Sexual reproduction relies on meiotic chromosome pairing to form bivalents, a process that is complicated in polyploids owing to the presence of multiple subgenomes1. Uneven ploidy mostly results in sterility due to unbalanced chromosome pairing and segregation during meiosis. However, pentaploid dogroses (Rosa sect. Caninae; 2n = 5x = 35) achieve stable sexual reproduction through a unique mechanism: 14 chromosomes form bivalents and are transmitted biparentally, while the remaining 21 chromosomes are maternally inherited as univalents2,3. Despite being studied for over a century, the role of centromeres in this process has remained unclear. Here we analyse haplotype-resolved chromosome-level genome assemblies for three pentaploid dogroses. Subgenome phasing revealed a bivalent-forming subgenome with two highly homozygous chromosome sets and three divergent subgenomes lacking homologous partners, therefore explaining their meiotic behaviour. Comparative analyses of chromosome synteny, phylogenetic relationships and centromere composition indicate that the subgenomes originated from two divergent clades of the genus Rosa. Pollen genome analysis shows that subgenomes from different evolutionary origins form bivalents, supporting multiple origins of dogroses and highlighting variation in subgenome contributions. We reveal that bivalent-forming centromeres are enriched with ATHILA retrotransposons, contrasting with larger tandem-repeat-based centromeres mainly found in univalents. This centromere structural bimodality possibly contributes to univalent drive during female meiosis. Our findings provide insights into the unique reproductive strategies of dogroses, advancing our understanding of genome evolution, centromere diversity and meiotic mechanisms in organisms with asymmetrical inheritance systems.

• MeSH
• Centromere * genetics   metabolism   MeSH
• Chromosomes, Plant genetics   MeSH
• Phylogeny MeSH
• Genome, Plant genetics   MeSH
• Haplotypes genetics   MeSH
• Meiosis * genetics   MeSH
• Polyploidy * MeSH
• Pollen genetics   cytology   MeSH
• Retroelements genetics   MeSH
• Synteny genetics   MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Retroelements MeSH

Baobab (Adansonia digitata) is a long-lived tree endemic to Africa with economic, ecological, and cultural importance, yet its genomic features are underexplored. Here, we report a chromosome-level reference genome anchored to 42 chromosomes for A. digitata, alongside draft assemblies for a sibling tree, two trees from distinct locations in Africa, and A. za from Madagascar. The baobab genome is uniquely rich in DNA transposons, which make up 33%, while LTR retrotransposons account for 10%. A. digitata experienced whole genome multiplication (WGM) around 30 million years ago (MYA), followed by a second WGM event 3-11 MYA, likely linked to autotetraploidy. Resequencing of 25 trees identify three subpopulations, with gene flow across West Africa distinct from East Africa. Gene enrichment and fixation index (Fst) analyses show baobab retained multiple circadian, flowering, and light-responsive genes, which likely support longevity through the UV RESISTANCE LOCUS 8 (UVR8) pathway. In sum, we provide genomic resources and insights for baobab breeding and conservation.

• MeSH
• Chromosomes, Plant * genetics   MeSH
• Phylogeny MeSH
• Adaptation, Physiological genetics   MeSH
• Genome, Plant * MeSH
• Evolution, Molecular * MeSH
• Retroelements genetics   MeSH
• Trees genetics   MeSH
• Gene Flow MeSH
• DNA Transposable Elements genetics   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• Madagascar MeSH
• Names of Substances
• Retroelements MeSH
• DNA Transposable Elements MeSH

Although both are salient features of genomes, at first glance ribosomal DNAs and transposable elements are genetic elements with not much in common: whereas ribosomal DNAs are mainly viewed as housekeeping genes that uphold all prime genome functions, transposable elements are generally portrayed as selfish and disruptive. These opposing characteristics are also mirrored in other attributes: organization in tandem (ribosomal DNAs) versus organization in a dispersed manner (transposable elements); evolution in a concerted manner (ribosomal DNAs) versus evolution by diversification (transposable elements); and activity that prolongs genomic stability (ribosomal DNAs) versus activity that shortens it (transposable elements). Re-visiting relevant instances in which ribosomal DNA-transposable element interactions have been reported, we note that both repeat types share at least four structural and functional hallmarks: (1) they are repetitive DNAs that shape genomes in evolutionary timescales, (2) they exchange structural motifs and can enter co-evolution processes, (3) they are tightly controlled genomic stress sensors playing key roles in senescence/aging, and (4) they share common epigenetic marks such as DNA methylation and histone modification. Here, we give an overview of the structural, functional, and evolutionary characteristics of both ribosomal DNAs and transposable elements, discuss their roles and interactions, and highlight trends and future directions as we move forward in understanding ribosomal DNA-transposable element associations.

• Keywords
• concerted evolution, genome size, genome stability, homogenization, housekeeping genes, long-read sequencing, molecular cytogenetics, recombination, repetitive DNA, ribosomal DNA, transposable elements, transposition,
• MeSH
• Cytogenetic Analysis MeSH
• Genomics * MeSH
• DNA Methylation MeSH
• Evolution, Molecular MeSH
• DNA, Ribosomal MeSH
• DNA Transposable Elements * MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• DNA, Ribosomal MeSH
• DNA Transposable Elements * MeSH

Chromosome painting (CP) refers to visualization of large chromosome regions, chromosome arms or entire chromosomes via fluorescence in situ hybridization (FISH) of chromosome-specific DNA sequences. For CP in crucifers (Brassicaceae), typically contigs of chromosome-specific bacterial artificial chromosomes (BAC) from Arabidopsis thaliana are applied as painting probes on chromosomes of A. thaliana or other species (comparative chromosome painting, CCP). CP/CCP enables to identify and trace particular chromosome regions and/or chromosomes throughout all mitotic and meiotic stages as well as corresponding interphase chromosome territories. However, extended pachytene chromosomes provide the highest resolution of CP/CCP. Fine-scale chromosome structure, structural chromosome rearrangements (such as inversions, translocations, centromere repositioning), and chromosome breakpoints can be investigated by CP/CCP. BAC DNA probes can be accompanied by other types of DNA probes, such as repetitive DNA, genomic DNA, or synthetic oligonucleotide probes. Here, we describe a robust step-by-step protocol of CP and CCP which proved to be efficient across the family Brassicaceae, but which is also applicable to other angiosperm families.

• Keywords
• Arabidopsis thaliana, BAC FISH, Brassicaceae, Chromosome painting, Fluorescence in situ hybridization (FISH), Nick translation,
• MeSH
• Arabidopsis * genetics   MeSH
• Brassicaceae * genetics   MeSH
• Clone Cells MeSH
• Chromosomes MeSH
• DNA Probes MeSH
• DNA MeSH
• In Situ Hybridization, Fluorescence methods   MeSH
• Chromosome Painting methods   MeSH
• Chromosomes, Artificial, Bacterial genetics   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• DNA Probes MeSH
• DNA MeSH

The centromere is the chromosome region where microtubules attach during cell division. In contrast to monocentric chromosomes with one centromere, holocentric species usually distribute hundreds of centromere units along the entire chromatid. We assembled the chromosome-scale reference genome and analyzed the holocentromere and (epi)genome organization of the lilioid Chionographis japonica. Remarkably, each of its holocentric chromatids consists of only 7 to 11 evenly spaced megabase-sized centromere-specific histone H3-positive units. These units contain satellite arrays of 23 and 28 bp-long monomers capable of forming palindromic structures. Like monocentric species, C. japonica forms clustered centromeres in chromocenters at interphase. In addition, the large-scale eu- and heterochromatin arrangement differs between C. japonica and other known holocentric species. Finally, using polymer simulations, we model the formation of prometaphase line-like holocentromeres from interphase centromere clusters. Our findings broaden the knowledge about centromere diversity, showing that holocentricity is not restricted to species with numerous and small centromere units.

• MeSH
• Cell Division MeSH
• Centromere * genetics   MeSH
• Chromatids MeSH
• Heterochromatin genetics   MeSH
• Cell Cycle Proteins * MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Heterochromatin MeSH
• Cell Cycle Proteins * MeSH

Centromeres are critical for cell division, loading CENH3 or CENPA histone variant nucleosomes, directing kinetochore formation and allowing chromosome segregation1,2. Despite their conserved function, centromere size and structure are diverse across species. To understand this centromere paradox3,4, it is necessary to know how centromeric diversity is generated and whether it reflects ancient trans-species variation or, instead, rapid post-speciation divergence. To address these questions, we assembled 346 centromeres from 66 Arabidopsis thaliana and 2 Arabidopsis lyrata accessions, which exhibited a remarkable degree of intra- and inter-species diversity. A. thaliana centromere repeat arrays are embedded in linkage blocks, despite ongoing internal satellite turnover, consistent with roles for unidirectional gene conversion or unequal crossover between sister chromatids in sequence diversification. Additionally, centrophilic ATHILA transposons have recently invaded the satellite arrays. To counter ATHILA invasion, chromosome-specific bursts of satellite homogenization generate higher-order repeats and purge transposons, in line with cycles of repeat evolution. Centromeric sequence changes are even more extreme in comparison between A. thaliana and A. lyrata. Together, our findings identify rapid cycles of transposon invasion and purging through satellite homogenization, which drive centromere evolution and ultimately contribute to speciation.

• MeSH
• Arabidopsis * genetics   metabolism   MeSH
• Centromere * genetics   metabolism   MeSH
• Gene Conversion MeSH
• Histones genetics   metabolism   MeSH
• Evolution, Molecular * MeSH
• Nucleosomes genetics   metabolism   MeSH
• DNA, Satellite * genetics   MeSH
• DNA Transposable Elements * genetics   MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Cid protein, Drosophila MeSH Browser
• Histones MeSH
• Nucleosomes MeSH
• DNA, Satellite * MeSH
• DNA Transposable Elements * MeSH

Centromeres in the legume genera Pisum and Lathyrus exhibit unique morphological characteristics, including extended primary constrictions and multiple separate domains of centromeric chromatin. These so-called metapolycentromeres resemble an intermediate form between monocentric and holocentric types, and therefore provide a great opportunity for studying the transitions between different types of centromere organizations. However, because of the exceedingly large and highly repetitive nature of metapolycentromeres, highly contiguous assemblies needed for these studies are lacking. Here, we report on the assembly and analysis of a 177.6 Mb region of pea (Pisum sativum) chromosome 6, including the 81.6 Mb centromere region (CEN6) and adjacent chromosome arms. Genes, DNA methylation profiles, and most of the repeats were uniformly distributed within the centromere, and their densities in CEN6 and chromosome arms were similar. The exception was an accumulation of satellite DNA in CEN6, where it formed multiple arrays up to 2 Mb in length. Centromeric chromatin, characterized by the presence of the CENH3 protein, was predominantly associated with arrays of three different satellite repeats; however, five other satellites present in CEN6 lacked CENH3. The presence of CENH3 chromatin was found to determine the spatial distribution of the respective satellites during the cell cycle. Finally, oligo-FISH painting experiments, performed using probes specifically designed to label the genomic regions corresponding to CEN6 in Pisum, Lathyrus, and Vicia species, revealed that metapolycentromeres evolved via the expansion of centromeric chromatin into neighboring chromosomal regions and the accumulation of novel satellite repeats. However, in some of these species, centromere evolution also involved chromosomal translocations and centromere repositioning.

• MeSH
• Centromere genetics   MeSH
• Chromatin genetics   MeSH
• Pisum sativum * genetics   MeSH
• Humans MeSH
• Chromosomes, Human, Pair 6 * MeSH
• DNA, Satellite genetics   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Chromatin MeSH
• DNA, Satellite MeSH

Telomeres are essential structures formed from satellite DNA repeats at the ends of chromosomes in most eukaryotes. Satellite DNA repeat sequences are useful markers for karyotyping, but have a more enigmatic role in the eukaryotic cell. Much work has been done to investigate the structure and arrangement of repetitive DNA elements in classical models with implications for species evolution. Still more is needed until there is a complete picture of the biological function of DNA satellite sequences, particularly when considering non-model organisms. Celebrating Gregor Mendel's anniversary by going to the roots, this review is designed to inspire and aid new research into telomeres and satellites with a particular focus on non-model organisms and accessible experimental and in silico methods that do not require specialized equipment or expensive materials. We describe how to identify telomere (and satellite) repeats giving many examples of published (and some unpublished) data from these techniques to illustrate the principles behind the experiments. We also present advice on how to perform and analyse such experiments, including details of common pitfalls. Our examples are a selection of recent developments and underexplored areas of research from the past. As a nod to Mendel's early work, we use many examples from plants and insects, especially as much recent work has expanded beyond the human and yeast models traditional in telomere research. We give a general introduction to the accepted knowledge of telomere and satellite systems and include references to specialized reviews for the interested reader.

• Keywords
• FISH, NGS, TRAP, eukaryotic tree of life, interstitial telomere sequences, retroelements, satellite, subtelomere structure, telomerase RNA, telomere evolution,
• MeSH
• DNA MeSH
• Humans MeSH
• Repetitive Sequences, Nucleic Acid MeSH
• DNA, Satellite * MeSH
• Base Sequence MeSH
• Telomere * genetics   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH
• Names of Substances
• DNA MeSH
• DNA, Satellite * MeSH

Satellite DNAs are present on every chromosome in the cell and are typically enriched in repetitive, heterochromatic parts of the human genome. Sex chromosomes represent a unique genomic and epigenetic context. In this review, we first report what is known about satellite DNA biology on human X and Y chromosomes, including repeat content and organization, as well as satellite variation in typical euploid individuals. Then, we review sex chromosome aneuploidies that are among the most common types of aneuploidies in the general population, and are better tolerated than autosomal aneuploidies. This is demonstrated also by the fact that aging is associated with the loss of the X, and especially the Y chromosome. In addition, supernumerary sex chromosomes enable us to study general processes in a cell, such as analyzing heterochromatin dosage (i.e. additional Barr bodies and long heterochromatin arrays on Yq) and their downstream consequences. Finally, genomic and epigenetic organization and regulation of satellite DNA could influence chromosome stability and lead to aneuploidy. In this review, we argue that the complete annotation of satellite DNA on sex chromosomes in human, and especially in centromeric regions, will aid in explaining the prevalence and the consequences of sex chromosome aneuploidies.

• Keywords
• Aneuploidy, Centromere, Satellite DNA, Sex chromosomes, X-inactivation,
• MeSH
• Aneuploidy MeSH
• Centromere genetics   MeSH
• Heterochromatin * genetics   MeSH
• Humans MeSH
• Chromosomes, Human MeSH
• Sex Chromosomes genetics   MeSH
• DNA, Satellite * genetics   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH
• Research Support, N.I.H., Extramural MeSH
• Names of Substances
• Heterochromatin * MeSH
• DNA, Satellite * MeSH

The first gapless, telomere-to-telomere (T2T) sequence assemblies of plant chromosomes were reported recently. However, sequence assemblies of most plant genomes remain fragmented. Only recent breakthroughs in accurate long-read sequencing have made it possible to achieve highly contiguous sequence assemblies with a few tens of contigs per chromosome, that is a number small enough to allow for a systematic inquiry into the causes of the remaining sequence gaps and the approaches and resources needed to close them. Here, we analyse sequence gaps in the current reference genome sequence of barley cv. Morex (MorexV3). Optical map and sequence raw data, complemented by ChIP-seq data for centromeric histone variant CENH3, were used to estimate the abundance of centromeric, ribosomal DNA, and subtelomeric repeats in the barley genome. These estimates were compared with copy numbers in the MorexV3 pseudomolecule sequence. We found that almost all centromeric sequences and 45S ribosomal DNA repeat arrays were absent from the MorexV3 pseudomolecules and that the majority of sequence gaps can be attributed to assembly breakdown in long stretches of satellite repeats. However, missing sequences cannot fully account for the difference between assembly size and flow cytometric genome size estimates. We discuss the prospects of gap closure with ultra-long sequence reads.

• Keywords
• CenH3, Cereba, ChIP-seq, PacBio HiFi reads, flow cytometry, nanopore, ribosomal DNA, satellite, telomeric repeats,
• MeSH
• Chromosomes, Plant genetics   MeSH
• Genome, Plant genetics   MeSH
• Hordeum * genetics   MeSH
• DNA, Ribosomal genetics   MeSH
• Sequence Analysis, DNA MeSH
• Telomere genetics   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• DNA, Ribosomal MeSH