoka Cancer Center Hospital, reflecting a multidisciplinary effort spanning surgical oncology, medical genetics and immunotherapy research. In the longer view, the study adds an important piece to one of oncology’s most consequential puzzles: why some tumors hide in plain sight from the immune system, and how the architecture of a broken genome may hold the key to making them visible again.

Subject of Research: Chromosomal instability and immune suppression in the tumor microenvironment of solid cancers

Article Title: Characterization of the immune status in the tumor microenvironment of solid cancers with chromosomal instability

Article References: Akiyama, Y., Ikeya, T., Iizuka, A., Miyata, H., Maeda, C., Ashizawa, T., Nagashima, T., Urakami, K., Shimoda, Y., Ohshima, K., Shiomi, A., Ohde, Y., Bando, E., Sugiura, T., Mukaigawa, T., Nishimura, S., Hirashima, Y., Mitsuya, K., Yoshikawa, S., … Yamaguchi, K. (2026). Characterization of the immune status in the tumor microenvironment of solid cancers with chromosomal instability. Cancer Immunology, Immunotherapy. https://doi.org/10.1007/s00262-026-04547-0

Image Credits: AI Generated

DOI: 10.1007/s00262-026-04547-0

Keywords: Characterization, immune, status, tumor, microenvironment, solid, cancers, chromosomal, instability, scientific research