Catastrophic chromosomal restructuring during genome elimination in plants.

Genome instability is associated with mitotic errors and cancer. This phenomenon can lead to deleterious rearrangements, but also genetic novelty, and many questions regarding its genesis, fate and evolutionary role remain unanswered. Here, we describe extreme chromosomal restructuring during genome elimination, a process resulting from hybridization of Arabidopsis plants expressing different centromere histones H3. Shattered chromosomes are formed from the genome of the haploid inducer, consistent with genomic catastrophes affecting a single, laggard chromosome compartmentalized within a micronucleus. Analysis of breakpoint junctions implicates breaks followed by repair through non-homologous end joining (NHEJ) or stalled fork repair. Furthermore, mutation of required NHEJ factor DNA Ligase 4 results in enhanced haploid recovery. Lastly, heritability and stability of a rearranged chromosome suggest a potential for enduring genomic novelty. These findings provide a tractable, natural system towards investigating the causes and mechanisms of complex genomic rearrangements similar to those associated with several human disorders

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

Biased retention of environment-responsive genes following genome fractionation.

The molecular underpinnings and consequences of cycles of whole-genome duplication (WGD) and subsequent gene loss through subgenome fractionation remain largely elusive. Endogenous drivers, such as transposable elements, have been postulated to shape genome-wide dominance and biased fractionation leading to a conserved least-fractionated (LF) and a degenerated most-fractionated (MF) subgenome. In contrast, the role of exogenous factors, such as those induced by environmental stresses, has been overlooked. A chromosome-scale assembly of the alpine Buckler Mustard (Biscutella laevigata; Brassicaceae) that underwent a WGD event about 11 million years ago is here coupled with transcriptional responses to heat, cold, drought and herbivory to assess how gene expression is associated with differential gene retention across the MF and LF subgenomes. Counteracting the impact of transposable elements in reducing the expression and retention of nearby genes across the MF subgenome, dosage balance is highlighted as a main endogenous promoter of the retention of duplicated gene products under purifying selection. Consistent with the "turn a hobby into a job" model, about one third of environment-responsive duplicates exhibit novel expression patterns, with one copy typically remaining conditionally-expressed, whereas the other copy has evolved constitutive expression, highlighting exogenous factors as a major driver of gene retention. Showing uneven patterns of fractionation, with regions remaining unbiased while others show high bias and significant enrichment in environment-responsive genes, this mesopolyploid genome presents evolutionary signatures consistent with an interplay of endogenous and exogenous factors having driven gene content following WGD-fractionation cycles

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

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

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

Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size.

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.Plants exhibit an extraordinary range of genome sizes, varying by > 2000-fold between the smallest and largest recorded values. In the absence of polyploidy, changes in the amount of repetitive DNA (transposable elements and tandem repeats) are primarily responsible for genome size differences between species. However, there is ongoing debate regarding the relative importance of amplification of repetitive DNA versus its deletion in governing genome size. Using data from 454 sequencing, we analysed the most repetitive fraction of some of the largest known genomes for diploid plant species, from members of Fritillaria. We revealed that genomic expansion has not resulted from the recent massive amplification of just a handful of repeat families, as shown in species with smaller genomes. Instead, the bulk of these immense genomes is composed of highly heterogeneous, relatively low-abundance repeat-derived DNA, supporting a scenario where amplified repeats continually accumulate due to infrequent DNA removal. Our results indicate that a lack of deletion and low turnover of repetitive DNA are major contributors to the evolution of extremely large genomes and show that their size cannot simply be accounted for by the activity of a small number of high-abundance repeat families.Thiswork was supported by the Natural Environment ResearchCouncil (grant no. NE/G017 24/1), the Czech Science Fou nda-tion (grant no. P501/12/G090), the AVCR (grant no.RVO:60077344) and a Beatriu de Pinos postdoctoral fellowshipto J.P. (grant no. 2011-A-00292; Catalan Government-E.U. 7thF.P.)

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