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Rhynchospora breviuscula

ABSTRACT: Rhynchospora breviuscula overview

PROVIDER: PRJNA1060412 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27934911_1.fastq.gz	Fastqsanger.gz
	SRR27934911_2.fastq.gz	Fastqsanger.gz
	SRR27962223_1.fastq.gz	Fastqsanger.gz
	SRR27962223_2.fastq.gz	Fastqsanger.gz
	SRR27962224_1.fastq.gz	Fastqsanger.gz

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Rhynchospora breviuscula

Project description:Meiotic recombination dynamics in holocentric Rhynchospora breviuscula

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Holocentromeres in Rhynchospora are associated with genome-wide centromere-specific repeat arrays interspersed among euchromatin

Project description:BAC sequencing of centromeric regions from Rhynchospora pubera

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Holocentromeres in Rhynchospora are associated with genome-wide centromere-specific repeat arrays interspersed among euchromatin

Project description:Pollen mother cell transcriptome sequencing (RNAseq) from Rhynchospora pubera

| PRJEB9645 | ENA

Holocentromeres in Rhynchospora are associated with genome-wide centromere-specific repeat arrays interspersed among euchromatin

Project description:CENH3 ChIP-sequencing (CENH3-ChIPseq) from Rhynchospora pubera leaves

| PRJEB9647 | ENA

Holocentromeres in Rhynchospora are associated with genome-wide centromere-specific repeat arrays interspersed among euchromatin

Project description:Illumina paired-end HiSeq2000 Sequencing of the genome from Rhynchospora pubera

| PRJEB9643 | ENA

Restructuring of Holocentric Centromeres During Meiosis in the Plant Rhynchospora pubera.

Project description:Centromeres are responsible for the correct segregation of chromosomes during mitosis and meiosis. Holocentric chromosomes, characterized by multiple centromere units along each chromatid, have particular adaptations to ensure regular disjunction during meiosis. Here we show by detecting CENH3, CENP-C, tubulin, and centromeric repeats that holocentromeres may be organized differently in mitosis and meiosis of Rhynchospora pubera Contrasting to the mitotic linear holocentromere organization, meiotic centromeres show several clusters of centromere units (cluster-holocentromeres) during meiosis I. They accumulate along the poleward surface of bivalents where spindle fibers perpendicularly attach. During meiosis II, the cluster-holocentromeres are mostly present in the midregion of each chromatid. A linear holocentromere organization is restored after meiosis during pollen mitosis. Thus, a not yet described case of a cluster-holocentromere organization, showing a clear centromere restructuration between mitosis and meiosis, was identified in a holocentric organism.

| S-EPMC5068846 | biostudies-literature

Developmental programmed cell death during asymmetric microsporogenesis in holocentric species of Rhynchospora (Cyperaceae).

Project description:Members of the Cyperaceae family exhibit an asymmetric microsporogenesis that results in the degeneration of three out of four meiotic products. Efforts have been made previously to describe the resulting structure, named the pseudomonad, but mechanisms concerning the establishment of cell domains, nuclear development, and programmed cell death are largely unknown. Using the Rhynchospora genus as a model, evidence for cell asymmetry, cytoplasmic isolation, and programmed cell death was obtained by a combination of electron microscopic, cytochemical, immunocytochemical, in situ hybridization, and flow cytometric methods. Degenerative cells were identified at the abaxial region, with the cytoskeleton marking their delimitation from the functional domain after meiosis. After attempting to initiate cell division with an unreplicated genome and abnormal spindle assembly, these cells exhibited a gradual process of cytoplasmic contraction associated with hypermethylation of cytosines and differential loss of DNA. These results indicate that the asymmetric tetrad establishes a functional cell, where one nucleus is preferentially selected to survive. Degenerative haploid cells are then eliminated in a multistep process associated with mitotic disorder, non-random elimination of repetitive DNA, vacuolar cell death, and DNA fragmentation.

| S-EPMC5049389 | biostudies-literature

Holocentromeres in Rhynchospora are associated with genome-wide centromere-specific repeat arrays interspersed among euchromatin.

Project description:Holocentric chromosomes lack a primary constriction, in contrast to monocentrics. They form kinetochores distributed along almost the entire poleward surface of the chromatids, to which spindle fibers attach. No centromere-specific DNA sequence has been found for any holocentric organism studied so far. It was proposed that centromeric repeats, typical for many monocentric species, could not occur in holocentrics, most likely because of differences in the centromere organization. Here we show that the holokinetic centromeres of the Cyperaceae Rhynchospora pubera are highly enriched by a centromeric histone H3 variant-interacting centromere-specific satellite family designated "Tyba" and by centromeric retrotransposons (i.e., CRRh) occurring as genome-wide interspersed arrays. Centromeric arrays vary in length from 3 to 16 kb and are intermingled with gene-coding sequences and transposable elements. We show that holocentromeres of metaphase chromosomes are composed of multiple centromeric units rather than possessing a diffuse organization, thus favoring the polycentric model. A cell-cycle-dependent shuffling of multiple centromeric units results in the formation of functional (poly)centromeres during mitosis. The genome-wide distribution of centromeric repeat arrays interspersing the euchromatin provides a previously unidentified type of centromeric chromatin organization among eukaryotes. Thus, different types of holocentromeres exist in different species, namely with and without centromeric repetitive sequences.

| S-EPMC4640781 | biostudies-literature

Holocentric Karyotype Evolution in <i>Rhynchospora</i> Is Marked by Intense Numerical, Structural, and Genome Size Changes.

Project description:Cyperaceae is a family of Monocotyledons comprised of species with holocentric chromosomes that are associated with intense dysploidy and polyploidy events. Within this family the genus Rhynchospora has recently become the focus of several studies that characterize the organization of the holocentric karyotype and genome structures. To broaden our understanding of genome evolution in this genus, representatives of Rhynchospora were studied to contrast chromosome features, C-CMA/DAPI band distribution and genome sizes. Here, we carried out a comparative analysis for 35 taxa of Rhynchospora, and generated new genome size estimates for 20 taxa. The DNA 2C-values varied up to 22-fold, from 2C = 0.51 pg to 11.32 pg, and chromosome numbers ranged from 2n = 4 to 61. At least 37% of our sampling exhibited 2n different from the basic number x = 5, and chromosome rearrangements were also observed. A large variation in C-CMA/DAPI band accumulation and distribution was observed as well. We show that genome variation in Rhynchospora is much larger than previously reported. Phylogenetic analysis showed that most taxa were grouped in clades corresponding to previously described taxonomic sections. Basic chromosome numbers are the same within every section, however, changes appeared in all the clades. Ancestral chromosome number reconstruction revealed n = 5 as the most likely ancestral complements, but n = 10 appears as a new possibility. Chromosome evolution models point to polyploidy as the major driver of chromosome evolution in Rhynchospora, followed by dysploidy. A negative correlation between chromosome size and diploid number open the discussion for holokinetic drive-based genome evolution. This study explores relationships between karyotype differentiation and genome size variation in Rhynchospora, and contrasts it against the phylogeny of this holocentric group.

| S-EPMC7533669 | biostudies-literature

Spring temperatures affect senescence and N uptake in autumn and N storage for winter in Rhynchospora alba (Cyperaceae).

Project description:Environmental and physiological factors underlying variation in timing of autumn senescence are not well known. We investigated how the time of the onset of the growth in spring affects senescence and its functional consequences for nitrogen (N) uptake in autumn and storage of N for the winter, in a species that each year develops its bulbils for storage and overwintering anew. Rhynchospora alba was grown outdoors with two treatments, identical except for a 3 week difference in the start of growth in May. Leaf and root growth and senescence, and N uptake were recorded from August to November. By August, late-starting plants had caught up in size and total N content, but had smaller bulbils. They had a higher δ 13C, indicating a higher stomatal conductance during growth. Leaf and root senescence were delayed, extending 15N tracer uptake by 4 weeks. Nevertheless, after senescence, plants with an early start had 55% more N in their overwintering bulbils, due to earlier and more efficient remobilization. We conclude that timing of senescence in R. alba is a result of an interplay between the status of winter storage and cold temperatures, constrained by a trade-off between prolonged nutrient uptake and efficient remobilization of nutrients.

| S-EPMC7031056 | biostudies-literature

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