Biology subjects

Karafiatova, M.

Publications and source records attributed to Karafiatova, M..

5 recordsLinked to original sources

bioRxiv2026

Programmed chromosome elimination correlates with the overexpression of cohesin and additional B chromosome-encoded genes in Aegilops speltoides

Programmed chromosome elimination is a highly controlled developmental process in which specific chromosomes are selectively lost from defined cell types during development. Despite its broad occurrence across plants and animals, the molecular mechanisms driving the tissue-specific elimination of chromosomes remain largely unresolved. Here, we exploit the root-specific elimination of supernumerary B chromosomes in Aegilops speltoides as a tractable model to identify the genetic basis of programmed chromosome loss. A high-quality, chromosome-scale genome assembly was generated, assigning 398 Mb of sequence to the Ae. speltoides B chromosome. Transcriptome profiling across seven tissue types representing chromosome elimination-active, elimination-negative, and B chromosome nondisjunction conditions identified 3,262 genes consistently upregulated in elimination-associated tissues, including 1,035 B genes. Stepwise subtraction of genes expressed in post-elimination and B chromosome-retaining reference tissues, followed by intersection with genes expressed during B nondisjunction in anthers, identified a candidate gene set enriched for chromosome segregation functions. From this set, we prioritized SYN2-B, a B chromosome-encoded cohesin -kleisin subunit whose Arabidopsis thaliana ortholog AtSYN2 induces chromosome bridges and micronucleus formation when misregulated. CENH3-B, an -type centromeric histone variant identified through GO enrichment analysis of B genes expressed in elimination-associated tissues, was shown to be incorporated in centromeres of both A and B chromosomes by transient gene expression assays using protoplasts and 3D structured illumination microscopy. These findings support a model in which B chromosome-encoded perturbations of cohesin activity and centromere composition contribute to selective B chromosome nondisjunction and their elimination in root tissues. Moreover, the SYN2-B promoter is enriched for ethylene response factor-binding sites compared to its A-encoded paralog, suggesting that ethylene is implicated in the root identity pathway driving root-specific B chromosome elimination.

genetics↗

bioRxiv2025

Single-nucleus transcriptome analysis provides new insights into B chromosome elimination in sorghum

B chromosomes (Bs) are supernumerary entities found in many plant species, with some exhibiting tissue-specific elimination. In Sorghum purpureosericeum, extensive level of the B chromosome elimination occurs during embryogenesis. It progresses quickly and affects most of the embryonic organs, leaving the B chromosome maintained mainly in limited regions of meristems. Dynamic of the process and rarity of the transcripts associated with elimination make its capturing challenging. To address this, we performed single-nucleus RNA sequencing (snRNA-seq) on embryos actively undergoing B chromosome elimination. The snRNA-seq approach enabled the detection of a greater number of B-linked transcripts compared to previous method. Among all, we identified the nuclei with B-specific transcripts, which prevalently clustered together forming cluster 10 and contributing to cluster G2/M. The detailed analysis of cluster 10 revealed two distinct subpopulations of B-containing nuclei with divergent transcriptional profiles. The genes expressed in one subpopulation (sCL10-1) indicated that elimination of the B chromosome might be a factor for the split of the two subpopulations; namely that nuclei in sCL10-1 prepare for / undergo elimination, while the other subpopulation is expected to exhibit regular segregation of the B chromosome. Our analysis shows a direction so far missing in current studies and highlights a clear benefit of the single-cell approaches for studying specific behaviour of the B chromosomes.

plant biology↗

bioRxiv2025

Sorghum embryos undergoing B chromosome elimination express B-variants of mitotic-related genes

BackgroundSelective DNA elimination occurs across diverse species and plays a crucial role in evolution and development. This process encompasses small deletions, complete removal of chromosomes, or even the elimination of entire parental genomes. Despite its importance, the molecular mechanisms governing selective DNA elimination remain poorly understood. Our study focused on the tissue-specific elimination of Sorghum purpureosericeum B chromosome(s) during embryo development. ResultsIn situ B chromosome visualisation, complemented by transcriptomic profiling and gene-enrichment analysis, allowed us to identify 28 candidate genes poten-tially linked to chromosome elimination. We show that elimination is a developmentally programmed process, peaking during mid-embryogenesis and nearly completed at later stages, leaving B chromosomes only in restricted meristematic regions. Genome sequencing revealed that the sorghum B chromosome is of multi-A chromosomal origin, has reduced gene density, is enriched in repetitive sequences, and carries a novel centromeric repeat (SpuCL166). Transcriptome analyses identified B-specific variants of kinetochore, cohesion, and checkpoint genes that are expressed during active elimination, while structural modeling of CENH3 and CENP-C indicated functional divergence at the kinetochore interface. ConclusionHere, we provide the first comprehensive genomic and transcriptomic characterization of B chromosome and its elimination in Sorghum purpureosericeum. Our findings suggest that B chromosomes express modified mitotic machinery to control their own fate. By establishing a framework of candidate genes, this study opens new avenues for dissecting the molecular mechanisms of chromosome elimination and provides a critical foundation for understanding how genomes evolve to regulate and tolerate supernumerary chromosomal elements.

plant biology↗

bioRxiv2019

Identification of a dominant chlorosis phenotype through a forward screen of the Triticum turgidum cv. Kronos TILLING population

Durum wheat (Triticum turgidum) derives from a hybridization event approximately 400,000 years ago which led to the creation of an allotetraploid genome. Unlike with more ancient whole genome duplications, the evolutionary recent origin of durum wheat means that its genome has not yet been fully diploidised. As a result, many of the genes present in the durum genome act in a redundant fashion, meaning that, in many cases, loss-of-function mutations must be present in both gene copies to observe a phenotypic effect. This redundancy has hindered the use of forward genetic screens in durum wheat. Here we use a novel set of induced variation within the cv. Kronos TILLING population to identify a locus controlling a dominant, environmentally-dependent chlorosis phenotype. We carried out a forward screen of the sequenced cv. Kronos TILLING lines for senescence phenotypes and identified a single line with a dominant early senescence and chlorosis phenotype. Mutant plants contained overall less chlorophyll throughout their development and displayed premature flag leaf senescence. A segregating population was classified into discrete phenotypic groups and subjected to bulked-segregant analysis using exome capture followed by next-generation sequencing. This allowed the identification of a single region on chromosome 3A, Yellow Early Senescence 1 (YES-1), which was associated with the mutant phenotype. To obtain further SNPs for fine-mapping, we isolated chromosome 3A using flow sorting and sequenced the entire chromosome. By mapping these reads against both the cv. Chinese Spring reference sequence and the cv. Kronos assembly, we could identify high-quality, novel EMS-induced SNPs in non-coding regions within YES-1 that were previously missed in the exome capture data. This allowed us to fine-map YES-1 to 4.3 Mb, containing 59 genes. Our study shows that populations containing induced variation can be sources of novel dominant variation in polyploid crop species, highlighting their importance in future genetic screens. We also demonstrate the value of using cultivar-specific genome assemblies alongside the gold-standard reference genomes particularly when working with non-coding regions of the genome. Further fine-mapping of the YES-1 locus will be needed to identify the causal SNP underpinning this dominant, environmentally dependent phenotype.

plant biology↗

bioRxiv2018

The Aquilegia genome: adaptive radiation and an extraordinarily polymorphic chromosome with a unique history

The columbine genus Aquilegia is a classic example of an adaptive radiation, involving a wide variety of pollinators and habitats. Here we present the genome assembly of A. coerulea Goldsmith, complemented by high-coverage sequencing data from 10 wild species covering the world-wide distribution. Our analyses reveal extensive allele sharing among species and demonstrate that introgression and selection played a role in the Aquilegia radiation. We also present the remarkable discovery that the evolutionary history of an entire chromosome differs from that of the rest of the genome - a phenomenon which we do not fully understand, but which highlights the need to consider chromosomes in an evolutionary context.

evolutionary biology↗