Hybridization and genome doubling (allopolyploidy) have led to evolutionary novelties as well as to the origin of new clades and species. Despite the importance of allopolyploidization, the dynamics of postpolyploid diploidization (PPD) at the genome level has been only sparsely studied. The Microlepidieae (MICR) is a crucifer tribe of 17 genera and c. 56 species endemic to Australia and New Zealand. Our phylogenetic and cytogenomic analyses revealed that MICR originated via an intertribal hybridization between ancestors of Crucihimalayeae (n = 8; maternal genome) and Smelowskieae (n = 7; paternal genome), both native to the Northern Hemisphere. The reconstructed ancestral allopolyploid genome (n = 15) originated probably in northeastern Asia or western North America during the Late Miocene (c. 10.6-7 million years ago) and reached the Australian mainland via long-distance dispersal. In Australia, the allotetraploid genome diverged into at least three main subclades exhibiting different levels of PPD and diversity: 1.25-fold descending dysploidy (DD) of n = 15 → n = 12 (autopolyploidy → 24) in perennial Arabidella (3 species), 1.5-fold DD of n = 15 → n = 10 in the perennial Pachycladon (11 spp.) and 2.1-3.75-fold DD of n = 15 → n = 7-4 in the largely annual crown-group genera (42 spp. in 15 genera). These results are among the first to demonstrate multispeed genome evolution in taxa descending from a common allopolyploid ancestor. It is suggested that clade-specific PPD can operate at different rates and efficacies and can be tentatively linked to life histories and the extent of taxonomic diversity.

• Klíčová slova
• Brassicaceae, comparative genomics, distant hybridization, long-distance dispersal, phylogeography, whole-genome duplication,
• MeSH
• biologická evoluce * MeSH
• Brassicaceae klasifikace   genetika   MeSH
• DNA rostlinná genetika   MeSH
• fylogeneze MeSH
• genom rostlinný MeSH
• genová přestavba MeSH
• hybridizace genetická * MeSH
• malování chromozomů MeSH
• polyploidie * MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Austrálie MeSH
• Nový Zéland MeSH
• Názvy látek
• DNA rostlinná MeSH

One of the major goals of contemporary evolutionary biology is to elucidate the relative roles of allopatric and ecological differentiation and polyploidy in speciation. In this study, we address the taxonomically intricate Sabulina verna group, which has a disjunct Arctic-alpine postglacial range in Europe and occupies a broad range of ecological niches, including substrates toxic to plants. Using genome-wide ddRAD sequencing combined with morphometric analyses based on extensive sampling of 111 natural populations, we aimed to disentangle internal evolutionary relationships and examine their correspondence with the pronounced edaphic and ploidy diversity within the group. We identified two spatially distinct groups of diploids: a widespread Arctic-alpine group and a spatially restricted yet diverse Balkan group. Most tetraploids exhibited a considerably admixed ancestry derived from both these groups, suggesting their allopolyploid origin. Four genetic clusters in congruence with geography and mostly supported by morphological traits were recognized in the diploid Arctic-alpine group. Tetraploids are split into two distinct and geographically vicariant groups, indicating their repeated polytopic origin. Furthermore, our results also revealed at least five-fold parallel colonization of toxic substrates (serpentine and metalliferous), altogether demonstrating a complex interaction between geography, challenging substrates and polyploidy in the evolution of the group. Finally, we propose a new taxonomic treatment of this complex.

• Klíčová slova
• Caryophyllaceae, Minuartia, Phylogeny, Polyploidy, Toxic substrates,
• MeSH
• Caryophyllaceae * genetika   MeSH
• fylogeneze MeSH
• polyploidie MeSH
• tetraploidie * MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Evropa MeSH

Repetitive elements have been identified in several amphibian genomes using whole genome sequencing, but few studies have used cytogenetic mapping to visualize these elements in this vertebrate group. Here, we used fluorescence in situ hybridization and genomic data to map the U1 and U2 small nuclear RNAs and histone H3 in six species of African clawed frog (genus Xenopus), including, from subgenus Silurana, the diploid Xenopus tropicalis and its close allotetraploid relative X. calcaratus and, from subgenus Xenopus, the allotetraploid species X. pygmaeus, X. allofraseri, X. laevis, and X. muelleri. Results allowed us to qualitatively evaluate the relative roles of polyploidization and divergence in the evolution of repetitive elements because our focal species include allotetraploid species derived from two independent polyploidization events - one that is relatively young that gave rise to X. calcaratus and another that is older that gave rise to the other (older) allotetraploids. Our results demonstrated conserved loci number and position of signals in the species from subgenus Silurana; allotetraploid X. calcaratus has twice as many signals as diploid X. tropicalis. However, the content of repeats varied among the other allotetraploid species. We detected almost same number of signals in X. muelleri as in X. calcaratus and same number of signals in X. pygmaeus, X. allofraseri, X. laevis as in the diploid X. tropicalis. Overall, these results are consistent with the proposal that allopolyploidization duplicated these tandem repeats and that variation in their copy number was accumulated over time through reduction and expansion in a subset of the older allopolyploids.

• Klíčová slova
• Allopolyploidization, Amphibians, Anura, Histone H3, In situ hybridization, snRNA,
• Publikační typ
• časopisecké články MeSH

Allopolyploid genomes are divided into compartments called subgenomes that are derived from lower ploidy ancestors. In African clawed frogs of the subgenus Xenopus (genus Xenopus), allotetraploid species have two subgenomes (L and S) with morphologically distinct homoeologous chromosomes. In allotetraploid species of the sister subgenus Silurana, independently evolved subgenomes also exist, but their cytogenetics has not been investigated in detail. We used a diverse suite of cytogenetic and molecular FISH techniques on an allotetraploid species in Silurana-Xenopus calcaratus-to explore evolutionary dynamics of chromosome morphology and rearrangements. We find that the subgenomes of X. calcaratus have distinctive characteristics, with a more conserved a-subgenome resembling the closely related genome of the diploid species X. tropicalis, and a more rapidly evolving b-subgenome having more pronounced changes in chromosome structure, including diverged heterochromatic blocks, repetitive sequences, and deletion of a nucleolar secondary constriction. Based on these cytogenetic differences, we propose a chromosome nomenclature for X. calcaratus that may apply to other allotetraploids in subgenus Silurana, depending on as yet unresolved details of their evolutionary origins. These findings highlight the potential for large-scale asymmetry in subgenome evolution following allopolyploidization.

• Klíčová slova
• Allopolyploidization, Chromosome, Chromosome length, Cytogenetics, FISH, Genome,
• MeSH
• chromozomy * genetika   MeSH
• diploidie * MeSH
• genom rostlinný MeSH
• genom genetika   MeSH
• molekulární evoluce MeSH
• Xenopus laevis MeSH
• Xenopus genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Pachycladon (Brassicaceae, tribe Camelineae) is a monophyletic genus of ten morphologically and ecogeographically differentiated, and presumably allopolyploid species occurring in the South Island of New Zealand and in Tasmania. All Pachycladon species possess ten chromosome pairs (2n = 20). The feasibility of comparative chromosome painting (CCP) in crucifer species allows the origin and genome evolution in this genus to be elucidated. We focus on the origin and genome evolution of Pachycladon as well as on its genomic relationship to other crucifer species, particularly to the allopolyploid Australian Camelineae taxa. As species radiation on islands is usually characterized by chromosomal stasis, i.e. uniformity of chromosome numbers/ploidy levels, the role of major karyotypic reshuffling during the island adaptive and species radiation in Pachycladon is investigated through whole-genome CCP analysis. RESULTS: The four analyzed Pachycladon species possess an identical karyotype structure. The consensual ancestral karyotype is most likely common to all Pachycladon species and corroborates the monophyletic origin of the genus evidenced by previous phylogenetic analyses. The ancestral Pachycladon karyotype (n = 10) originated through an allopolyploidization event between two genomes structurally resembling the Ancestral Crucifer Karyotype (ACK, n = 8). The primary allopolyploid (apparently with n = 16) has undergone genome reshuffling by descending dysploidy toward n = 10. Chromosome "fusions" were mediated by inversions, translocations and centromere inactivation/loss. Pachycladon chromosome 3 (PC3) resulted from insertional fusion, described in grasses. The allopolyploid ancestor originated in Australia, from the same or closely related ACK-like parental species as the Australian Camelineae allopolyploids. However, the two whole-genome duplication (WGD) events were independent, with the Pachycladon WGD being significantly younger. The long-distance dispersal of the diploidized Pachycladon ancestor to New Zealand was followed by the Pleistocene species radiation in alpine habitats and characterized by karyotypic stasis. CONCLUSIONS: Karyotypic stasis in Pachycladon suggests that the insular species radiation in this genus proceeded through homoploid divergence rather than through species-specific gross chromosomal repatterning. The ancestral Pachycladon genome originated in Australia through an allopolyploidization event involving two closely related parental genomes, and spread to New Zealand by a long-distance dispersal. We argue that the chromosome number decrease mediated by inter-genomic reshuffling (diploidization) could provide the Pachycladon allopolyploid founder with an adaptive advantage to colonize montane/alpine habitats. The ancestral Pachycladon karyotype remained stable during the Pleistocene adaptive radiation into ten different species.

• MeSH
• biologická evoluce * MeSH
• Brassicaceae klasifikace   genetika   MeSH
• DNA rostlinná genetika   MeSH
• fylogeneze MeSH
• genom rostlinný * MeSH
• karyotypizace MeSH
• malování chromozomů MeSH
• vznik druhů (genetika) * MeSH
• zeměpis MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Nový Zéland MeSH
• Tasmánie MeSH
• Názvy látek
• DNA rostlinná MeSH

Sex chromosomes of some closely related species are not homologous, and sex chromosome turnover is often attributed to mechanisms that involve linkage to or recombination arrest around sex-determining loci. We examined sex chromosome turnover and recombination landscapes in African clawed frogs (genus Xenopus) with reduced representation genome sequences from 929 individuals from 19 species. We recovered extensive variation in sex chromosomes, including at least eight nonhomologous sex-associated regions-five newly reported here, with most maintaining female heterogamety, but two independent origins of Y chromosomes. Seven of these regions are found in allopolyploid species in the subgenus Xenopus, and all of these reside in one of their two subgenomes, which highlights functional asymmetry between subgenomes. In three species with chromosome-scale genome assemblies (Xenopus borealis, Xenopus laevis, and Xenopus tropicalis), sex-specific recombination landscapes have similar patterns of sex differences in rates and locations of recombination. Across these Xenopus species, sex-associated regions are significantly nearer chromosome ends than expected by chance, even though this is where the ancestral recombination rate is highest in both sexes before the regions became sex associated. As well, expansions of sex-associated recombination arrest occurred multiple times. New information on sex linkage along with among-species variation in female specificity of the sex-determining gene dm-w argues against a "jumping gene" model, where dm-w moves around the genome. The diversity of sex chromosomes in Xenopus raises questions about the roles of natural and sexual selection, polyploidy, the recombination landscape, and neutral processes in driving sex chromosome turnover in animal groups with mostly heterogametic females.

• Klíčová slova
• allopolyploidization, genetic linkage, recombination landscape, sex chromosome turnover, sex determination,
• MeSH
• pohlavní chromozomy * genetika   MeSH
• procesy určující pohlaví MeSH
• rekombinace genetická MeSH
• Xenopus * genetika   MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Allopolyploidization entailing the merger of two distinct genomes in a single hybrid organism, is an important process in plant evolution and a valuable tool in breeding programs. Newly established hybrids often experience massive genomic perturbations, including karyotype reshuffling and gene expression modifications. These phenomena may be asymmetric with respect to the two progenitors, with one of the parental genomes being "dominant." Such "genome dominance" can manifest in several ways, including biased homoeolog gene expression and expression level dominance. Here we employed a k-mer-based approach to study gene expression in reciprocal Festuca pratensis Huds. × Lolium multiflorum Lam. allopolyploid grasses. Our study revealed significantly more genes where expression mimicked that of the Lolium parent compared with the Festuca parent. This genome dominance was heritable to successive generation and its direction was only slightly modified by environmental conditions and plant age. Our results suggest that Lolium genome dominance was at least partially caused by its more efficient trans-acting gene expression regulatory factors. Unraveling the mechanisms responsible for propagation of parent-specific traits in hybrid crops contributes to our understanding of allopolyploid genome evolution and opens a way to targeted breeding strategies.

• Klíčová slova
• Gene expression, allopolyploidy, cis/trans regulation, genome dominance, homoeolog, interspecific hybrids,
• MeSH
• databáze genetické MeSH
• Festuca genetika   růst a vývoj   MeSH
• genom rostlinný * MeSH
• jílek genetika   růst a vývoj   MeSH
• polyploidie * MeSH
• regulace genové exprese u rostlin * MeSH
• regulační oblasti nukleových kyselin MeSH
• sekvenční analýza RNA MeSH
• stanovení celkové genové exprese MeSH
• zemědělské plodiny MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Reticulate evolution is characterized by occasional hybridization between two species, creating a network of closely related taxa below and at the species level. In the present research, we aimed to verify the hypothesis of the allopolyploid origin of hexaploid C. album s. str., identify its putative parents and estimate the frequency of allopolyploidization events. We sampled 122 individuals of the C. album aggregate, covering most of its distribution range in Eurasia. Our samples included putative progenitors of C. album s. str. of both ploidy levels, i.e. diploids (C. ficifolium, C. suecicum) and tetraploids (C. striatiforme, C. strictum). To fulfil these objectives, we analysed sequence variation in the nrDNA ITS region and the rpl32-trnL intergenic spacer of cpDNA and performed genomic in-situ hybridization (GISH). Our study confirms the allohexaploid origin of C. album s. str. Analysis of cpDNA revealed tetraploids as the maternal species. In most accessions of hexaploid C. album s. str., ITS sequences were completely or nearly completely homogenized towards the tetraploid maternal ribotype; a tetraploid species therefore served as one genome donor. GISH revealed a strong hybridization signal on the same eighteen chromosomes of C. album s. str. with both diploid species C. ficifolium and C. suecicum. The second genome donor was therefore a diploid species. Moreover, some individuals with completely unhomogenized ITS sequences were found. Thus, hexaploid individuals of C. album s. str. with ITS sequences homogenized to different degrees may represent hybrids of different ages. This proves the existence of at least two different allopolyploid lineages, indicating a polyphyletic origin of C. album s. str.

• MeSH
• Chenopodium album genetika   MeSH
• cytogenetické vyšetření metody   MeSH
• DNA rostlinná genetika   MeSH
• fylogeneze MeSH
• genetická variace genetika   MeSH
• genomika MeSH
• molekulární evoluce * MeSH
• polyploidie * MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• DNA rostlinná MeSH

Plants rely on tight coordination between nuclear, mitochondrial, and chloroplast genomes to form essential multi-enzyme cytonuclear complexes. Whole-genome duplication (WGD) doubles the nuclear genome, potentially disrupting cytonuclear stoichiometry unless organellar genomes respond accordingly. Targeted analyses of chloroplasts and mitochondria enabled us to dissect the extent and mechanisms of adjustments in both organelles immediately after WGD and across generations in Arabidopsis auto- and allopolyploids. We observed a substantial overcompensation of organellar genome copies in both organelles in early-generation autotetraploids primarily through multiplication of DNA copies within organelles rather than increasing the number of organelles. Despite higher DNA content, mitochondria maintained their volume, and chloroplasts were even smaller. In successive generations, chloroplast DNA copy numbers continued to rise, whereas mitochondrial DNA copies declined. Gene expression patterns also differed between chloroplasts and mitochondria and between auto- and allopolyploids. In autopolyploids, immediate transcriptional changes were minimal, but by the fourth generation after WGD, nuclear genes involved in mitochondria-nuclear complexes were downregulated. In allopolyploids, transcriptional changes appeared immediately in the first generation (chloroplast genes were upregulated and mitochondrial genes were downregulated). Our findings demonstrate that cytonuclear balance is restored through dynamic, organelle-specific, and polyploid-type-specific mechanisms. These insights advance our understanding of the evolution of polyploid genomes.

• Klíčová slova
• chloroplasts, cytonuclear interactions, gene expression, interspecific hybridization, mitochondria, organellar DNA, stoichiometry, whole genome duplication,
• MeSH
• Arabidopsis * genetika   MeSH
• buněčné jádro * genetika   MeSH
• chloroplasty genetika   MeSH
• DNA chloroplastová genetika   MeSH
• genom chloroplastový genetika   MeSH
• genom rostlinný genetika   MeSH
• mitochondriální DNA genetika   MeSH
• mitochondrie genetika   metabolismus   MeSH
• polyploidie * MeSH
• regulace genové exprese u rostlin MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• DNA chloroplastová MeSH
• mitochondriální DNA MeSH

Whole-genome duplication coupled with hybridization is of prime importance in plant evolution. Here we reinvestigate Müntzing's classical example of allopolyploid speciation; the first report of experimental synthesis of a naturally occurring allopolyploid species, Galeopsis tetrahit. Various molecular markers (cpDNA, NRPA2, amplified fragment length polymorphisms (AFLPs)) and flow cytometry were surveyed in population samples of subgenus Galeopsis, including two allopolyploid species and their potential diploid parents. The presence of two divergent copies of single-copy NRPA2 confirms the allopolyploid origins of G. tetrahit and Galeopsis bifida. However, the two allopolyploids do not share the same maternal genome, as originally suggested by Müntzing. The results support independent origins, but not recurrent formation, of the two allotetraploids. Data further indicate frequent gene flow and introgression within ploidy levels, but less so between ploidy levels. Our results confirm and elaborate on Müntzing's classical conclusion about allopolyploid origins of G. tetrahit and G. bifida. We address questions of general interest within polyploidy research, such as recurrent formation, gene flow and introgression within and between ploidy levels.

• MeSH
• analýza polymorfismu délky amplifikovaných restrikčních fragmentů MeSH
• Bayesova věta MeSH
• buněčné jádro genetika   MeSH
• chloroplasty genetika   MeSH
• DNA chloroplastová genetika   MeSH
• DNA rostlinná genetika   MeSH
• fylogeneze MeSH
• genetické markery MeSH
• hluchavkovité genetika   MeSH
• polyploidie * MeSH
• průtoková cytometrie MeSH
• rostlinné geny * MeSH
• sekvenční analýza DNA metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA chloroplastová MeSH
• DNA rostlinná MeSH
• genetické markery MeSH