Stem rust is an important disease of wheat that can be controlled using resistance genes. The gene SuSr-D1 identified in cultivar 'Canthatch' suppresses stem rust resistance. SuSr-D1 mutants are resistant to several races of stem rust that are virulent on wild-type plants. Here we identify SuSr-D1 by sequencing flow-sorted chromosomes, mutagenesis, and map-based cloning. The gene encodes Med15, a subunit of the Mediator Complex, a conserved protein complex in eukaryotes that regulates expression of protein-coding genes. Nonsense mutations in Med15b.D result in expression of stem rust resistance. Time-course RNAseq analysis show a significant reduction or complete loss of differential gene expression at 24 h post inoculation in med15b.D mutants, suggesting that transcriptional reprogramming at this time point is not required for immunity to stem rust. Suppression is a common phenomenon and this study provides novel insight into suppression of rust resistance in wheat.
- MeSH
- Basidiomycota patogenita MeSH
- chromozomy rostlin genetika MeSH
- duplikace genu MeSH
- exprese genu MeSH
- fenotyp MeSH
- imunita rostlin genetika MeSH
- lipnicovité klasifikace genetika MeSH
- mapování chromozomů MeSH
- mediátorový komplex genetika MeSH
- mutace MeSH
- nemoci rostlin genetika imunologie mikrobiologie MeSH
- odolnost vůči nemocem genetika MeSH
- pšenice genetika imunologie mikrobiologie MeSH
- regulace genové exprese u rostlin MeSH
- rostlinné geny genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
Many grasslands have disappeared over the last century as a result of anthropogenic land use intensification, while new patches are emerging through abandonment of arable fields. Here, we compared species (SD), functional (FD) and phylogenetic (PD) (alpha) diversity among 272 dry grassland patches of two age-classes: old and new, with the new patches being dry grasslands established on previous intensively managed fields during the last 30 years. We first compared SD, FD and PD, between patches of different age. Then, we performed generalized linear models to determine the influence of abiotic, present-day and historical landscape configuration variables on SD, FD and PD. By measuring abiotic variables, we explained the effect of environmental filtering on species diversity, whereas the present-day and historical landscape configuration variables were included to describe how the spatial and temporal configuration of the patches influence patterns of species. Finally, we applied partial regressions to explore the relative importance of abiotic, present-day and historical variables in explaining the diversity metrics and how this varies between patches of different ages. We found higher SD in the old compared to the new patches, but no changes in FD and PD. SD was mostly affected by abiotic and present-day landscape configuration variables in the new and the old patches, respectively. In the new patches, historical variables explained variation in the FD, while present-day variables explained the PD. In the old patches, historical variables accounted for most of the variation in both FD and PD. Our evidence suggests that the relative importance of assembly processes has changed over time, showing that environmental filtering and changes in the landscape configuration prevented the establishment of species in the new patches. However, the loss of species (i.e. SD) is not necessarily linked to a loss of functions and evolutionary potential.
Background and Aims: Knowledge of diploid phylogeny and ecogeography provide a foundation for understanding plant evolutionary history, diversification patterns and taxonomy. The genus Anthoxanthum (vernal grasses, Poaceae) represents a taxonomically intricate polyploid complex with large phenotypic variation and poorly resolved evolutionary relationships. The aims of the study were to reveal: (1) evolutionary lineages of the diploid taxa and their genetic differentiation; (2) the past distribution of the rediscovered 'Mediterranean diploid'; and (3) possible migration routes of diploids in the Mediterranean. Methods: A combined approach involving sequencing of two plastid regions ( trnL-trnF and rpl32-trnL ), nrDNA ITS, rDNA FISH analyses, climatic niche characterization and spatio-temporal modelling was used. Key Results: Among the examined diploid species, only two well-differentiated evolutionary lineages were recognized: Anthoxanthum gracile and A. alpinum . The other taxa - A. aristatum, A. ovatum, A. maderense and the 'Mediterranean diploid' - form a rather intermixed group based on the examined molecular data. In situ rDNA localization enabled identification of the ancestral Anthoxanthum karyotype, shared by A. gracile and two taxa from the crown group. For the studied taxa, ancestral location probabilities for six discrete geographical regions in the Mediterranean were proposed and likely scenarios of gradual expansion from them were suggested. Modelling past and present distributions shows that the 'Mediterranean diploid' has already been occurring in the same localities for 120 000 years. Conclusions: Highly congruent results were obtained and dated the origin and first diversification of Anthoxanthum to the Miocene. The later divergence probably took place in the Pleistocene and started polyploid evolution within the genus. The most recent diversification event is still occurring, and incomplete lineage sorting prevents full diversification of taxa at the molecular level, despite clear separation based on climatic niches. The 'Mediterranean diploid' is hypothesized to be a possible relic of the most recent common ancestor of Anthoxanthum due to their sharing of ancestral features.
- MeSH
- biologická evoluce * MeSH
- diploidie * MeSH
- DNA chloroplastová genetika MeSH
- fylogeneze * MeSH
- lipnicovité klasifikace MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Středomoří MeSH
High tropical mountains harbour remarkable and fragmented biodiversity thought to a large degree to have been shaped by multiple dispersals of cold-adapted lineages from remote areas. Few dated phylogenetic/phylogeographic analyses are however available. Here, we address the hypotheses that the sub-Saharan African sweet vernal grasses have a dual colonization history and that lineages of independent origins have established secondary contact. We carried out rangewide sampling across the eastern African high mountains, inferred dated phylogenies from nuclear ribosomal and plastid DNA using Bayesian methods, and performed flow cytometry and AFLP (amplified fragment length polymorphism) analyses. We inferred a single Late Pliocene western Eurasian origin of the eastern African taxa, whose high-ploid populations in one mountain group formed a distinct phylogeographic group and carried plastids that diverged from those of the currently allopatric southern African lineage in the Mid- to Late Pleistocene. We show that Anthoxanthum has an intriguing history in sub-Saharan Africa, including Late Pliocene colonization from southeast and north, followed by secondary contact, hybridization, allopolyploidization and local extinction during one of the last glacial cycles. Our results add to a growing body of evidence showing that isolated tropical high mountain habitats have a dynamic recent history involving niche conservatism and recruitment from remote sources, repeated dispersals, diversification, hybridization and local extinction.
- MeSH
- analýza polymorfismu délky amplifikovaných restrikčních fragmentů MeSH
- Bayesova věta MeSH
- biologická evoluce * MeSH
- fylogeneze * MeSH
- fylogeografie MeSH
- lipnicovité klasifikace MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- severní Afrika MeSH
The movement of nuclear DNA from one vascular plant species to another in the absence of fertilization is thought to be rare. Here, nonnative rRNA gene [ribosomal DNA (rDNA)] copies were identified in a set of 16 diploid barley (Hordeum) species; their origin was traceable via their internal transcribed spacer (ITS) sequence to five distinct Panicoideae genera, a lineage that split from the Pooideae about 60 Mya. Phylogenetic, cytogenetic, and genomic analyses implied that the nonnative sequences were acquired between 1 and 5 Mya after a series of multiple events, with the result that some current Hordeum sp. individuals harbor up to five different panicoid rDNA units in addition to the native Hordeum rDNA copies. There was no evidence that any of the nonnative rDNA units were transcribed; some showed indications of having been silenced via pseudogenization. A single copy of a Panicum sp. rDNA unit present in H. bogdanii had been interrupted by a native transposable element and was surrounded by about 70 kbp of mostly noncoding sequence of panicoid origin. The data suggest that horizontal gene transfer between vascular plants is not a rare event, that it is not necessarily restricted to one or a few genes only, and that it can be selectively neutral.
- MeSH
- buněčné jádro genetika MeSH
- diploidie MeSH
- DNA rostlinná chemie genetika MeSH
- fylogeneze * MeSH
- ječmen (rod) klasifikace genetika MeSH
- lipnicovité klasifikace genetika MeSH
- mezerníky ribozomální DNA chemie genetika MeSH
- molekulární evoluce MeSH
- přenos genů horizontální * MeSH
- ribozomální DNA chemie genetika MeSH
- rostlinné geny genetika MeSH
- sekvenční analýza DNA MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The structure of the Stipa lipskyi (GenBank accession no. KT692644) plastid genome is similar to that of closely related Poaceae species: it has a total length of 137 755 bp, the base composition of the plastome is the following: A (30.7%), C (19.3%), G (19.4%) and T (30.5%). The S. lipskyi plastid genome contains 71 genes, excluding second IR region. A complete plastome sequence of S. lipskyi will help the development of primers for examining phylogeny and hybridization events in this taxonomically difficult genus.
Upward migration of plants to barren subnival areas is occurring worldwide due to raising ambient temperatures and glacial recession. In summer 2012, the presence of six vascular plants, growing in a single patch, was recorded at an unprecedented elevation of 6150 m.a.s.l. close to the summit of Mount Shukule II in the Western Himalayas (Ladakh, India). Whilst showing multiple signs of stress, all plants have managed to establish stable growth and persist for several years. To learn about the role of microbes in the process of plant upward migration, we analysed the root-associated microbial community of the plants (three individuals from each) using microscopy and tagged amplicon sequencing. No mycorrhizae were found on the roots, implying they are of little importance to the establishment and early growth of the plants. However, all roots were associated with a complex bacterial community, with richness and diversity estimates similar or even higher than the surrounding bare soil. Both soil and root-associated communities were dominated by members of the orders Sphingomonadales and Sphingobacteriales, which are typical for hot desert soils, but were different from communities of temperate subnival soils and typical rhizosphere communities. Despite taxonomic similarity on the order level, the plants harboured a unique set of highly dominant operational taxonomic units which were not found in the bare soil. These bacteria have been likely transported with the dispersing seeds and became part of the root-associated community following germination. The results indicate that developing soils act not only as a source of inoculation to plant roots but also possibly as a sink for plant-associated bacteria.
- MeSH
- Bacteria klasifikace izolace a purifikace MeSH
- biomasa MeSH
- Brassicaceae klasifikace mikrobiologie MeSH
- DNA bakterií genetika MeSH
- DNA fungální genetika MeSH
- kořeny rostlin mikrobiologie MeSH
- lipnicovité klasifikace mikrobiologie MeSH
- mykorhiza klasifikace izolace a purifikace MeSH
- půdní mikrobiologie MeSH
- rhizosféra MeSH
- RNA ribozomální 16S genetika MeSH
- Saussurea klasifikace mikrobiologie MeSH
- sekvenční analýza DNA MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Indie MeSH
Gene and whole-genome duplications are widespread in plant nuclear genomes, resulting in sequence heterogeneity. Identification of duplicated genes may be particularly challenging in highly redundant genomes, especially when there are no diploid parents as a reference. Here, we developed a pipeline to detect the different copies in the ribosomal RNA gene family in the hexaploid grass Spartina maritima from next-generation sequencing (Roche-454) reads. The heterogeneity of the different domains of the highly repeated 45S unit was explored by identifying single nucleotide polymorphisms (SNPs) and assembling reads based on shared polymorphisms. SNPs were validated using comparisons with Illumina sequence data sets and by cloning and Sanger (re)sequencing. Using this approach, 29 validated polymorphisms and 11 validated haplotypes were reported (out of 34 and 20, respectively, that were initially predicted by our program). The rDNA domains of S. maritima have similar lengths as those found in other Poaceae, apart from the 5'-ETS, which is approximately two-times longer in S. maritima. Sequence homogeneity was encountered in coding regions and both internal transcribed spacers (ITS), whereas high intragenomic variability was detected in the intergenic spacer (IGS) and the external transcribed spacer (ETS). Molecular cytogenetic analysis by fluorescent in situ hybridization (FISH) revealed the presence of one pair of 45S rDNA signals on the chromosomes of S. maritima instead of three expected pairs for a hexaploid genome, indicating loss of duplicated homeologous loci through the diploidization process. The procedure developed here may be used at any ploidy level and using different sequencing technologies.
- MeSH
- anotace sekvence MeSH
- fylogeneze * MeSH
- genom rostlinný MeSH
- genomika metody MeSH
- haplotypy * MeSH
- hybridizace in situ fluorescenční MeSH
- jednonukleotidový polymorfismus MeSH
- lipnicovité klasifikace genetika MeSH
- otevřené čtecí rámce MeSH
- polyploidie * MeSH
- reprodukovatelnost výsledků MeSH
- ribozomální DNA MeSH
- RNA ribozomální genetika MeSH
- rostlinné geny MeSH
- výpočetní biologie metody MeSH
- vysoce účinné nukleotidové sekvenování * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The genus Anthoxanthum (sweet vernal grass, Poaceae) represents a taxonomically intricate polyploid complex with large phenotypic variation and its evolutionary relationships still poorly resolved. In order to get insight into the geographic distribution of ploidy levels and assess the taxonomic value of genome size data, we determined C- and Cx-values in 628 plants representing all currently recognized European species collected from 197 populations in 29 European countries. The flow cytometric estimates were supplemented by conventional chromosome counts. In addition to diploids, we found two low (rare 3x and common 4x) and one high (~16x-18x) polyploid levels. Mean holoploid genome sizes ranged from 5.52 pg in diploid A. alpinum to 44.75 pg in highly polyploid A. amarum, while the size of monoploid genomes ranged from 2.75 pg in tetraploid A. alpinum to 9.19 pg in diploid A. gracile. In contrast to Central and Northern Europe, which harboured only limited cytological variation, a much more complex pattern of genome sizes was revealed in the Mediterranean, particularly in Corsica. Eight taxonomic groups that partly corresponded to traditionally recognized species were delimited based on genome size values and phenotypic variation. Whereas our data supported the merger of A. aristatum and A. ovatum, eastern Mediterranean populations traditionally referred to as diploid A. odoratum were shown to be cytologically distinct, and may represent a new taxon. Autopolyploid origin was suggested for 4x A. alpinum. In contrast, 4x A. odoratum seems to be an allopolyploid, based on the amounts of nuclear DNA. Intraspecific variation in genome size was observed in all recognized species, the most striking example being the A. aristatum/ovatum complex. Altogether, our study showed that genome size can be a useful taxonomic marker in Anthoxathum to not only guide taxonomic decisions but also help resolve evolutionary relationships in this challenging grass genus.
- MeSH
- biologická evoluce MeSH
- buněčné jádro chemie MeSH
- chromozomy rostlin genetika MeSH
- diploidie MeSH
- distribuce rostlin MeSH
- DNA rostlinná genetika MeSH
- druhová specificita MeSH
- genom rostlinný * MeSH
- hybridizace genetická MeSH
- kořeny rostlin MeSH
- lipnicovité klasifikace genetika MeSH
- polyploidie MeSH
- průtoková cytometrie MeSH
- vznik druhů (genetika) MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
- Geografické názvy
- Evropa MeSH
All grass species evolved from an ancestor that underwent a whole-genome duplication (WGD) approximately 70 million years ago. Interestingly, the short arms of rice chromosomes 11 and 12 (and independently their homologs in sorghum) were found to be much more similar to each other than other homeologous regions within the duplicated genome. Based on detailed analysis of rice chromosomes 11 and 12 and their homologs in seven grass species, we propose a mechanism that explains the apparently 'younger' age of the duplication in this region of the genome, assuming a small number of reciprocal translocations at the chromosome termini. In each case the translocations were followed by unbalanced transmission and subsequent lineage sorting of the involved chromosomes to offspring. Molecular dating of these translocation events also allowed us to date major chromosome 'fusions' in the evolutionary lineages that led to Brachypodium and Triticeae. Furthermore, we provide evidence that rice is exceptional regarding the evolution of chromosomes 11 and 12, inasmuch as in other species the process of sequence exchange between homeologous chromosomes ceased much earlier than in rice. We presume that random events rather than selective forces are responsible for the observed high similarity between the short arm ends of rice chromosomes 11 and 12.
- MeSH
- časové faktory MeSH
- chromozomy rostlin genetika MeSH
- druhová specificita MeSH
- duplikace genu MeSH
- fylogeneze MeSH
- genetická variace MeSH
- genom rostlinný genetika MeSH
- lipnicovité klasifikace genetika MeSH
- molekulární evoluce * MeSH
- molekulární sekvence - údaje MeSH
- rekombinace genetická MeSH
- sekvence nukleotidů MeSH
- sekvenční analýza DNA MeSH
- sekvenční homologie nukleových kyselin MeSH
- selekce (genetika) MeSH
- syntenie MeSH
- translokace genetická MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
