Cytotaxonomy and ecology of Aster amellus agg. in the Czech Republic

Katedra botanikyDepartment of BotanyPřírodovědecká fakultaFaculty of Scienc

Multiple hybridization events in Cardamine (Brassicaceae) during the last 150 years: revisiting a textbook example of neoallopolyploidy

Background and Aims Recently formed allopolyploid species represent excellent subjects for exploring early stages of polyploid evolution. The hexaploid Cardamine schulzii was regarded as one of the few nascent allopolyploid species formed within the past ∼150 years that presumably arose by autopolyploidization of a triploid hybrid, C. × insueta; however, the most recent investigations have shown that it is a trigenomic hybrid. The aims of this study were to explore the efficiency of progenitor-specific microsatellite markers in detecting the hybrid origins and genome composition of these two allopolyploids, to estimate the frequency of polyploid formation events, and to outline their evolutionary potential for long-term persistence and speciation. Methods Flow-cytometric ploidy-level screening and genotyping by progenitor-specific microsatellite markers (20 microsatellite loci) were carried out on samples focused on hybridizing populations at Urnerboden, Switzerland, but also including comparative material of the parental species from other sites in the Alps and more distant areas. Key Results It was confirmed that hybridization between the diploids C. amara and C. rivularis auct. gave rise to triploid C. × insueta, and it is inferred that this has occurred repeatedly. Evidence is provided that C. schulzii comprises three parental genomes and supports its origin from hybridization events between C. × insueta and the locally co-occurring hypotetraploid C. pratensis, leading to two cytotypes of C. schulzii: hypopentaploid and hypohexaploid. Each cytotype of C. schulzii is genetically uniform, suggesting their single origins. Conclusions Persistence of C. schulzii has presumably been achieved only by perennial growth and clonal reproduction. This contrasts with C. × insueta, in which multiple origins and occasional sexual reproduction have generated sufficient genetic variation for long-term survival and evolutionary success. This study illustrates a complex case of recurrent hybridization and polyploidization events, and highlights the role of triploids that promoted the origin of trigenomic hybrid

Camelina neglecta (Brassicaceae, Camelineae), a new diploid species from Europe

Camelina neglecta is described as a new diploid species and its relationship to the other diploids of the genus and to the somewhat superficially similar tetraploid C. rumelica and hexaploid C. microcarpa, are discussed. SEM of seed and stem trichomes of the new species are presented

Chromosomal Evolution and Apomixis in the Cruciferous Tribe Boechereae

The mustard family (Brassicaceae) comprises several dozen monophyletic clades usually ranked as tribes. The tribe Boechereae plays a prominent role in plant research due to the incidence of apomixis and its close relationship to Arabidopsis. This tribe, largely confined to western North America, harbors nine genera and c. 130 species, with \u3e90% of species belonging to the genus Boechera. Hundreds of apomictic diploid and triploid Boechera hybrids have spurred interest in this genus, but the remaining Boechereae genomes remain virtually unstudied. Here we report on comparative genome structure of six genera (Borodinia, Cusickiella, Phoenicaulis, Polyctenium, Nevada, and Sandbergia) and three Boechera species as revealed by comparative chromosome painting (CCP). All analyzed taxa shared the same seven-chromosome genome structure. Comparisons with the sister Halimolobeae tribe (n = 8) showed that the ancestral Boechereae genome (n = 7) was derived from an older n = 8 genome by descending dysploidy followed by the divergence of extant Boechereae taxa. As tribal divergence post-dated the origin of four tribe-specific chromosomes, it is proposed that these chromosomal rearrangements were a key evolutionary innovation underlaying the origin and diversification of the Boechereae in North America. Although most Boechereae genera exhibit genomic conservatism, intra-tribal cladogenesis has occasionally been accompanied by chromosomal rearrangements (particularly inversions). Recently, apomixis was reported in the Boechereae genera Borodinia and Phoenicaulis. Here, we report sexual reproduction in diploid Nevada, diploid Sandbergia, and tetraploid Cusickiella and aposporous apomixis in tetraploids of Polyctenium and Sandbergia. In sum, apomixis is now known to occur in five of the nine Boechereae genera

Gradual evolution of allopolyploidy in Arabidopsis suecica.

Most diploid organisms have polyploid ancestors. The evolutionary process of polyploidization is poorly understood but has frequently been conjectured to involve some form of 'genome shock', such as genome reorganization and subgenome expression dominance. Here we study polyploidization in Arabidopsis suecica, a post-glacial allopolyploid species formed via hybridization of Arabidopsis thaliana and Arabidopsis arenosa. We generated a chromosome-level genome assembly of A. suecica and complemented it with polymorphism and transcriptome data from all species. Despite a divergence around 6 million years ago (Ma) between the ancestral species and differences in their genome composition, we see no evidence of a genome shock: the A. suecica genome is colinear with the ancestral genomes; there is no subgenome dominance in expression; and transposon dynamics appear stable. However, we find changes suggesting gradual adaptation to polyploidy. In particular, the A. thaliana subgenome shows upregulation of meiosis-related genes, possibly to prevent aneuploidy and undesirable homeologous exchanges that are observed in synthetic A. suecica, and the A. arenosa subgenome shows upregulation of cyto-nuclear processes, possibly in response to the new cytoplasmic environment of A. suecica, with plastids maternally inherited from A. thaliana. These changes are not seen in synthetic hybrids, and thus are likely to represent subsequent evolution

Stofn gæsamatar (Arabidopsis thaliana) frá Íslandi greindur með aðferðum frumuerfðafræði og raðgreiningu erfðamengis

In this paper, we report the first discovery of Arabidopsis thaliana in Iceland. In May 2015, the plants were located growing on warm geothermal soil around the hot spring Deildartunguhver in Reykholt, West Iceland. Flower buds and leaves were collected and used for subsequent cytogenetic analyses and DNA sequencing. Whole plant specimens were deposited at the Icelandic AMNH herbarium and were assigned accession number VA21379. The accession was found to be diploid with 2n=2x=10, as expected for this species. At meiosis I (diakinesis) it formed five normal bivalents. Ribosomal FISH mapping revealed two pairs of 5S rDNA loci and two pairs of NORs. Fine-scale chromosome painting using BAC clones specific for chromosomes At1 and At4 confirmed the standard structure of these chromosomes. Furthermore, the painting revealed an absence of the 1.17-Mb paracentric inversion on the At4 short arm in the Icelandic accession, in contrast to the inversionbearing A. thaliana accessions more prevalent in North America. The sequencing of multiplexed whole-genome libraries identified the Swedish accession Ham-1 as the closest relative of the Icelandic accession, with, however, a markedly low SNPmatch score. We conclude that although the Icelandic accession appears to be more genetically related to populations from Scandinavia than to other European accessions, it did not originate from any of the populations represented in the global collection of the 1001 Genomes accessions of A. thaliana.Hér verður greint frá fyrsta fundi gæsamatar (Arabidopsis thaliana) á Íslandi. Tegundin fannst í maí 2015 á jarðhitasvæði við Deildartunguhver. Blómknöppum og laufblöðum var safnað fyrir litningagreiningu og raðgreiningu erfðamengis. Einnig var eintökum safnað til þurrkunar og þeim síðan komið fyrir í plöntusafni AMNH þar sem þau fengu númerið VA21379. Eins og fyrri rannsóknir gæsamatar hafa leitt í ljós reyndust sýnin vera tvílitna (2n=2x=10) og við greiningu á rýriskiptingu komu í ljós fimm eðlileg tvígilda litningapör. Þáttatenging flúrljómandi rDNA (FISH) þreifara á litningum í mítósu leiddi í ljós tvö 5S ríbósóm genapör og tvö pör NOR svæða sem jafnframt eru dæmigerð fyrir arfgerð tegundarinnar. Nánari greining með notkun BACFISH þreifara á litningunum At1 og At4 sýndi að uppbygging litninganna úr sýnunum frá Deildartungu væri eðlileg. Greiningin leiddi jafnframt í ljós vöntun á 1.17-Mb þráðhefta umhverfu á At4 litningi en þessi umhverfa er algeng meðal stofna gæsamatar í Norður-Ameríku. Raðgreining erfðamengis íslensku sýnanna leiddi í ljós mestan skyldleika við sýni frá Svíþjóð en þó með lágum skyldleikastuðli. Því er niðurstaða þessarar greiningar sú að þótt plöntur sem fundust á Íslandi séu skyldari stofnum frá Skandinavíu en stofnum annars staðar frá, hafa þær upphaflega ekki borist frá neinum af stofnum í þekktu safni 1001 erfðamengja gæsamatar víðsvegar að úr heiminum.This work was supported by EEA collaborative grant number EHP-CZ07-MOP-1-1052014.Peer Reviewe

Novelty and Convergence in Adaptation to Whole Genome Duplication

Whole genome duplication (WGD) can promote adaptation but is disruptive to conserved processes, especially meiosis. Studies in Arabidopsis arenosa revealed a coordinated evolutionary response to WGD involving interacting proteins controlling meiotic crossovers, which are minimized in an autotetraploid (within-species polyploid) to avoid missegregation. Here, we test whether this surprising flexibility of a conserved essential process, meiosis, is recapitulated in an independent WGD system, Cardamine amara, 17 My diverged from A. arenosa. We assess meiotic stability and perform population-based scans for positive selection, contrasting the genomic response to WGD in C. amara with that of A. arenosa. We found in C. amara the strongest selection signals at genes with predicted functions thought important to adaptation to WGD: meiosis, chromosome remodeling, cell cycle, and ion transport. However, genomic responses to WGD in the two species differ: minimal ortholog-level convergence emerged, with none of the meiosis genes found in A. arenosa exhibiting strong signal in C. amara. This is consistent with our observations of lower meiotic stability and occasional clonal spreading in diploid C. amara, suggesting that nascent C. amara autotetraploid lineages were preadapted by their diploid lifestyle to survive while enduring reduced meiotic fidelity. However, in contrast to a lack of ortholog convergence, we see process-level and network convergence in DNA management, chromosome organization, stress signaling, and ion homeostasis processes. This gives the first insight into the salient adaptations required to meet the challenges of a WGD state and shows that autopolyploids can utilize multiple evolutionary trajectories to adapt to WGD

The genetic and epigenetic landscape of the Arabidopsis centromeres.

Centromeres attach chromosomes to spindle microtubules during cell division and, despite this conserved role, show paradoxically rapid evolution and are typified by complex repeats. We used longread sequencing to generate the Col-CEN Arabidopsis thaliana genome assembly that resolves all five centromeres. The centromeres consist of megabase-scale tandemly repeated satellite arrays, which support CENH3 occupancy and are densely DNA methylated, with satellite variants private to each chromosome. CENH3 preferentially occupies satellites that show least divergence and occur in higherorder repeats. The centromeres are invaded by ATHILA retrotransposons, which disrupt genetic and epigenetic organization. Centromeric crossover recombination is suppressed, yet low levels of meiotic DSBs occur that are regulated by DNA methylation. We propose that Arabidopsis centromeres are evolving via cycles of satellite homogenization and retrotransposon-driven diversification.BBSRC grants BB/S006842/1, BB/S020012/1 and BB/V003984/1

Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation

This document is the Accepted Manuscript version, made available in accordance to Springer Nature Terms of reuse of archived manuscripts.Despite evolutionary conserved mechanisms to silence transposable element activity, there are drastic differences in the abundance of transposable elements even among closely related plant species. We conducted a de novo assembly for the 375 .Mb genome of the perennial model plant, Arabis alpina. Analysing this genome revealed long-lasting and recent transposable element activity predominately driven by Gypsy long terminal repeat retrotransposons, which extended the low-recombining pericentromeres and transformed large formerly euchromatic regions into repeat-rich pericentromeric regions. This reduced capacity for long terminal repeat retrotransposon silencing and removal in A. alpina co-occurs with unexpectedly low levels of DNA methylation. Most remarkably, the striking reduction of symmetrical CG and CHG methylation suggests weakened DNA methylation maintenance in A. alpina compared with Arabidopsis thaliana. Phylogenetic analyses indicate a highly dynamic evolution of some components of methylation maintenance machinery that might be related to the unique methylation in A. alpina.Peer reviewe