Crucifers Dotaz Zobrazit nápovědu
A decade ago the concept of the Ancestral Crucifer Karyotype (ACK) and the definition of 24 conserved genomic blocks was presented. Subsequently, 35 cytogenetic reconstructions and/or draft genome sequences of crucifer species (members of the Brassicaceae family) have been analyzed in the context of this system; placing crucifers at the forefront of plant phylogenomics. In this review, we highlight how the ACK and genomic blocks have facilitated and guided genomic analysis of crucifers in the last 10 years and provide an update of this robust model.
Cleomaceae is a diverse group well-suited to addressing fundamental genomic and evolutionary questions as the sister group to Brassicaceae, facilitating transfer of knowledge from the model Arabidopsis thaliana. Phylogenetic and taxonomic revisions provide a framework for examining the evolution of substantive morphological and physiology diversity in Cleomaceae, but not necessarily in Brassicaceae. The investigation of both nested and contrasting whole-genome duplications (WGDs) between Cleomaceae and Brassicaceae allows comparisons of independently duplicated genes and investigation of whether they may be drivers of the observed innovations. Further, a wealth of outstanding genetic research has provided insight into how the important alternative carbon fixation pathway, C4 photosynthesis, has evolved via differential expression of a suite of genes, of which the underlying mechanisms are being elucidated.
- Klíčová slova
- Brassicaceae, C(4) photosynthesis, Cleomaceae, floral evolution, whole-genome duplications,
- MeSH
- Brassicaceae klasifikace genetika MeSH
- fylogeneze MeSH
- genom rostlinný genetika MeSH
- genomika * MeSH
- Magnoliopsida klasifikace genetika MeSH
- molekulární evoluce MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
In crucifer cytogenomics, BAC contigs of Arabidopsis thaliana have been used as probes for comparative chromosome painting among species. Here we successfully tested chromosome-specific BAC contigs of A. thaliana (n = 5) and A. halleri (n = 8) as probes for reciprocal BAC painting. Furthermore, BAC contigs of both Arabidopsis species were applied as multi-species painting probes to a third crucifer species, Noccaea caerulescens (n = 7), revealing their shared chromosome homeology. Specifically, we found homeology across portions of chromosomes At2, Ah4, and Nc4, which reflects their shared common origin with chromosome AK4 of the Ancestral Crucifer Karyotype (n = 8). We argue that multi-species and multi-directional painting will significantly expedite comparative cytogenomics in Brassicaceae and other plant families.
- MeSH
- Arabidopsis klasifikace genetika MeSH
- Brassicaceae klasifikace genetika MeSH
- chromozomy rostlin genetika MeSH
- druhová specificita MeSH
- hybridizace in situ fluorescenční MeSH
- karyotypizace MeSH
- malování chromozomů metody MeSH
- umělé bakteriální chromozomy genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
PREMISE: The monotypic Idahoa (I. scapigera) and the bispecific Subularia (S. aquatica and S. monticola) belong to Brassicaceae with unclear phylogenetic relationships and no tribal assignment. To fill this knowledge gap, we investigated these species and their closest relatives by combining cytogenomic and phylogenomic methods. METHODS: We used whole plastome sequences in maximum likelihood and Bayesian inference analyses. We tested the phylogenetic informativeness of shared genomic repeats. We combined nuclear gene tree reconciliation and comparative chromosome painting (CCP) to examine the occurrence of past whole-genome duplications (WGDs). RESULTS: The plastid data set corroborated the sister relationship between Idahoa and Subularia within the crucifer Lineage V but failed to resolve consistent topologies using both inference methods. The shared repetitive sequences provided conflicting pwhylogenetic signals. CCP analysis unexpectedly revealed that Idahoa (2n = 16) has a diploidized mesotetraploid genome, whereas two Subularia species (2n = 28 and 30) have diploidized mesoctoploid genomes. Several ancient allopolyploidy events have also been detected in closely related taxa (Chamira circaeoides, Cremolobeae, Eudemeae, and Notothlaspideae). CONCLUSIONS: Our results suggest that the contentious phylogenetic placement of Idahoa and Subularia is best explained by two WGDs involving one or more shared parental genomes. The newly identified mesopolyploid genomes highlight the challenges of studying plant clades with complex polyploidy histories and provide a better framework for understanding genome evolution in the crucifer family.
- Klíčová slova
- Brassicaceae, CES clade, Cruciferae, Hyb-Seq, Lineage V, Subularieae, mesopolyploidy, plastome phylogeny, repeatome, whole-genome duplication,
- MeSH
- Bayesova věta MeSH
- Brassicaceae * genetika MeSH
- fylogeneze MeSH
- genom MeSH
- molekulární evoluce MeSH
- polyploidie * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND AND AIMS: Cardamine occulta (Brassicaceae) is an octoploid weedy species (2n = 8x = 64) originated in Eastern Asia. It has been introduced to other continents including Europe and considered to be an invasive species. Despite its wide distribution, the polyploid origin of C. occulta remained unexplored. The feasibility of comparative chromosome painting (CCP) in crucifers allowed us to elucidate the origin and genome evolution in Cardamine species. We aimed to investigate the genome structure of C. occulta in comparison with its tetraploid (2n = 4x = 32, C. kokaiensis and C. scutata) and octoploid (2n = 8x = 64, C. dentipetala) relatives. METHODS: Genomic in situ hybridization (GISH) and large-scale CCP were applied to uncover the parental genomes and chromosome composition of the investigated Cardamine species. KEY RESULTS: All investigated species descended from a common ancestral Cardamine genome (n = 8), structurally resembling the Ancestral Crucifer Karyotype (n = 8), but differentiated by a translocation between chromosomes AK6 and AK8. Allotetraploid C. scutata originated by hybridization between two diploid species, C. parviflora and C. amara (2n = 2x = 16). By contrast, C. kokaiensis has an autotetraploid origin from a parental genome related to C. parviflora. Interestingly, octoploid C. occulta probably originated through hybridization between the tetraploids C. scutata and C. kokaiensis. The octoploid genome of C. dentipetala probably originated from C. scutata via autopolyploidization. Except for five species-specific centromere repositionings and one pericentric inversion post-dating the polyploidization events, the parental subgenomes remained stable in the tetra- and octoploids. CONCLUSIONS: Comparative genome structure, origin and evolutionary history was reconstructed in C. occulta and related species. For the first time, whole-genome cytogenomic maps were established for octoploid plants. Post-polyploid evolution in Asian Cardamine polyploids has not been associated with descending dysploidy and intergenomic rearrangements. The combination of different parental (sub)genomes adapted to distinct habitats provides an evolutionary advantage to newly formed polyploids by occupying new ecological niches.
- Klíčová slova
- Allopolyploidy, Asian Cardamine, Brassicaceae, GISH (genomic in situ hybridization), autopolyploidy, centromere repositioning, chromosome rearrangements, comparative chromosome painting, diploidization, genome collinearity, hybridization, invasive species,
- MeSH
- Brassicaceae * MeSH
- Cardamine * MeSH
- genom rostlinný MeSH
- lidé MeSH
- polyploidie MeSH
- zavlečené druhy MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Dálný východ MeSH
- Evropa MeSH
BACKGROUND: Hairy roots constitute a valuable tissue culture system for species that are difficult to propagate through conventional seed-based methods. Moreover, the generation of transgenic plants derived from hairy roots can be facilitated by employing carefully designed hormone-containing media. RESULTS: We initiated hairy root formation in the rare crucifer species Asperuginoides axillaris via an injection-based protocol using the Agrobacterium strain C58C1 harboring a hairy root-inducing (Ri) plasmid and successfully regenerated plants from established hairy root lines. Our study confirms the genetic stability of both hairy roots and their derived regenerants and highlights their utility as a permanent source of mitotic chromosomes for cytogenetic investigations. Additionally, we have developed an effective embryo rescue protocol to circumvent seed dormancy issues in A. axillaris seeds. By using inflorescence primary stems of Arabidopsis thaliana and Cardamine hirsuta as starting material, we also established hairy root lines that were subsequently used for regeneration studies. CONCLUSION: We developed efficient hairy root transformation and regeneration protocols for various crucifers, namely A. axillaris, A. thaliana, and C. hirsuta. Hairy roots and derived regenerants can serve as a continuous source of plant material for molecular and cytogenetic analyses.
- Klíčová slova
- Arabidopsis thaliana, Asperuginoides axillaris, Brassicaceae, Cardamine hirsuta, Crucifers, Cytogenetics, Hairy root, Plant regeneration, Transformation,
- Publikační typ
- časopisecké články MeSH
Arabidopsis thaliana has become a major plant research model, where interphase nuclear organization exhibits unique features, including nucleolus-associated telomere clustering. The chromocenter (CC)-loop model, or rosette-like configuration, describes intranuclear chromatin organization in Arabidopsis as megabase-long loops anchored in, and emanating from, peripherally positioned CCs, with those containing telomeres associating with the nucleolus. To investigate whether the CC-loop organization is universal across the mustard family (crucifers), the nuclear distributions of centromeres, telomeres and nucleoli were analyzed by fluorescence in situ hybridization in seven diploid species (2n = 10-16) representing major crucifer clades with an up to 26-fold variation in genome size (160-4260 Mb). Nucleolus-associated telomere clustering was confirmed in Arabidopsis (157 Mb) and was newly identified as the major nuclear phenotype in other species with a small genome (215-381 Mb). In large-genome species (2611-4264 Mb), centromeres and telomeres adopted a Rabl-like configuration or dispersed distribution in the nuclear interior; telomeres only rarely associated with the nucleolus. In Arabis cypria (381 Mb) and Bunias orientalis (2611 Mb), tissue-specific patterns deviating from the major nuclear phenotypes were observed in anther and stem tissues, respectively. The rosette-like configuration, including nucleolus-associated telomere clustering in small-genome species from different infrafamiliar clades, suggests that genomic properties rather than phylogenetic position determine the interphase nuclear organization. Our data suggest that nuclear genome size, average chromosome size and degree of longitudinal chromosome compartmentalization affect interphase chromosome organization in crucifer genomes.
- Klíčová slova
- Arabidopsis thaliana, Crucifereae, Rabl, centromere, chromocenter-loop model, interphase, nucleolus, telomere,
- MeSH
- Arabidopsis genetika MeSH
- Arabis genetika MeSH
- Brassicaceae genetika MeSH
- buněčné jadérko genetika MeSH
- centromera genetika MeSH
- chromatin genetika MeSH
- délka genomu MeSH
- fylogeneze MeSH
- genom rostlinný * MeSH
- heterochromatin genetika MeSH
- hybridizace in situ fluorescenční MeSH
- interfáze MeSH
- ribozomální DNA genetika MeSH
- telomery genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- chromatin MeSH
- heterochromatin MeSH
- ribozomální DNA MeSH
Clade E, or the Hesperis clade, is one of the major Brassicaceae (Crucifereae) clades, comprising some 48 genera and 351 species classified into seven tribes and is distributed predominantly across arid and montane regions of Asia. Several taxa have socioeconomic significance, being important ornamental but also weedy and invasive species. From the comparative genomic perspective, the clade is noteworthy as it harbors species with the largest crucifer genomes but low numbers of chromosomes (n = 5-7). By applying comparative cytogenetic analysis and whole-chloroplast phylogenetics, we constructed, to our knowledge, the first partial and complete cytogenetic maps for selected representatives of clade E tribes and investigated their relationships in a family-wide context. The Hesperis clade is a well-supported monophyletic lineage comprising seven tribes: Anchonieae, Buniadeae, Chorisporeae, Dontostemoneae, Euclidieae, Hesperideae, and Shehbazieae. The clade diverged from other Brassicaceae crown-group clades during the Oligocene, followed by subsequent Miocene tribal diversifications in central/southwestern Asia. The inferred ancestral karyotype of clade E (CEK; n = 7) originated from an older n = 8 genome, which also was the purported progenitor of tribe Arabideae (KAA genome). In most taxa of clade E, the seven linkage groups of CEK either remained conserved (Chorisporeae) or were reshuffled by chromosomal translocations (Euclidieae). In 50% of Anchonieae and Hesperideae species, the CEK genome has undergone descending dysploidy toward n = 6 (-5). These genomic data elucidate early genome evolution in Brassicaceae and pave the way for future whole-genome sequencing and assembly efforts in this as yet genomically neglected group of crucifer plants.
- MeSH
- Brassicaceae genetika MeSH
- fylogeneze * MeSH
- genom rostlinný * MeSH
- karyotyp MeSH
- molekulární evoluce * MeSH
- Publikační typ
- časopisecké články MeSH
Karyotype evolution in species with identical chromosome number but belonging to distinct phylogenetic clades is a long-standing question of plant biology, intractable by conventional cytogenetic techniques. Here, we apply comparative chromosome painting (CCP) to reconstruct karyotype evolution in eight species with x=7 (2n=14, 28) chromosomes from six Brassicaceae tribes. CCP data allowed us to reconstruct an ancestral Proto-Calepineae Karyotype (PCK; n=7) shared by all x=7 species analyzed. The PCK has been preserved in the tribes Calepineae, Conringieae, and Noccaeeae, whereas karyotypes of Eutremeae, Isatideae, and Sisymbrieae are characterized by an additional translocation. The inferred chromosomal phylogeny provided compelling evidence for a monophyletic origin of the x=7 tribes. Moreover, chromosomal data along with previously published gene phylogenies strongly suggest the PCK to represent an ancestral karyotype of the tribe Brassiceae prior to its tribe-specific whole-genome triplication. As the PCK shares five chromosomes and conserved associations of genomic blocks with the putative Ancestral Crucifer Karyotype (n=8) of crucifer Lineage I, we propose that both karyotypes descended from a common ancestor. A tentative origin of the PCK via chromosome number reduction from n=8 to n=7 is outlined. Comparative chromosome maps of two important model species, Noccaea caerulescens and Thellungiella halophila, and complete karyotypes of two purported autotetraploid Calepineae species (2n=4x=28) were reconstructed by CCP.
- MeSH
- Brassicaceae genetika MeSH
- chromozomy rostlin * MeSH
- druhová specificita MeSH
- fylogeneze MeSH
- heterochromatin MeSH
- karyotypizace MeSH
- malování chromozomů MeSH
- molekulární evoluce * MeSH
- translokace genetická MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- heterochromatin MeSH
Repetitive sequences are ubiquitous components of all eukaryotic genomes. They contribute to genome evolution and the regulation of gene transcription. However, the uncontrolled activity of repetitive sequences can negatively affect genome functions and stability. Therefore, repetitive DNAs are embedded in a highly repressive heterochromatic environment in plant cell nuclei. Here, we analyzed the sequence, composition and the epigenetic makeup of peculiar non-pericentromeric heterochromatic segments in the genome of the Australian crucifer Ballantinia antipoda. By the combination of high throughput sequencing, graph-based clustering and cytogenetics, we found that the heterochromatic segments consist of a mixture of unique sequences and an A-T-rich 174 bp satellite repeat (BaSAT1). BaSAT1 occupies about 10% of the B. antipoda nuclear genome in >250 000 copies. Unlike many other highly repetitive sequences, BaSAT1 repeats are hypomethylated; this contrasts with the normal patterns of DNA methylation in the B. antipoda genome. Detailed analysis of several copies revealed that these non-methylated BaSAT1 repeats were also devoid of heterochromatic histone H3K9me2 methylation. However, the factors decisive for the methylation status of BaSAT1 repeats remain currently unknown. In summary, we show that even highly repetitive sequences can exist as hypomethylated in the plant nuclear genome.
- Klíčová slova
- Brassicaceae, DNA methylation, comparative genomics, heterochromatin, satellite repeats,
- MeSH
- Arabidopsis genetika MeSH
- cévnaté rostliny chemie genetika metabolismus MeSH
- epigeneze genetická MeSH
- fylogeneze MeSH
- genom rostlinný MeSH
- heterochromatin genetika metabolismus MeSH
- histony chemie metabolismus MeSH
- metylace DNA genetika MeSH
- satelitní DNA chemie genetika metabolismus MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- heterochromatin MeSH
- histony MeSH
- satelitní DNA MeSH
