Chromosome Size Research Articles

Diversity of genome size and chromosome number in homothallic and heterothallic strains of the Closterium peracerosum-strigosum-littorale complex (Desmidiales, Zygnematophyceae, Streptophyta).

The evolutionary transitions of mating systems between outcrossing and self-fertilization are often suggested to associate with the cytological and genomic changes, but the empirical reports are limited in multicellular organisms. Here we used the unicellular zygnematophycean algae, the Closterium peracerosum-strigosum-littorale (C. psl.) complex, to address whether genomic properties such as genome sizes and chromosome numbers are associated with mating system transitions between homothallism (self-fertility) and heterothallism (self-sterility). Phylogenetic analysis revealed the polyphyly of homothallic strains, suggesting multiple transitions between homothallism and heterothallism in the C. psl. complex. Flow cytometry analysis identified a more than 2-fold genome size variation, ranging from 0.53 to 1.42 Gbp, which was positively correlated with chromosome number variation between strains. Although we did not find consistent trends in genome size change and mating system transitions, the mean chromosome sizes tend to be smaller in homothallic strains than in their relative heterothallic strains. This result suggests that homothallic strains possibly have more fragmented chromosomes, which is consistent with the argument that self-fertilizing populations may tolerate more chromosomal rearrangements.

Karyological analyses in several Algerian populations of six species of the genus Vicia L. (Fabaceae)

As part of the evaluation and valorization of plant genetic resources of fodder and pastoral interest in Algeria, seventeen (17) natural populations belonging to six (06) species of the genus Vicia (Vicia sativa, Vicia disperma, Vicia monardii, Vicia ohchroleuca, Vicia onobrychioides and Vicia lutea), originated from different ecological regions in the North-Eastern of the country, were considered. The populations have been the subject of mitotic and meiotic studies. Haploid and diploid numbers and chromosome measurements were determined. Original results were observed for the first time in some species. In fact, chromosome counts have revealed some new chromosome numbers. The first number (2n=14, n=7) was observed in the endemic subspecies of Algeria, V. ochroleuca subsp. atlantica and in the species Vicia onobrychioides. The second number (n=6) was observed in the species Vicia disperma. Within Vicia monardii, the three new chromosome numbers, previously observed only in mitosis by our research team, were confirmed for the first time through the present meiosis study (n=6, 7 and 8), indicating that they are A type chromosomes. The base number x=7 is the most frequently observed number in the six Vicia species. The observed chromosome numbers would be related to some ecological factors (altitude, rainfall) of the origin environment of the populations. Chromosome measurements and established karyotypes were determined for the first time in V. monardii, V. onobrychioides and V. ochroleuca subsp. atlantica. Chromosome size and karyotype formula are variable among the studied species and subspecies. Karyotypes vary from symmetrical to asymmetrical and the intrachromosomal asymmetry is higher than interchromosomal one. The new cytogenetic data would contribute to a better understanding of the evolution mechanism of the species in the genus Vicia L.

Chromosomal and genome size variations in Opium poppy (Papaver somniferum L.) from Afghanistan

The genus Papaver classified in the Papaveraceae family, is a valuable, non-alternative medicinal plant which has illustrated a massive variety of pharmacologically important alkaloids. Chromosomal and monoploid genome size diversity of seven populations collected from different districts of Balkh Province in northern parts of Afghanistan were studied. All populations were diploid, six of which (P1-P6) had 22 chromosomes, while P7 had 20 larger chromosomes. The mean chromosome length (CL) of P1-P6 populations was 1.32 μm (0.91-1.74 μm), but that of P7 population was 2.24 μm. The results of flow cytometric analysis showed that the mean monoploid 2Cx DNA of P1-P6 populations was 5.701 pg (5.574-5.901 pg), whereas that of P7 population was 5.795 pg, confirming intraspecific variation. This study is being reported for the first time from the northern part of Afghanistan’s opium cultivation area, and P7 population is also being reported for the first time in terms of chromosome number. Valuable information on Cytogenetics can be used in some research fields, including polygenetic analysis, taxonomic relationships, evolutionary characteristics, and plant breeding.

Genomic insights into the chromosomal elongation in a family of Collembola.

Collembola is a highly diverse and abundant group of soil arthropods with chromosome numbers ranging from 5 to 11. Previous karyotype studies indicated that the Tomoceridae family possesses an exceptionally long chromosome. To better understand chromosome size evolution in Collembola, we obtained a chromosome-level genome of Yoshiicerus persimilis with a size of 334.44 Mb and BUSCO completeness of 97.0% (n = 1013). Both genomes of Y. persimilis and Tomocerus qinae (recently published) have an exceptionally large chromosome (ElChr greater than 100 Mb), accounting for nearly one-third of the genome. Comparative genomic analyses suggest that chromosomal elongation occurred independently in the two species approximately 10 million years ago, rather than in the ancestor of the Tomoceridae family. The ElChr elongation was caused by large tandem and segmental duplications, as well as transposon proliferation, with genes in these regions experiencing weaker purifying selection (higher dN/dS) than conserved regions. Moreover, inter-genomic synteny analyses indicated that chromosomal fission/fusion events played a crucial role in the evolution of chromosome numbers (ranging from 5 to 7) within Entomobryomorpha. This study provides a valuable resource for investigating the chromosome evolution of Collembola.

Cytogenetic characteristics of Microtus daghestanicus (Rodentia: Arvicolinae) from Northeast Anatolia, Türkiye: Conventional Karyotype, C-Banding

Conventionally stained and C-banded karyotypes of Microtus daghestanicus were studied from Kars village, Turkey. The diploid chromosome number of M. daghestanicus was found as 2n=54, NFa=54. M. daghestanicus karyotype has a pair of small metacentric and 25 pairs of different sizes of acrocentric chromosomes. X chromosome is large submetacentric. Autosomal and X chromosomes were found have to pericentromeric C-band positive characteristics. Additionally, there is a wide interstitial heterochromatin block on the long arm of the X chromosome.

Chromosome counts and karyotype features of different ecotypes of Allium L. species (Amaryllidaceae – Subg. Melanocrommyum) in Iran

This study aimed to investigate the karyotypes of five Allium species, which belong to three sections of the subgenus Melanocrommyum. Bulbs from these species were collected from natural habitats in Iran, and their somatic chromosomes were analysed. The results revealed that all examined members of subg. Melanocrommyum had a basic chromosome number of x=8 and were diploid (2n=2x=16). Chromosomal data for A. saralicum and A. shatakiense are reported here for the first time. The karyotypes exhibited a variety of chromosome types and sizes, including variations observed among different accessions of the same species. In particular, A. saralicum showed satellite chromosomes ranging in size from 2.2 to 3.71 µm, located on the short arm. Seven accessions of A. saralicum, A. stipitatum, and A. haemanthoides demonstrated the presence of 1-3 B chromosomes with centromeres located in the median or subterminal position. Notably, the number of B chromosomes varied even among different accessions of the same species. Based on various indices, the karyotypes of the species were classified into symmetric and asymmetric groups. All karyotype asymmetry methods consistently identified A. stipitatum as the species with the most asymmetric chromosomes, while A. ubipetrense was recognized as the most symmetric species. This study contributes to the karyological knowledge of the genus Allium and provides valuable data for future taxonomic research. It emphasizes the significance of chromosomal characteristics in understanding plant evolution and species diversity within the Allium genus.

Understanding the chromosomal evolution in cuckoos (Aves, Cuculiformes): a journey through unusual rearrangements.

The Cuculiformes are a family of over 150 species that live in a range of habitats, such as forests, savannas, and deserts. Here, bacterial artificial chromosome (BAC) probes (75 from chicken and 14 from zebra finch macrochromosomes 1-10 +ZW and for microchromosomes 11-28 (except 16)) were used to investigate chromosome homologies between chicken and the squirrel cuckoo (Piaya cayana). In addition, repetitive DNA probes were applied to characterize the chromosome organization and to explore the role of these sequences in the karyotype evolution of P. cayana. We also applied BAC probes for chicken chromosome 17 and Z to the guira cuckoo (Guira guira) to test whether this species has an unusual Robertsonian translocation between a microchromosome and the Z chromosome, recently described in the smooth-billed ani (Crotophaga ani). Our results revealed extensive chromosome reorganization with inter- and intrachromosomal rearrangements in P. cayana, including a conspicuous chromosome size and heterochromatin polymorphism on chromosome pair 20. Furthermore, we confirmed that the Z-autosome Robertsonian translocation found in C. ani is also found in G. guira, not P. cayana. These findings suggest that this translocation occurred prior to the divergence between C. ani and G. guira, but after the divergence with P. cayana.

Fine-Scale Map Reveals Highly Variable Recombination Rates Associated with Genomic Features in the Eurasian Blackcap.

Recombination is responsible for breaking up haplotypes, influencing genetic variability, and the efficacy of selection. Bird genomes lack the protein PR domain-containing protein 9, a key determinant of recombination dynamics in most metazoans. Historical recombination maps in birds show an apparent stasis in positioning recombination events. This highly conserved recombination pattern over long timescales may constrain the evolution of recombination in birds. At the same time, extensive variation in recombination rate is observed across the genome and between different species of birds. Here, we characterize the fine-scale historical recombination map of an iconic migratory songbird, the Eurasian blackcap (Sylvia atricapilla), using a linkage disequilibrium-based approach that accounts for population demography. Our results reveal variable recombination rates among and within chromosomes, which associate positively with nucleotide diversity and GC content and negatively with chromosome size. Recombination rates increased significantly at regulatory regions but not necessarily at gene bodies. CpG islands are associated strongly with recombination rates, though their specific position and local DNA methylation patterns likely influence this relationship. The association with retrotransposons varied according to specific family and location. Our results also provide evidence of heterogeneous intrachromosomal conservation of recombination maps between the blackcap and its closest sister taxon, the garden warbler. These findings highlight the considerable variability of recombination rates at different scales and the role of specific genomic features in shaping this variation. This study opens the possibility of further investigating the impact of recombination on specific population-genomic features.

Can ploidy levels explain the variation of Herbertia lahue (Iridaceae)?

Polyploidy is often related with phenotypic variation, as observed in Herbertia lahue, a geophyte species. This study examined the H. lahue polyploid series and departure in cytogenetic, morphometric, and pollen data. Diploids (2n=2x=14) present bimodal karyotype with two long and five short chromosome pairs, while hexaploids (2n=6x=42) and octoploids (2n=8x=56) present a gradual decrease in chromosome size. All cytotypes have CMA+/DAPI- bands co-localized with 18S rDNA sites in the satellite region (no DAPI+ bands in any cytotype). Unlike diploids and octoploids, 5S rDNA interstitial sites in hexaploids are not in a syntenic position with 18S rDNA sites. Genome size is effective as an indirect predictor of the cytotypes since 2C-values increased according to ploidy level. The reduction in the number of the rDNA sites in polyploids associated with their lower 1Cx-values compared to diploids may suggest a genome downsizing process. Morphometric analysis revealed significant differences among cytotypes, and discriminant analysis identified three morphometric groupings corresponding to the cytotypes. The phenotypic variation observed in pollen grains, bulbs, and ovary characters suggested the gigas effect. Concluding, remarkable differentiation was observed at both genomic and phenotypic characters in all the cytotypes analyzed, suggesting a possible ongoing speciation process in H. lahue.

Molecular Dynamics Simulation of a Feather-Boa Model of a Bacterial Chromosome.

The chromosome of a bacterium consists of a mega-base pair-long circular DNA, which self-organizes within the micron-sized bacterial cell volume, compacting itself by three orders of magnitude. Unlike eukaryotic chromosomes, it lacks a nuclear membrane and freely floats in the cytosol confined by the cell membrane. It is believed that strong confinement, cross-linking by associated proteins, and molecular crowding all contribute to determine chromosome size and morphology. Modelling the chromosome simply as a circular polymer decorated with closed side loops in a cylindrical confining volume has been shown to already recapture some of the salient properties observed experimentally. Here we describe how a computer simulation can be set up to study structure and dynamics of bacterial chromosomes using this model.

The chromosome number and heterochromatin distribution pattern suggest differentiation among species of the Stylosanthes scabra-seabrana complex.

The genus Stylosanthes has economic importance in semi-arid regions and requires studies that reveal complex relationships between species involving different ploidies. The aim of this study was to cytogenetically investigate accessions of Stylosanthes identified as S. scabra, in order to properly identify the number, morphology, and pattern of distribution of heterochromatin, analyzing the karyological variability of these species. Accessions with 2n=40 and 2n=20 were identified, exhibiting semi-reticulate interphase nuclei, symmetric karyotype, varied morphology, with differences in average chromosomal size, and genome length. The analysis with the fluorochromes chromomycin (CMA) and 4',6-diamidino-2-phenylindole (DAPI) allowed the visualization of two CMA+ blocks in the subterminal region of the short arm in all accessions, and DAPI+/CMA- bands in S. scabra accessions. This suggests that not only chromosomal rearrangements, but also changes in the composition of heterochromatin, may have occurred during the speciation of this genus, and that S. scabra may be undergoing chromosomal evolution based on the observed karyological differences. In addition to the ploidy level, the distribution pattern of CMA+ heterochromatin reinforces the separation between S. scabra and S. seabrana. Thus, this genus represents an interesting group of plants for further studies on the content and quantity of repetitive and non-repetitive DNA sequences.

Escherichia coli O157:H7 tir 255 T > A allele strains differ in chromosomal and plasmid composition.

Shiga toxin-producing Escherichia coli (STEC) O157:H7 strains with the T allele in the translocated intimin receptor polymorphism (tir) 255 A > T gene associate with human disease more than strains with an A allele; however, the allele is not thought to be the direct cause of this difference. We sequenced a diverse set of STEC O157:H7 strains (26% A allele, 74% T allele) to identify linked differences that might underlie disease association. The average chromosome and pO157 plasmid size and gene content were significantly greater within the tir 255 A allele strains. Eighteen coding sequences were unique to tir 255 A allele chromosomes, and three were unique to tir 255 T allele chromosomes. There also were non-pO157 plasmids that were unique to each tir 255 allele variant. The overall average number of prophages did not differ between tir 255 allele strains; however, there were different types between the strains. Genomic and mobile element variation linked to the tir 255 polymorphism may account for the increased frequency of the T allele isolates in human disease.

Complete genomic sequencing of a Pseudomonas putida isolate derived from a patient suffering from chronic diarrheal infection in Hangzhou, China.

This study presents a comprehensive analysis of the genomic sequence of Pseudomonas putida isolate L2890hy, having a 6,733,472 bp chromosome size. This particular strain was obtained from a fecal sample of a patient suffering from acute diarrhea in Hangzhou, China, in 2020.

Cell culture and karyotypic description of Pseudophrynecoriacea (Keferstein, 1868) (Amphibia, Anura) from the New South Wales Central Coast.

The karyotype of the IUCN least concern red-backed toadlet Pseudophryne (P.) coriacea (Keferstein, 1868) from the New South Wales Central Coast is described following tissue culture of toe clipping macerates and conventional DAPI staining. The diploid number is 2n = 24. The karyotype is represented by six large and five small chromosomal pairs and one very small chromosomal pair. The very small chromosome 12 is 12% the size of chromosome 1. One of the large chromosomes is subtelocentric, two of the large chromosomes are submetacentric and the remaining chromosomes are metacentric. The putative nucleolus organiser region (NOR) is observed on chromosome 4. The diploid number and location of the putative NOR correlates to that of the previously published IUCN critically endangered P.corroboree (Moore 1953) and unpublished descriptions of the P.coriacea karyotype. This is the first described cell culture of a species from the genus Pseudophryne Fitzinger, 1843, first published analysis of the P.coriacea karyotype and the first published analysis of centromeric allocation of this genus. Globally there exists a large inventory of tissue samples in cryobanks that are not associated with known recovery mechanisms such as basic cell culture techniques. Detailed cytogenetic analyses of these cryobanked samples are therefore not possible. This work therefore enables: (i) a comparison of the P.coriacea karyotype with that of the critically endangered P.corroboree and (ii) a benchmark for repeat and future cytogenetic and genomic analyses of cryostored samples of this genus.

Variation in the Incidence and Type of Full versus Mosaic Segmental Aneuploidies Identified in Blastocysts Undergoing PGT-A

Objectives: The primary aim of this study was to investigate the incidence of segmental aneuploidies (full vs. mosaic) in embryos biopsied for Preimplantation Genetic Testing with Aneuploidy (PGT-A) screening using low-coverage whole genome sequencing (WGS). The secondary aim was to investigate factors that may be associated with segmental aneuploidy rates, including blastocyst developmental stage and quality. Methods: This study involved a retrospective analysis of cycle and PGT-A data from 8,153 blastocysts biopsied from 2,522 patients at four Monash IVF Victorian clinics between January 2015 and June 2021. All biopsies were processed using the Veriseq PGS Kit (Illumina) and analyzed using Bluefuse Multi software (Illumina) with a conclusive PGT-A result. Segmental aneuploidy was reported with a minimum resolution of greater than or equal to 10[Formula: see text]Mb. The reporting range for mosaicism was 20%–70% loss/gain in copy number. Statistical significance was established at a P-value of less than 0.05. Results: Segmental aneuploidies (full and/or mosaic) were reported in 682/8,153 (8.4%) biopsied embryos. Analysis of the types of segmental aneuploidy showed a higher proportion of deletions (423/8,153; 5.2%) compared to duplications (210/8,153; 2.6% [[Formula: see text]] plus a small portion with both duplications and deletions detected 49/8153; 0.6% [[Formula: see text]]). The incidence of segmental aneuploidies appeared to increase in correlation with chromosome size. Segregation of embryos by blastocyst stage indicated an increase in the incidence of segmental aneuploidies in early blastocysts (9/64; 14.1%) compared with expanding/expanded (39/475, 8.2%, [[Formula: see text]] and hatching/hatched blastocysts [634/7614, 8.3%; [Formula: see text]]). Furthermore, the incidence of segmental aneuploidies significantly increased as blastocyst overall grade decreased (Grade A 71/1,429, 5.0%; Grade B 298/3,764, 7.9%; Grade C 313/2,960, 10.6%; [Formula: see text]). Of the segmental aneuploidies detected, 425/682 (62.3%) were present at a mosaic level. Conclusions: Segmental aneuploidy rates varied between blastocyst stage and grades, with a significant proportion of segmental aneuploidies being detected at the mosaic level. Our data highlights that segmental aneuploidies, both at the full and mosaic level, are associated with lower blastocyst quality and poorer embryo development.

Hidden prevalence of deletion-inversion bi-alleles in CRISPR-mediated deletions of tandemly arrayed genes in plants

Tandemly arrayed genes (TAGs) with functional redundancy and chromosomal linkage constitute 14 ~ 35% in sequenced plant genomes. The multiplex CRISPR system is the tool of choice for creating targeted TAG deletions. Here, we show that up to ~80% of CRISPR-mediated TAG knockout alleles in Arabidopsis and rice are deletion-inversion (delinver) bi-alleles, which are easily misidentified as homozygous deletion alleles by routine PCR-based genotyping. This can lead to misinterpretation of experimental data and production of progenies with genetic heterogeneity in an unnoticed manner. In ~2,650 transgenic events, delinver mutation frequencies are predominantly correlated with deletion frequencies but unrelated to chromosomal locations or deletion sizes. Delinver mutations also occur frequently at genomic non-TAG loci during multiplexed CRISPR editing. Our work raises the alarm about delinver mutations as common unwanted products of targeted TAG deletions in plants and helps prevent false interpretation of plant TAG functions due to this hidden genotype issue.

A cytosystematic study of the Dianthus virgineus complex (Caryophyllaceae) in the Central Mediterranean

AbstractEuropean wild carnations (Dianthus) are represented by a high number of taxa organized in unresolved taxonomies. In particular, taxa belonging to the Dianthus virgineus L. complex in the Central Mediterranean have been delimited mainly with qualitative morphological data and still await quantitative investigations, which are vital to understand boundaries and relations among plant diversity groups. Here, we examine the phenotypic features of nuclear genome organization testing for species boundaries in this complex. We have studied the chromosome number, the total haploid length (THL), and the relative genome size (RGS) in 122 populations belonging to 25 out of 33 taxa of the complex. All the studied populations have 2n = 2x = 30 chromosomes, and the THL ranges from 14.09 to 20.71 μm. Genome size estimations support the absence of polyploidization events, but show a certain degree of variation (0.318–0.423 arbitrary units). The RGS variation is not in agreement with current taxonomic treatment, but rather shows a geographical pattern, with higher values in Sicily and Sardinia. No correlation between the THL and the RGS was detected, possibly due to the stable chromosome number and the small size of chromosomes. A number of evolutionary unique groups lower than the number of currently accepted taxa may be hypothesized.

A Modified Quantum-Inspired Genetic Algorithm Using Lengthening Chromosome Size and an Adaptive Look-Up Table to Avoid Local Optima

The quantum-inspired genetic algorithm (QGA), which combines quantum mechanics concepts and GA to enhance search capability, has been popular and provides an efficient search mechanism. This paper proposes a modified QGA, called dynamic QGA (DQGA). The proposed algorithm utilizes a lengthening chromosome strategy for a balanced and smooth transition between exploration and exploitation phases to avoid local optima and premature convergence. Apart from that, a novel adaptive look-up table for rotation gates is presented to boost the algorithm’s optimization abilities. To evaluate the effectiveness of these ideas, DQGA is tested by various mathematical benchmark functions as well as real-world constrained engineering problems against several well-known and state-of-the-art algorithms. The obtained results indicate the merits of the proposed algorithm and its superiority for solving multimodal benchmark functions and real-world constrained engineering problems.

Comparative genomics of Mycoplasma feriruminatoris, a fast-growing pathogen of wild Caprinae.

Mycoplasma feriruminatoris is a fast-growing Mycoplasma species isolated from wild Caprinae and first described in 2013. M. feriruminatoris isolates have been associated with arthritis, kerato conjunctivitis, pneumonia and septicemia, but were also recovered from apparently healthy animals. To better understand what defines this species, we performed a genomic survey on 14 strains collected from free-ranging or zoo-housed animals between 1987 and 2017, mostly in Europe. The average chromosome size of the M. feriruminatoris strains was 1,040±0,024 kbp, with 24 % G+C and 852±31 CDS. The core genome and pan-genome of the M. feriruminatoris species contained 628 and 1312 protein families, respectively. The M. feriruminatoris strains displayed a relatively closed pan-genome, with many features and putative virulence factors shared with species from the M. mycoides cluster, including the MIB-MIP Ig cleavage system, a repertoire of DUF285 surface proteins and a complete biosynthetic pathway for galactan. M. feriruminatoris genomes were found to be mostly syntenic, although repertoires of mobile genetic elements, including Mycoplasma Integrative and Conjugative Elements, insertion sequences, and a single plasmid varied. Phylogenetic- and gene content analyses confirmed that M. feriruminatoris was closer to the M. mycoides cluster than to the ruminant species M. yeatsii and M. putrefaciens. Ancestral genome reconstruction showed that the emergence of the M. feriruminatoris species was associated with the gain of 17 gene families, some of which encode defence enzymes and surface proteins, and the loss of 25 others, some of which are involved in sugar transport and metabolism. This comparative study suggests that the M. mycoides cluster could be extended to include M. feriruminatoris. We also find evidence that the specific organization and structure of the DnaA boxes around the oriC of M. feriruminatoris may contribute to drive the remarkable fast growth of this minimal bacterium.

Modelo matemático basado en algoritmos genéticos para optimizar las utilidades en una empresa de transporte interprovincial de pasajeros

The main objective of this research was to improve profits in an interprovincial passenger transport company, having designed a mathematical programming model and a genetic algorithm model with the purpose of reaching solutions for a future optimization of the company's profits. The type of research was applied, the technique that was applied was the survey and the sample was made up of all the variables of income, costs and profits of an interprovincial passenger transport company in the Peruvian territory. The results confirmed that the implementation of a mathematical model based on genetic algorithms contributes significantly to the optimization of profits, since the profit associated with the economic bus was improved, to the sleeper bus, to the mixed bus and to the super sleeper bus, achieving an optimal occupancy rate of 58.33%, 85.00%, 58.33% and 95.00%, respectively. The implemented model was based on a chromosome size of 19 bits, the population size was 10 chromosomes, the selection method is probabilistic with 4 chromosomes, crossing with four chromosomes, type of multipoint crossing and mutation process a from the second iteration of probabilistic type.