Dactylorhiza majalis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1151607 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31528900_1.fastq.gz | Fastqsanger.gz | |||
| SRR31528900_2.fastq.gz | Fastqsanger.gz | |||
| SRR31528901_1.fastq.gz | Fastqsanger.gz | |||
| SRR31528901_2.fastq.gz | Fastqsanger.gz | |||
| SRR31528902_1.fastq.gz | Fastqsanger.gz |
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Project description:Whole-genome duplication has shaped the evolution of angiosperms and other organisms, and is important for many crops. Structural reorganization of chromosomes and repatterning of gene expression are frequently observed in allopolyploids, with physiological and ecological consequences. Recurrent origins from different parental populations are widespread among polyploids, resulting in an array of lineages that provide excellent models to uncover mechanisms of adaptation to divergent environments in early phases of polyploid evolution. We integrate here transcriptomic and ecophysiological comparative studies to show that sibling allopolyploid marsh orchid species (Dactylorhiza, Orchidaceae) occur in different habitats (low nutrient fens vs. meadows with mesic soils) and are characterized by a complex suite of intertwined, pronounced ecophysiological differences between them. We uncover distinct features in leaf elemental chemistry, light-harvesting, photoprotection, nutrient transport and stomata activity of the two sibling allopolyploids, which appear to match their specific ecologies, in particular soil chemistry differences at their native sites. We argue that the phenotypic divergence between the sibling allopolyploids has a clear genetic basis, generating ecological barriers that maintain distinct, independent lineages, despite pervasive interspecific gene flow. This suggests that recurrent origins of polyploids bring about a long-term potential to trigger and maintain functional and ecological diversity in marsh orchids and other groups.
| S-EPMC10947288 | biostudies-literature
Project description:Allopolyploidization often happens recurrently, but the evolutionary significance of its iterative nature is not yet fully understood. Of particular interest are the gene flow dynamics and the mechanisms that allow young sibling polyploids to remain distinct while sharing the same ploidy, heritage and overlapping distribution areas. By using eight highly variable nuclear microsatellites, newly reported here, we investigate the patterns of divergence and gene flow between 386 polyploid and 42 diploid individuals, representing the sibling allopolyploids Dactylorhiza majalis s.s. and D. traunsteineri s.l. and their parents at localities across Europe. We make use in our inference of the distinct distribution ranges of the polyploids, including areas in which they are sympatric (that is, the Alps) or allopatric (for example, Pyrenees with D. majalis only and Britain with D. traunsteineri only). Our results show a phylogeographic signal, but no clear genetic differentiation between the allopolyploids, despite the visible phenotypic divergence between them. The results indicate that gene flow between sibling Dactylorhiza allopolyploids is frequent in sympatry, with potential implications for the genetic patterns across their entire distribution range. Limited interploidal introgression is also evidenced, in particular between D. incarnata and D. traunsteineri. Altogether the allopolyploid genomes appear to be porous for introgression from related diploids and polyploids. We conclude that the observed phenotypic divergence between D. majalis and D. traunsteineri is maintained by strong divergent selection on specific genomic areas with strong penetrance, but which are short enough to remain undetected by genotyping dispersed neutral markers.
| S-EPMC4787024 | biostudies-literature
Project description:To provide insights into the fate of transposable elements (TEs) across timescales in a post-polyploidization context, we comparatively investigate five sibling Dactylorhiza allotetraploids (Orchidaceae) formed independently and sequentially between 500 and 100K generations ago by unidirectional hybridization between diploids D. fuchsii and D. incarnata. Our results first reveal that the paternal D. incarnata genome shows a marked increased content of LTR retrotransposons compared to the maternal species, reflected in its larger genome size and consistent with a previously hypothesized bottleneck. With regard to the allopolyploids, in the youngest D. purpurella both genome size and TE composition appear to be largely additive with respect to parents, whereas for polyploids of intermediate ages we uncover rampant genome expansion on a magnitude of multiple entire genomes of some plants such as Arabidopsis. The oldest allopolyploids in the series are not larger than the intermediate ones. A putative tandem repeat, potentially derived from a non-autonomous miniature inverted-repeat TE (MITE) drives much of the genome dynamics in the allopolyploids. The highly dynamic MITE-like element is found in higher proportions in the maternal diploid, D. fuchsii, but is observed to increase in copy number in both subgenomes of the allopolyploids. Altogether, the fate of repeats appears strongly regulated and therefore predictable across multiple independent allopolyploidization events in this system. Apart from the MITE-like element, we consistently document a mild genomic shock following the allopolyploidizations investigated here, which may be linked to their relatively large genome sizes, possibly associated with strong selection against further genome expansions.
| S-EPMC9366187 | biostudies-literature
Project description:The complete chloroplast genome of Dactylorhiza majalis (Rchb.) P.F. Hunt et Summerh. (Orchidaceae:Orchidoideae) was assembled and characterized using next-generation sequencing data. The plastome (154,108?bp) possesses the typical circular structure consisting of a large single-copy region (LSC; 83,196?bp), a small single-copy region (SSC; 26,580?bp), and two copies of inverted repeats (17,752?bp each). Its overall GC content is 36.99% and the plastome encodes 134 genes. Reconstruction of phylogenetic relationships using complete plastome sequences of Orchidaceae representatives showed that D. majalis was nested within the Orchidoideae tribe Orchideae. The complete plastome comprises a valuable tool in elucidating taxonomic uncertainties within the genus Dactylorhiza.
| S-EPMC7706816 | biostudies-literature
Project description:The goals of these studies are to explore the mechanisms that enable extreme physiological plasticity and that may account for evolutionary divergence of adaptive osmotic physiologies among taxa that occupy different osmotic niches. In a common-garden environment, we track physiological and genome expression responses to hypo-osmotic (freshwater) challenge during a time-course of acclimation, and contrast these responses within and between species. We seek to identify mechanisms that facilitate osmotic acclimation that are evolutionarily conserved between basal and derived physiologies, and identify mechanisms that are uniquely derived to enable the extreme osmotic plasticity exhibited by F. heteroclitus. Importantly, previous studies using a comparable experimental design have identified physiological changes and genome expression responses that are adaptive for populations of F. heteroclitus that live in fresh water. As such, this enables us to test whether mechanisms of adaptive micro-evolutionary divergence across osmotic gradients within F. heteroclitus are shared with the mechanisms that account for patterns of macro-evolutionary divergence between F. heteroclitus and F. majalis that we identify in this study. That is, are the targets of micro-evolutionary fine-tuning the same or different as the targets of macro-evolutionary divergence across osmotic boundaries? Population comparisons include between populations from Chesapeake Bay (CB), coastal Virginia (VA), and coastal Georgia (GA).
2013-04-23 | E-MTAB-1551 | biostudies-arrayexpress
Project description:Background and aimsThe island of Gotland in the Baltic Sea has had no contact with surrounding continental areas since the withdrawal of the Weichselian ice sheet at approx. 17 ka BP. Plants present on Gotland must have arrived by long-distance dispersal, so populations are expected to exhibit reduced levels of genetic diversity compared with populations on surrounding mainlands. However, orchids have very small seeds, which appear well adapted to long-distance dispersal, and they should therefore be less affected than other plant species by colonization bottlenecks. The aim of this study was to analyse the genetic structure of orchids colonizing isolated islands, using the marsh orchid Dactylorhiza majalis ssp. lapponica as a case study.MethodsMore than 500 samples from 27 populations were analysed for 15 plastid and eight nuclear marker loci. Population diversity and differentiation patterns were compared for nuclear and plastid marker systems and analysed in relation to geographical location.Key resultsWe found high genetic diversity but no clear geographical structure of genetic differentiation between populations on Gotland. However, the between-population differentiation in plastid and nuclear markers were correlated and the greatest diversity was found at sites at comparatively high elevations, which were the first to emerge above the water after the Ice Age.ConclusionsThe regional population on Gotland has been established by a minimum of four dispersal events from continental regions. Subsequent gene flow between sites has not yet homogenized the differentiation pattern originating from initial colonization. We conclude that long-distance seed dispersal in orchids has a strong impact on structuring genetic diversity during periods of expansion and colonization, but contributes less to gene flow between populations once a stable population structure has been achieved.
| S-EPMC6266126 | biostudies-literature
Project description:To explore the mechanisms governing the leaf color variations in Chinese orchids, we analyzed gene expression differences between a wild-type and an albino-type cultivar of Cymbidium longibracteatum
2018-04-03 | GSE100180 | GEO