Biology subjects

Tomaszewska, P.

Publications and source records attributed to Tomaszewska, P..

13 recordsLinked to original sources

bioRxiv2026

Acellular starch domains in the endosperm of wheat and oat

The transformation of the free nuclear syncytium into cellular endosperm tissue with starch and protein accumulation is a well-established phenomenon, at least in the fruits of cereals of the Triticeae tribe. The present article demonstrates that there is considerable diversity inherent in this type of caryopsis morphogenesis. By examining various taxa (species, varieties, and cultivars) of wheat, oats, and some wild grasses, this research reveals significant deviations in endosperm morphogenesis from the typical state. A new developmental pattern of endosperm was identified, characterized by several distinctive features such as incomplete cellularization of the syncytium and starch accumulation within the acellular endosperm domains and the endosperm cavity. A large number of plastids were observed in the syncytium stage, which served as the basis for the later amyloplast stage. The acellular endosperm domains and the cavity domain exhibited connections at specific discontinuities in the modified aleurone layer surrounding the cavity. The peripheral parts of the caryopsis received fewer assimilates necessary for starch synthesis, which was attributed to their increased distance from the transfer system and a likely reduction in the efficiency of assimilate transport through the apoplast in these areas. The starch cavity volume constituted a few percent of the overall caryopsis volume, which could serve as a foundation for potential breeding improvements to enhance starch yields across different varieties.

plant biology↗

bioRxiv2025

Comparative functional profiling of plant ACR3 orthologs reveals metalloid-sensitive trafficking and arsenic efflux capabilities

Arsenic contamination poses a major environmental and public health challenge. In liverworts and ferns, ACR3 transporters mediate arsenite efflux and contribute to arsenic tolerance. We recently showed that ACR3 from Marchantia polymorpha (MpACR3) contains an extended N-terminal region that couples arsenic sensing to membrane trafficking. However, the function and regulation of ACR3 transporters across photosynthetic lineages remain unclear. Here, we characterize ACR3 transporters from phylogenetically distant algae and land plants using heterologous expression in yeast. All examined ACR3 proteins function as arsenic efflux transporters but display two distinct trafficking modes: constitutive plasma membrane localization or metalloid-driven relocalization from the endomembrane system. Like the previously characterized MpACR3, we show that this inducible trafficking is governed by an extended N-terminal domain unique to plant ACR3 proteins, integrating a conserved di-arginine ER/Golgi retention signal with cysteine-based arsenic sensing. These findings establish a direct mechanistic link between metalloid perception and subcellular targeting. Functional assays in Arabidopsis thaliana demonstrated that Physcomitrium patens ACR3 confers arsenic tolerance, reduces root arsenic accumulation, and retains metalloid-dependent trafficking, supporting its physiological relevance. Together, our findings uncover a conserved mechanism linking arsenic sensing to ACR3 trafficking and provide new insight into the evolution of arsenic tolerance in plants. Summary statementPlant ACR3 transporters mediate arsenic efflux and exhibit distinct trafficking modes. An N-terminal domain links arsenic sensing to the endomembrane system-plasma membrane relocalization, revealing a conserved mechanism controlling ACR3 function and arsenic tolerance across plant lineages.

plant biology↗

bioRxiv2025

Arsenic-sensing domain controls ACR3 transporter trafficking and function in Marchantia polymorpha

Arsenic, a toxic and carcinogenic metalloid, is a pervasive environmental contaminant that threatens human health through contaminated water and food. The efflux of As(III) via ACR3 transporters is an ancient detoxification mechanism conserved across prokaryotes, fungi, and plants, with the notable exception of angiosperms. Despite their evolutionary significance, plant ACR3s remain largely uncharacterized. Here, we demonstrate that MpACR3, the ACR3 orthologue from the liverwort Marchantia polymorpha, functions as a metalloid/proton antiporter, conferring resistance to arsenicals and moderate tolerance to antimony. Additionally, we uncover an arsenic-sensing domain within MpACR3 that regulates its intracellular trafficking. Under normal conditions, MpACR3 sorting to the plasma membrane is delayed, resulting in its retention within Golgi bodies. However, As(III) binding to three cysteine residues in the N-terminal cytosolic domain induces a conformational change that facilitates MpACR3 trafficking to the plasma membrane. Furthermore, mutational analysis of a conserved arginine-based motif reveals that the N-terminal domain not only controls MpACR3 accumulation at the plasma membrane but also modulates its transport activity. Importantly, this arsenic-sensing domain is conserved among plant ACR3 transporters, suggesting a plant-specific adaptation to arsenic toxicity.

plant biology↗

bioRxiv2024

Multi-character assessment of caryopsis in diverse common wheat germplasm,including high protein breeds

In 15 varieties and hybrids of common wheat, including high-protein, varieties such as Atlas 66, Nap Hal, and Lancota, the microstructural characters of the caryopsis were analysed. Among the wheats, a high variability in the correlation matrices of characters was observed. A variable relationship between the specific gravity of the caryopsis and the size of the endosperm cavity was demonstrated. Some principal components (I, II, IV and V) contained the majority of the information regarding the weight, quality, vitreousness, and aleurone layer of the caryopsis, respectively. In the ordination space of nonmetric multidimensional scaling (nmMDS), two groups of wheat were distinguished: high-protein and low-protein subaleurone layers. Endosperm morphotypes were characterised by the proportion of two types of starch tissue, cylindric and isodiametric. In the nmMDS ordination space, wheat was described by the frequency distributions of six endosperm cavity morphotypes, with more (leptokurtosis) or less (platykurtosis) cumulated variation. In the case of endosperm developmental anomalies, the intrusive growth of cell walls, particularly in the aleurone layer, was identified as playing a significant role in the formation of endosperm mosaic architecture and domains. Varietal developmental specificity was discovered in the development of acellular starch domains within the endosperm tissue and starch grain storage in the cavity (as observed in cv. Purdue).

plant biology↗

bioRxiv2023

Phylogenomic analysis reveals the evolutionary origins of five independent clades of forage grasses within the African genus Urochloa

Background and AimsThe grass genus Urochloa (Brachiaria) includes forage crops that are important for beef and dairy industries in tropical and sub-tropical Africa, South America, and Oceania/Australia. Economically important species include U. brizantha, U. decumbens, U. humidicola, U. mutica, U. arrecta, U. trichopus, U. mosambicensis, and M. maximus, all native to the African continent. Perennial growth habits, large, fast growing palatable leaves, intra- and interspecific morphological variability, apomictic reproductive systems, and frequent polyploidy are widely shared within the genus. The combination of these traits likely favoured the selection for forage domestication and weediness, but trait emergence across Urochloa cannot be modelled, as a robust phylogenetic assessment of the genus has not been conducted. MethodsUsing a target enrichment sequencing approach (Angiosperms353 baits), we inferred a species level phylogeny for Urochloa sensu lato, encompassing 57 species ([~]50% of the genus) and outgroups. We determined the phylogenetic placement of agriculturally important species and identify their closest wild relatives. Further, we mapped key traits associated with forage crop potential to the species tree, exploring trait distribution across the genus. Key ResultsAgricultural species belong to five independent clades, including U. brizantha and U. decumbens lying in a previously defined species complex. Crop wild relatives were identified for these clades supporting previous sub-generic groupings in Urochloa based on morphology. Using ancestral trait estimation models, we find that five morphological traits that correlate with forage potential (perennial growth habits, culm height, leaf size, a winged rachis, and large seeds) independently evolved in forage clades. ConclusionsUrochloa s.l. is a highly diverse genus that contains numerous species with agricultural potential, including crop wild relatives that are currently underexploited. The African continent is the centre of origin for these clades and their conservation across their native distributions is essential. Genomic and phenotypic diversity in forage clade species and their wild relatives needs to be better assessed to improve sustainability in Urochloa cultivar production.

evolutionary biology↗

bioRxiv2023

Oat species and interspecific amphiploids show predominance of diploid nuclei in the syncytial endosperm

Apart from apomictic types, the Polygonum-type eight-nuclear embryo sac is considered to be dominant in grasses. A triploid endosperm is formed as a result of double fertilisation. This study showed, for the first time, the dominance of diploid nuclei in the syncytial stage of the central cell of embryo sac in oat species and amphiploids. The dominance of diploid nuclei, which were the basis for the formation of polyploid nuclei, was weaker in amphiploids due to aneuploid events. The genomic in situ hybridisation method applied in the study did not distinguish the maternal and paternal haploid nuclei of embryo sac. However, this method demonstrated the lack of a set of genomes of one haploid nucleus. It can be assumed that the formation of diploid oat endosperm occurred after the fusion of one polar nucleus and the nucleus of a sperm cell, while the second polar nucleus formed 1n nuclei. The levels of syncytial ploidy were not influenced by both aneuploid events and correlated with pollen developmental anomalies. The differences in the analysed cytogenetic events distinguished amphiploids and their parental species in the ordination space.

plant biology↗

bioRxiv2022

Oat chromosome and genome evolution defined by widespread terminal intergenomic translocations in polyploids

Structural chromosome rearrangements involving translocations, fusions and fissions lead to evolutionary variation between species and potentially reproductive isolation and variation in gene expression. While the wheats (Triticeae, Poaceae) and oats (Aveneae) all maintain a basic chromosome number of x=7, genomes of oats show frequent intergenomic translocations, in contrast to wheats where these translocations are relatively rare. We aimed to show genome structural diversity and genome relationships in tetraploid, hexaploid and octoploid Avena species and amphiploids, establishing patterns of intergenomic translocations across different oat taxa using fluorescence in situ hybridization (FISH) with four well-characterized repetitive DNA sequences: pAs120, AF226603, Ast-R171 and Ast-T116. In A. agadiriana (2n=4x=28), the selected probes hybridized to all chromosomes indicating that this species originated from one (autotetraploid) or closely related ancestors with the same genomes. Hexaploid amphiploids were confirmed as having the genomic composition AACCDD, while octoploid amphiploids showed three different genome compositions: AACCCCDD, AAAACCDD or AABBCCDD. The A, B, C, and D genomes of oats differ significantly in their involvement in non-centromeric, intercalary translocations. There was a predominance of distal intergenomic translocations from the C-into the D-genome chromosomes. Translocations from A- to C-, or D- to C-genome chromosomes were less frequent, proving that at least some of the translocations in oat polyploids are non-reciprocal. Rare translocations from A- to D-, D- to A- and C- to B-genome chromosomes were also visualized. The fundamental research has implications for exploiting genomic biodiversity in oat breeding to through introgression from wild species potentially with contrasting chromosomal structures and hence deleterious segmental duplications or large deletions in amphiploid parental lines.

plant biology↗

bioRxiv2022

The repetitive DNA sequence landscape and DNA methylation in chromosomes of an apomictic tropical forage grass, Cenchrus ciliaris

Cenchrus ciliaris is an apomictic, allotetraploid pasture grass widely distributed in tropical and subtropical regions of Africa and Asia. In this work, we aim to investigate the genomic organization and characterize the nature of repetitive DNA sequences in this species. Because of the apomictic propagation, various aneuploid genotypes are found and we analysed here a 2n=4x+3=39 accession. The physical mapping of Ty1-copia and Ty3-gypsy retroelements through fluorescence in situ hybridization with global assessment of 5-methylcytosine DNA methylation through immunostaining revealed the genome-wide distribution pattern of retroelements and their association with DNA methylation. About a third of Ty1-copia sites overlapped or spanned centromeric DAPI positive heterochromatin, while the centromeric regions and arms of some chromosomes were labeled with Ty3-gypsy. Most of the retroelement sites overlapped with 5-methycytosine signals, except some Ty3-gypsy on the arms of chromosomes which did not overlap with anti-5-mC signals. Universal retrotransposon probes did not distinguish genomes of C. ciliaris showing signals in pericentromeric regions of all 39 chromosomes, unlike highly abundant repetitive DNA motifs found in survey genome sequences of C. ciliaris using graph-based clustering. Probes developed from RepeatExplorer clusters gave strong signals mostly in pericentromeric regions of about half of the chromosomes, and we suggested that they differentiate the two ancestral genomes in the allotetraploid C. ciliaris likely having different repeat sequence variants amplified before the genome came together in the tetraploid.

genomics↗

bioRxiv2021

Variability of pollen grains quality in oat amphiploids and their parental species

The reproductive potential of oat species and their hybrid progeny (amphiploids) was evaluated during three vegetation seasons. Morphotypes and viability of pollen grains were described by means of correlations and regression, while relationships between taxa were analysed with the use of numerical taxonomy methods. Size of pollen grains varied between the growing seasons, but the relations between the taxa appeared to be stable. Viability of pollen grains was environmentally modified and showed no correlation with pollen length. In an ordination space, amphiploids were discriminated from parental species. In both group of plants, a positive correlation between the pollen size and the level of ploidy was maintained; however, along a regression line, amphiploids were located among species with a high level of ploidy and were extreme units deviating from the regression line. Developmental anomalies of pollen grains had a low frequency, with the formation of micrograins being the most common event. Such a pattern of development can prove that some pollen grains were chromosomally unbalanced. Anomalous morphotypes of pollen were more common in hybrid types than in species, including pollens with many poruses, which were found only in amphiploids. Frequencies of multiporate grains and micropollens were strongly correlated. In an ordination space, monoporate types (species) were discriminated from multiporate types (amphiploids). In general, the high level of pollen viability in amphiploids can prove their genomic stabilisation through many generations of their reproduction.

plant biology↗

bioRxiv2021

The five Urochola spp. used in development of tropical forage cultivars originate from defined subpopulations with differentiated gene pools

Background and AimsUrochloa (syn. Brachiaria, and including some Panicum and Megathyrus) is a genus of tropical and subtropical grasses widely sown as forage to feed ruminants in the tropics. A better understanding of the diversity among Urochloa spp. allow us to leverage its varying ploidy levels and genome composition to accelerate its improvement, following the example from other crop genera. MethodsWe explored the genetic make-up and population structure in 111 accessions, which comprise the five Urochloa species used for the development of commercial cultivars. These accessions are conserved from wild materials from collection sites at their centre of origin in Africa. We used RNA-seq, averaging 40M reads per accession, to generate 1,167,542 stringently selected SNP markers that tentatively encompassed the complete Urochloa gene pool used in breeding. Key ResultsWe identified ten subpopulations, which had no relation with geographical origin and represented ten independent gene pools, and two groups of admixed accessions. Our results support a division in U. decumbens by ploidy, with a diploid subpopulation closely related to U. ruziziensis, and a tetraploid subpopulation closely related to U. brizantha. We observed highly differentiated gene pools in U. brizantha, which were not related with origin or ploidy. Particularly, one U. brizantha subpopulation clustered distant from the other U. brizantha and U. decumbens subpopulations, so likely containing unexplored alleles. We also identified a well-supported subpopulation containing both polyploid U. decumbens and U. brizantha accessions; this was the only group containing more than one species and tentatively constitutes an independent "mixed" gene pool for both species. We observed two gene pools in U. humidicola. One subpopulation, "humidicola-2", was much less common but likely includes the only known sexual accession in the species. ConclusionsOur results offered a definitive picture of the available diversity in Urochloa to inform breeding and resolve questions raised by previous studies. It also allowed us identifying prospective founders to enrich the breeding gene pool and to develop genotyping and genotype-phenotype association mapping experiments. HIGHLIGHTWe clarified the genetic make-up and population structure of 111 Urochloa spp. forage grasses to inform cultivar development.

plant biology↗

bioRxiv2021

Flow cytometry-based determination of ploidy from dried leaf specimens in genomically complex collections of the tropical forage grass Urochloa s. l.

We aimed to develop an optimized approach to determine ploidy for dried leaf material in a germplasm collection of a tropical forage grass group, including approaches to collect, dry and preserve plant samples for flow cytometry analysis. Urochloa (including Brachiaria, Megathyrus and some Panicum) tropical grasses are native to Africa and are now, after selection and breeding, planted worldwide, particularly in South America, as important forages with huge potential for further sustainable improvement and conservation of grasslands. The methods enable robust identification of ploidy levels (coefficient of variation, CV, typically <5%). Ploidy of some 353 forage grass accessions (ploidy range from 2 to 9), from international genetic resource collections, showing variation in basic chromosome numbers and reproduction modes (apomixis and sexual), were determined using our defined standard protocol. Two major Urochloa agamic complexes used in the current breeding programs at CIAT and EMBRAPA: the brizantha and humidicola agamic complexes are variable, with multiple ploidy levels and DNA content. U. brizantha has odd level of ploidy (x=5), and the relative differences in nuclear DNA content between adjacent cytotypes is reduced, thus more precise examination of this species is required. Ploidy measurement of U. humidicola revealed some aneuploidy.

genomics↗

bioRxiv2021

Complex polyploid and hybrid species in an apomictic and sexual tropical forage grass group: genomic composition and evolution in Urochloa (Brachiaria) species

Background and AimsDiploid and polyploid Urochloa (including Brachiaria, Panicum and Megathyrsus species) C4 tropical forage grasses originating from Africa and now planted worldwide are important for food security and the environment, often being planted in marginal lands. We aimed to characterize the nature of their genomes, the repetitive DNA, and the genome composition of polyploids, leading to a model of the evolutionary pathways within the group including many apomictic species. MethodsSome 362 forage grass accessions from international germplasm collections were studied, and ploidy determined using an optimized flow cytometry method. Whole-genome survey sequencing and molecular cytogenetic analysis with in situ hybridization to chromosomes were used to identify chromosomes and genomes in Urochloa accessions belonging to the different agamic complexes. Key ResultsGenome structures are complex and variable, with multiple ploidies and genome compositions within the species, and no clear geographical patterns. Sequence analysis of nine diploid and polyploid accessions enabled identification of abundant genome-specific repetitive DNA motifs. In situ hybridization with a combination of repetitive DNA and genomic DNA probes, identified evolutionary divergence and allowed us to discriminate the different genomes present in polyploids. ConclusionsWe suggest a new coherent nomenclature for the genomes present. We develop a model of evolution at the whole-genome level in diploid and polyploid accessions showing processes of grass evolution. We support the retention of narrow species concepts for U. brizantha, U. decumbens, and U. ruziziensis. The results and model will be valuable in making rational choices of parents for new hybrids, assist in use of the germplasm for breeding and selection of Urochloa with improved sustainability and agronomic potential, and will assist in measuring and conserving biodiversity in grasslands.

genomics↗

bioRxiv2021

Cytogenetic events in the endosperm of amphiploid Avena maroccana x A. longiglumis

This study analysed cytogenetic events occurring in the syncytial endosperm of the Avena maroccana Gand. x Avena longiglumis Dur. amphiploid, which is a product of two wild species having different genomes. Selection through the elimination of chromosomes and their fragments, including those translocated, decreased the level of ploidy in the endosperm below the expected 3n, leading to the modal number close to 2n. During intergenomic translocations, fragments of the heterochromatin-rich C-genome were transferred to the A and Al genomes. Terminal and non-reciprocal exchanges dominated, whereas other types of translocations, including microexchanges, were less common. Using two probes and by counterstaining with DAPI, the A. longiglumis and the rare exchanges between the A and Al genomes were detected by GISH. The large discontinuity in the probe labelling in the C chromosomes demonstrated inequality in the distribution of repetitive sequences along the chromosome and probable intragenomic rearrangements. In the nucleus, the spatial arrangement of genomes was non-random and showed a sectorial-concentric pattern, which can vary during the cell cycle, especially in the less stable tissue like the hybrid endosperm.

genetics↗