Deserts exert strong selection pressures on plants, but the underlying genomic drivers of ecological adaptation and subsequent speciation remain largely unknown. Here, we generated de novo genome assemblies and conducted population genomic analyses of the psammophytic genus Pugionium (Brassicaceae). Our results indicated that this bispecific genus had undergone an allopolyploid event, and the two parental genomes were derived from two ancestral lineages with different chromosome numbers and structures. The postpolyploid expansion of gene families related to abiotic stress responses and lignin biosynthesis facilitated environmental adaptations of the genus to desert habitats. Population genomic analyses of both species further revealed their recent divergence with continuous gene flow, and the most divergent regions were found to be centered on three highly structurally reshuffled chromosomes. Genes under selection in these regions, which were mainly located in one of the two subgenomes, contributed greatly to the interspecific divergence in microhabitat adaptation.
Angiosperms have become the dominant terrestrial plant group by diversifying for ~145 million years into a broad range of environments. During the course of evolution, numerous morphological innovations arose, often preceded by whole genome duplications (WGD). The mustard family (Brassicaceae), a successful angiosperm clade with ~4000 species, has been diversifying into many evolutionary lineages for more than 30 million years. Here we develop a species inventory, analyze morphological variation, and present a maternal, plastome-based genus-level phylogeny. We show that increased morphological disparity, despite an apparent absence of clade-specific morphological innovations, is found in tribes with WGDs or diversification rate shifts. Both are important processes in Brassicaceae, resulting in an overall high net diversification rate. Character states show frequent and independent gain and loss, and form varying combinations. Therefore, Brassicaceae pave the way to concepts of phylogenetic genome-wide association studies to analyze the evolution of morphological form and function.
Centromere position may change despite conserved chromosomal collinearity. Centromere repositioning and evolutionary new centromeres (ENCs) were frequently encountered during vertebrate genome evolution but only rarely observed in plants. The largest crucifer tribe, Arabideae (∼550 species; Brassicaceae, the mustard family), diversified into several well-defined subclades in the virtual absence of chromosome number variation. Bacterial artificial chromosome-based comparative chromosome painting uncovered a constancy of genome structures among 10 analyzed genomes representing seven Arabideae subclades classified as four genera: Arabis, Aubrieta, Draba, and Pseudoturritis Interestingly, the intra-tribal diversification was marked by a high frequency of ENCs on five of the eight homoeologous chromosomes in the crown-group genera, but not in the most ancestral Pseudoturritis genome. From the 32 documented ENCs, at least 26 originated independently, including 4 ENCs recurrently formed at the same position in not closely related species. While chromosomal localization of ENCs does not reflect the phylogenetic position of the Arabideae subclades, centromere seeding was usually confined to long chromosome arms, transforming acrocentric chromosomes to (sub)metacentric chromosomes. Centromere repositioning is proposed as the key mechanism differentiating overall conserved homoeologous chromosomes across the crown-group Arabideae subclades. The evolutionary significance of centromere repositioning is discussed in the context of possible adaptive effects on recombination and epigenetic regulation of gene expression.
Complexes of diploid and polyploid species have formed frequently during the evolution of land plants. In false flax (Camelina sativa), an important hexaploid oilseed crop closely related to Arabidopsis (Arabidopsis thaliana), the putative parental species as well as the origin of other Camelina species remained unknown. By using bacterial artificial chromosome-based chromosome painting, genomic in situ hybridization, and multi-gene phylogenetics, we aimed to elucidate the origin and evolution of the polyploid complex. Genomes of diploid camelinas (Camelina hispida, n = 7; Camelina laxa, n = 6; and Camelina neglecta, n = 6) originated from an ancestral n = 7 genome. The allotetraploid genome of Camelina rumelica (n = 13, N6H) arose from hybridization between diploids related to C. neglecta (n = 6, N6) and C. hispida (n = 7, H), and the N subgenome has undergone a substantial post-polyploid fractionation. The allohexaploid genomes of C. sativa and Camelina microcarpa (n = 20, N6N7H) originated through hybridization between an auto-allotetraploid C. neglecta-like genome (n = 13, N6N7) and C. hispida (n = 7, H), and the three subgenomes have remained stable overall since the genome merger. Remarkably, the ancestral and diploid Camelina genomes were shaped by complex chromosomal rearrangements, resembling those associated with human disorders and resulting in the origin of genome-specific shattered chromosomes.plantcell;31/11/2596/FX1F1fx1.
- MeSH
- Arabidopsis genetika MeSH
- Brassicaceae klasifikace genetika MeSH
- chromothripsis * MeSH
- chromozomy rostlin MeSH
- diploidie * MeSH
- fylogeneze MeSH
- genom rostlinný * MeSH
- hybridizace genetická MeSH
- molekulární evoluce * MeSH
- polyploidie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: RNA-sequencing analysis is increasingly utilized to study gene expression in non-model organisms without sequenced genomes. Aethionema arabicum (Brassicaceae) exhibits seed dimorphism as a bet-hedging strategy - producing both a less dormant mucilaginous (M+) seed morph and a more dormant non-mucilaginous (NM) seed morph. Here, we compared de novo and reference-genome based transcriptome assemblies to investigate Ae. arabicum seed dimorphism and to evaluate the reference-free versus -dependent approach for identifying differentially expressed genes (DEGs). RESULTS: A de novo transcriptome assembly was generated using sequences from M+ and NM Ae. arabicum dry seed morphs. The transcripts of the de novo assembly contained 63.1% complete Benchmarking Universal Single-Copy Orthologs (BUSCO) compared to 90.9% for the transcripts of the reference genome. DEG detection used the strict consensus of three methods (DESeq2, edgeR and NOISeq). Only 37% of 1533 differentially expressed de novo assembled transcripts paired with 1876 genome-derived DEGs. Gene Ontology (GO) terms distinguished the seed morphs: the terms translation and nucleosome assembly were overrepresented in DEGs higher in abundance in M+ dry seeds, whereas terms related to mRNA processing and transcription were overrepresented in DEGs higher in abundance in NM dry seeds. DEGs amongst these GO terms included ribosomal proteins and histones (higher in M+), RNA polymerase II subunits and related transcription and elongation factors (higher in NM). Expression of the inferred DEGs and other genes associated with seed maturation (e.g. those encoding late embryogenesis abundant proteins and transcription factors regulating seed development and maturation such as ABI3, FUS3, LEC1 and WRI1 homologs) were put in context with Arabidopsis thaliana seed maturation and indicated that M+ seeds may desiccate and mature faster than NM. The 1901 transcriptomic DEG set GO-terms had almost 90% overlap with the 2191 genome-derived DEG GO-terms. CONCLUSIONS: Whilst there was only modest overlap of DEGs identified in reference-free versus -dependent approaches, the resulting GO analysis was concordant in both approaches. The identified differences in dry seed transcriptomes suggest mechanisms underpinning previously identified contrasts between morphology and germination behaviour of M+ and NM seeds.
- MeSH
- anotace sekvence MeSH
- Brassicaceae genetika růst a vývoj MeSH
- genom rostlinný MeSH
- genová ontologie MeSH
- klíčení MeSH
- regulace genové exprese u rostlin * MeSH
- rostlinné proteiny genetika MeSH
- semena rostlinná genetika růst a vývoj MeSH
- stanovení celkové genové exprese MeSH
- transkriptom * MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- Publikační typ
- časopisecké články MeSH
Habitats with alkaline edaphic substrates are often associated with plant speciation and diversification. The tribe Alysseae, in the family Brassicaceae, epitomizes this evolutionary trend. In this lineage, some genera, like Hormathophylla, can serve as a good case for testing the evolutionary framework. This genus is centered in the western Mediterranean. It grows on different substrates, but mostly on alkaline soils. It has been suggested that diversification in many lineages of the tribe Alysseae and in the genus Hormathophylla is linked to a tolerance for high levels of Mg+2 in xeric environments. In this study, we investigated the controversial phylogenetic placement of Hormathophylla in the tribe, the generic limits and the evolutionary relationships between the species using ribosomal and plastid DNA sequences. We also examined the putative association between the evolution of different ploidy levels, trichome morphology and the type of substrates. Our analyses demonstrated the monophyly of the genus Hormathophylla including all previously described species. Nuclear sequences revealed two lineages that differ in basic chromosome numbers (x = 7 and x = 8 or derived 11, 15) and in their trichome morphology. Contrasting results with plastid genes indicates more complex relationships between these two lineages involving recent hybridization processes. We also found an association between chloroplast haplotypes and substrate, especially in populations growing on dolomites. Finally, our dated phylogeny demonstrates that the origin of the genus took place in the mid-Miocene, during the establishment of temporal land bridges between the Tethys and Paratethys seas, with a later diversification during the upper Pliocene.
- MeSH
- alkálie chemie MeSH
- Bayesova věta MeSH
- Brassicaceae genetika ultrastruktura MeSH
- buněčné jádro genetika MeSH
- časové faktory MeSH
- chromozomy rostlin genetika MeSH
- druhová specificita MeSH
- fylogeneze * MeSH
- fylogeografie MeSH
- genetická variace MeSH
- haplotypy genetika MeSH
- hořčík chemie MeSH
- plastidy genetika MeSH
- ploidie MeSH
- pravděpodobnostní funkce MeSH
- půda chemie MeSH
- ribozomy genetika MeSH
- sekvence nukleotidů MeSH
- trichomy ultrastruktura MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Středomoří MeSH
The small genus Ricotia (nine species, Brassicaceae) is confined to the eastern Mediterranean. By comparative chromosome painting and a dated multi-gene chloroplast phylogeny, we reconstructed the origin and subsequent evolution of Ricotia. The ancestral Ricotia genome originated through hybridization between two older genomes with n = 7 and n = 8 chromosomes, respectively, on the Turkish mainland during the Early Miocene (c. 17.8 million years ago, Ma). Since then, the allotetraploid (n = 15) genome has been altered by two independent descending dysploidies (DD) to n = 14 in Ricotia aucheri and the Tenuifolia clade (2 spp.). By the Late Miocene (c. 10 Ma), the latter clade started to evolve in the most diverse Ricotia core clade (6 spp.), the process preceded by a DD event to n = 13. It is noteworthy that this dysploidy was mediated by a unique chromosomal rearrangement, merging together the same two chromosomes as were merged during the origin of a fusion chromosome within the paternal n = 7 genome c. 20 Ma. This shows that within a time period of c. 8 Myr genome evolution can repeat itself and that structurally very similar chromosomes may originate repeatedly from the same ancestral chromosomes by different pathways (end-to-end translocation versus nested chromosome insertion).
- MeSH
- Brassicaceae klasifikace genetika MeSH
- chromozomální aberace MeSH
- chromozomy rostlin * MeSH
- fylogeneze MeSH
- genom rostlinný MeSH
- hybridizace genetická * MeSH
- karyotypizace MeSH
- malování chromozomů MeSH
- molekulární evoluce * MeSH
- ploidie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Turecko MeSH
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.
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.
- 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
Clade E, or theHesperisclade, 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. TheHesperisclade 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 oldern= 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 towardn= 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
