The centromere has a conserved function across eukaryotes; however, the associated DNA sequences exhibit remarkable diversity in both size and structure. In plants, some species possess well-defined centromeres dominated by tandem satellite repeats and centromeric retrotransposons, while others have centromeric regions composed almost entirely of retrotransposons. Using a combination of bioinformatic, molecular, and cytogenetic approaches, we analyzed the centromeric landscape of Humulus lupulus. We identified novel centromeric repeats and characterized two types of centromeric organization. Cytogenetic localization on metaphase chromosomes confirmed the genomic distribution of the major repeats and revealed unique centromeric organization specifically on chromosomes 2, 8, and Y. Two centromeric types are composed of the major repeats SaazCEN and SaazCRM1 (Ty3/Gypsy) which are further accompanied by chromosome-specific centromeric satellites, Saaz40, Saaz293, Saaz85, and HuluTR120. Chromosome 2 displays unbalanced segregation during mitosis and meiosis, implicating an important role for its centromere structure in segregation patterns. Moreover, chromosome 2-specific centromeric repeat Saaz293 is a new marker for studying aneuploidy in hops. Our findings provide new insights into chromosome segregation in hops and highlight the diversity and complexity of the centromere organization in H. lupulus.

• Keywords
• Cannabaceae, asymmetric cell division, centromere, retrotransposons, sex chromosomes,
• MeSH
• Centromere * genetics   MeSH
• Chromosomes, Plant genetics   MeSH
• Humulus * genetics   MeSH
• Meiosis genetics   MeSH
• Repetitive Sequences, Nucleic Acid * genetics   MeSH
• Retroelements * genetics   MeSH
• Chromosome Segregation genetics   MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Retroelements * 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 evolution of eukaryotic genomes is accompanied by fluctuations in chromosome number, reflecting cycles of chromosome number increase (polyploidy and centric fissions) and decrease (chromosome fusions). Although all chromosome fusions result from DNA recombination between two or more nonhomologous chromosomes, several mechanisms of descending dysploidy are exploited by eukaryotes to reduce their chromosome number. Genome sequencing and comparative genomics have accelerated the identification of inter-genome chromosome collinearity and gross chromosomal rearrangements and have shown that end-to-end chromosome fusions (EEFs) and nested chromosome fusions (NCFs) may have played a more important role in the evolution of eukaryotic karyotypes than previously thought. The present review aims to summarize the limited knowledge on the origin, frequency, and evolutionary implications of EEF and NCF events in eukaryotes and especially in land plants. The interactions between nonhomologous chromosomes in interphase nuclei and chromosome (mis)pairing during meiosis are examined for their potential importance in the origin of EEFs and NCFs. The remaining open questions that need to be addressed are discussed.

• MeSH
• Genomics MeSH
• Karyotype MeSH
• Meiosis MeSH
• Evolution, Molecular * MeSH
• Polyploidy * MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH

Pervasive hybridization and whole-genome duplications (WGDs) influenced genome evolution in several eukaryotic lineages. Although frequent and recurrent hybridizations may result in reticulate phylogenies, the evolutionary events underlying these reticulations, including detailed structure of the ancestral diploid and polyploid genomes, were only rarely reconstructed. Here, we elucidate the complex genomic history of a monophyletic clade from the mustard family (Brassicaceae), showing contentious relationships to the early-diverging clades of this model plant family. Genome evolution in the crucifer tribe Biscutelleae (∼60 species, 5 genera) was dominated by pervasive hybridizations and subsequent genome duplications. Diversification of an ancestral diploid genome into several divergent but crossable genomes was followed by hybridizations between these genomes. Whereas a single genus (Megadenia) remained diploid, the four remaining genera originated by allopolyploidy (Biscutella, Lunaria, Ricotia) or autopolyploidy (Heldreichia). The contentious relationships among the Biscutelleae genera, and between the tribe and other early diverged crucifer lineages, are best explained by close genomic relatedness among the recurrently hybridizing ancestral genomes. By using complementary cytogenomics and phylogenomics approaches, we demonstrate that the origin of a monophyletic plant clade can be more complex than a parsimonious assumption of a single WGD spurring postpolyploid cladogenesis. Instead, recurrent hybridization among the same and/or closely related parental genomes may phylogenetically interlink diploid and polyploid genomes despite the incidence of multiple independent WGDs. Our results provide new insights into evolution of early-diverging Brassicaceae lineages and elucidate challenges in resolving the contentious relationships within and between land plant lineages with pervasive hybridization and WGDs.

• Keywords
• chromosome rearrangements, diploidization, dysploidy, hybridization, phylogenetics, polyploidy, reticulate evolution, whole-genome duplication,
• MeSH
• Biological Evolution * MeSH
• Brassicaceae genetics   MeSH
• Chromosomes, Plant * MeSH
• Gene Duplication MeSH
• Genome, Plant * MeSH
• Hybridization, Genetic MeSH
• Polyploidy * MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

The Arctic is one of the most extreme terrestrial environments on the planet. Here, we present the first chromosome-scale genome assembly of a plant adapted to the high Arctic, Draba nivalis (Brassicaceae), an attractive model species for studying plant adaptation to the stresses imposed by this harsh environment. We used an iterative scaffolding strategy with data from short-reads, single-molecule long reads, proximity ligation data, and a genetic map to produce a 302 Mb assembly that is highly contiguous with 91.6% assembled into eight chromosomes (the base chromosome number). To identify candidate genes and gene families that may have facilitated adaptation to Arctic environmental stresses, we performed comparative genomic analyses with nine non-Arctic Brassicaceae species. We show that the D. nivalis genome contains expanded suites of genes associated with drought and cold stress (e.g., related to the maintenance of oxidation-reduction homeostasis, meiosis, and signaling pathways). The expansions of gene families associated with these functions appear to be driven in part by the activity of transposable elements. Tests of positive selection identify suites of candidate genes associated with meiosis and photoperiodism, as well as cold, drought, and oxidative stress responses. Our results reveal a multifaceted landscape of stress adaptation in the D. nivalis genome, offering avenues for the continued development of this species as an Arctic model plant.

• Keywords
• Arctic, Brassicaceae, adaptation, chromosome-scale assembly, linkage map,
• MeSH
• Brassicaceae * genetics   MeSH
• Adaptation, Physiological * MeSH
• Genome, Plant * MeSH
• Genomics MeSH
• Publication type
• Journal Article MeSH
• Geographicals
• Arctic Regions MeSH

The tribe Aethionemeae is sister to all other crucifers, making it a crucial group for unraveling genome evolution and phylogenetic relationships within the crown group Brassicaceae. In this study, we extend the analysis of Brassicaceae genomic blocks (GBs) to Aethionema whereby we identified unique block boundaries shared only with the tribe Arabideae. This was achieved using bioinformatic methods to analyze synteny between the recently updated genome sequence of Aethionema arabicum and other high-quality Brassicaceae genome sequences. We show that compared to the largely conserved genomic structure of most non-polyploid Brassicaceae lineages, GBs are highly rearranged in Aethionema. Furthermore, we detected similarities between the genomes of Aethionema and Arabis alpina, in which also a high number of genomic rearrangements compared to those of other Brassicaceae was found. These similarities suggest that tribe Arabideae, a clade showing conflicting phylogenetic position between studies, may have diverged before diversification of the other major lineages, and highlight the potential of synteny information for phylogenetic inference.

• Keywords
• Aethionema, Arabideae, Brassicaceae, comparative genomics, genomic blocks, synteny,
• Publication type
• Journal Article MeSH