RNAseq Poa annua
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB75376 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR13033500_1.fastq.gz | Fastqsanger.gz | |||
| ERR13033500_2.fastq.gz | Fastqsanger.gz | |||
| ERR13033501_1.fastq.gz | Fastqsanger.gz | |||
| ERR13033501_2.fastq.gz | Fastqsanger.gz | |||
| ERR13033502_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:BackgroundPoa annua (annual bluegrass) is an allotetraploid turfgrass, an agronomically significant weed, and one of the most widely dispersed plant species on earth. Here, we report the chromosome-scale genome assemblies of P. annua's diploid progenitors, P. infirma and P. supina, and use multi-omic analyses spanning all three species to better understand P. annua's evolutionary novelty.ResultsWe find that the diploids diverged from their common ancestor 5.5 - 6.3 million years ago and hybridized to form P. annua ≤ 50,000 years ago. The diploid genomes are similar in chromosome structure and most notably distinguished by the divergent evolutionary histories of their transposable elements, leading to a 1.7 × difference in genome size. In allotetraploid P. annua, we find biased movement of retrotransposons from the larger (A) subgenome to the smaller (B) subgenome. We show that P. annua's B subgenome is preferentially accumulating genes and that its genes are more highly expressed. Whole-genome resequencing of several additional P. annua accessions revealed large-scale chromosomal rearrangements characterized by extensive TE-downsizing and evidence to support the Genome Balance Hypothesis.ConclusionsThe divergent evolutions of the diploid progenitors played a central role in conferring onto P. annua its remarkable phenotypic plasticity. We find that plant genes (guided by selection and drift) and transposable elements (mostly guided by host immunity) each respond to polyploidy in unique ways and that P. annua uses whole-genome duplication to purge highly parasitized heterochromatic sequences. The findings and genomic resources presented here will enable the development of homoeolog-specific markers for accelerated weed science and turfgrass breeding.
| S-EPMC10291818 | biostudies-literature
Project description:Haloxyfop is one of two acetyl-coenzyme A carboxylase (ACCase) inhibitors that is recommended for controlling Poa annua. We have characterised a population of P. annua that had developed resistance to haloxyfop. This resistant population was found to be almost 20 times less sensitive to haloxyfop than a susceptible population based on percentage survival of individuals in two dose-response experiments. However, the haloxyfop-resistant population was still susceptible to clethodim. Pre-treatment of resistant individuals with a cytochrome P450 inhibitor, malathion, did not change the sensitivity level of the resistant plants to haloxyfop, suggesting that a non-target site mechanism of resistance involving enhanced metabolism, was not responsible for this resistance in P. annua. Gene sequencing showed that a target site mutation at position 2041, which replaced isoleucine with threonine in the carboxyltransferase (CT) domain of the ACCase enzyme, was associated with resistance to haloxyfop in the resistant population. An evaluation of the 3-D structure of the CT domain suggested that, unlike Asn-2041, which is the most common mutation at this position reported to date, Thr-2041 does not change the conformational structure of the CT domain. This is the first study investigating the molecular mechanism involved with haloxyfop resistance in P. annua.
| S-EPMC7060245 | biostudies-literature
Project description:Poa annua L. is a globally distributed grass with economic and horticultural significance as a weed and as a turfgrass. This dual significance, and its phenotypic plasticity and ecological adaptation, have made P. annua an intriguing plant for genetic and evolutionary studies. Because of the lack of genomic resources and its allotetraploid (2n = 4x = 28) nature, a reference genome sequence would be a valuable asset to better understand the significance and polyploid origin of P. annua. Here we report a genome assembly with scaffolds representing the 14 haploid chromosomes that are 1.78 Gb in length with an N50 of 112 Mb and 96.7% of BUSCO orthologs. Seventy percent of the genome was identified as repetitive elements, 91.0% of which were Copia- or Gypsy-like long-terminal repeats. The genome was annotated with 76,420 genes spanning 13.3% of the 14 chromosomes. The two subgenomes originating from Poa infirma (Knuth) and Poa supina (Schrad) were sufficiently divergent to be distinguishable but syntenic in sequence and annotation with repetitive elements contributing to the expansion of the P. infirma subgenome.
| S-EPMC9838796 | biostudies-literature
Project description:BackgroundPoa annua L. is an example of a plant characterized by abundant, worldwide distribution from polar to equatorial regions. Due to its high plasticity and extraordinary expansiveness, P. annua is considered an invasive species capable of occupying and surviving in a wide range of habitats including pioneer zones, areas intensively transformed by human activities, remote subarctic meadows and even the Antarctic Peninsula region.MethodsIn the present study, we evaluated the utility of inter-primer binding site (iPBS) markers for assessing the genetic variation of P. annua populations representing contrasting environments from the worldwide range of this species. The electrophoretic patterns of polymerase chain reaction products obtained for each individual were used to estimate the genetic diversity and differentiation between populations.ResultsiPBS genotyping revealed a pattern of genetic variation differentiating the six studied P. annua populations characterized by their different climatic conditions. According to the analysis of molecular variance, the greatest genetic variation was recorded among populations, whereas 41.75% was observed between individuals within populations. The results of principal coordinates analysis (PCoA) and model-based clustering analysis showed a clear subdivision of analyzed populations. According to PCoA, populations from Siberia and the Kola Peninsula were the most different from each other and showed the lowest genetic variability. The application of STRUCTURE software confirmed the unique character of the population from the Kola Peninsula.DiscussionThe lowest variability of the Siberia population suggested that it was subjected to genetic drift. However, although demographic expansion was indicated by negative values of Fu's FS statistic and analysis of mismatch distribution, it was not followed by significant traces of a bottleneck or a founder effect. For the Antarctic population, the observed level of genetic variation was surprisingly high, despite the observed significant traces of bottleneck/founder effect following demographic expansion, and was similar to that observed in populations from Poland and the Balkans. For the Antarctic population, the multiple introduction events from different sources are considered to be responsible for such an observation. Moreover, the results of STRUCTURE and PCoA showed that the P. annua from Antarctica has the highest genetic similarity to populations from Europe.ConclusionsThe observed polymorphism should be considered as a consequence of the joint influence of external abiotic stress and the selection process. Environmental changes, due to their ability to induce transposon activation, lead to the acceleration of evolutionary processes through the production of genetic variability.
| S-EPMC6525586 | biostudies-literature
Project description:Poa annua (annual bluegrass) is one of the most ubiquitous grass species in the world. In isolated regions of maritime Antarctica, it has become an invasive organism threatening native tundra communities. In this study, we have explored and compared the rhizosphere and root-endosphere dwelling microbial community of P. annua specimens of maritime Antarctic and Central European origin in terms of bacterial phylogenetic diversity and microbial metabolic activity with a geochemical soil background. Our results show that the rhizospheric bacterial community was unique for each sampling site, yet the endosphere communities were similar to each other. However, key plant-associated bacterial taxa such as the Rhizobiaceae family were poorly represented in Antarctic samples, probably due to high salinity and heavy metal concentrations in the soil. Metabolic activity in the Antarctic material was considerably lower than in Central European samples. Antarctic root endosphere showed unusually high numbers of certain opportunistic bacterial groups, which proliferated due to low competition conditions. Thirteen bacterial families were recognized in this study to form a core microbiome of the P. annua root endosphere. The most numerous were the Flavobacteriaceae, suspected to be major contributors to the ecological success of annual bluegrass, especially in harsh, Antarctic conditions.
| S-EPMC8069831 | biostudies-literature
Project description:Puccinellia tenuiflora is an alkaline salt-tolerant monocot found in saline-alkali soil in China. To identify the genes which are determining the higher tolerance of P. tenuiflora compared to bicarbonate sensitive species, we examined the responses of P. tenuiflora and a related bicarbonate-sensitive Poeae plant, Poa annua, to two days of 20 mM NaHCO3 stress by RNA-seq analysis. We obtained 28 and 38 million reads for P. tenuiflora and P. annua, respectively. For each species, the reads of both unstressed and stressed samples were combined for de novo assembly of contigs. We obtained 77,329 contigs for P. tenuiflora and 115,335 contigs for P. annua. NaHCO3 stress resulted in greater than two-fold absolute expression value changes in 157 of the P. tenuiflora contigs and 1090 of P. annua contigs. Homologs of the genes involved in Fe acquisition, which are important for the survival of plants under alkaline stress, were up-regulated in P. tenuiflora and down-regulated in P. annua. The smaller number of the genes differentially regulated in P. tenuiflora suggests that the genes regulating bicarbonate tolerance are constitutively expressed in P. tenuiflora.
| S-EPMC4307258 | biostudies-literature
Project description:BackgroundPoa annua is a pervasive grassy, self-pollinating, weed that has evolved resistance to 10 different herbicide modes-of-action, third most of all weed species. We investigated constitutive overexpression of genes associated with non-target site resistance (NTSR) in POAAN-R3 and the response of those genes when treated with trifloxysulfuron despite the biotype having a known target site mutation in acetolactate synthase (ALS).ResultsDespite having an ALS target site mutation, POAAN-R3 still had a transcriptomic response to herbicide application that differed from a susceptible biotype. We observed differential expression of genes associated with transmembrane transport and oxidation-reduction activities, with differences being most pronounced prior to herbicide treatment.ConclusionsIn the P. annua biotype we studied with confirmed target site resistance to ALS inhibitors, we also observed constitutive expression of genes regulating transmembrane transport, as well as differential expression of genes associated with oxidative stress after treatment with trifloxysulfuron. This accumulation of mechanisms, in addition to the manifestation of target site resistance, could potentially increase the chance of survival when plants are challenged by different modes of action.
| S-EPMC8518846 | biostudies-literature