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40 results for “Eragrostis curvula”
Differentially methylated genes involved in reproduction and ploidy levels in recent diploidized and tetraploidized Eragrostis curvula genotypes
<p>Epigenetics studies changes in gene activity without changes in the DNA sequence. Methylation is an epigenetic mechanism important in many pathways, such as biotic and abiotic stresses, cell division, and reproduction. <em>Eragrostis curvula</em> is a grass species reproducing by apomixis, a clonal reproduction by seeds. This work employed the MCSeEd technique to identify deferentially methylated positions, regions, and genes in the CG, CHG, and CHH contexts in <em>E</em>. <em>curvula</em> genotypes with similar genomic backgrounds but with different reproductive modes and ploidy levels. In this way, we focused the analysis on the cvs. Tanganyika INTA (4x, apomictic), Victoria (2x, sexual), and Bahiense (4x, apomictic). Victoria was obtained from the diploidization of Tanganyika INTA, while Bahiense was produced from the tetraploidization of Victoria. This study showed that polyploid/apomictic genotypes had more differentially methylated positions and regions than the diploid sexual ones. Interestingly, it was possible to observe fewer differentially methylated positions and regions in CG than in the other contexts, meaning CG methylation is conserved across the genotypes regardless of the ploidy level and reproductive mode. In the comparisons between sexual and apomictic genotypes, we identified differentially methylated genes involved in the reproductive pathways, specifically in meiosis, cell division, and fertilization. Another interesting observation was that several differentially methylated genes between the diploid and the original tetraploid genotype recovered their methylation status after tetraploidization, suggesting that methylation is an important mechanism involved in reproduction and ploidy changes.</p>
Differential methylation patterns in apomictic vs. sexual genotypes of the diplosporous grass Eragrostis curvula.
<p>Methylation is an epigenetic mechanism where a methyl group take place over the C5 of cytosine or C6 of adenine repressing or de-repressing genes depending on the context, position (coding or non-coding) and species. Eragrostis curvula is a forage grass that reproduces by apomixis. Increases of the frequency of sexual pistils in facultative genotypes of this grass has been associated to epigenetic changes triggered by different biotic and abiotic stresses. The aim of the present study was to associate differences in the reproductive mode with specific methylated regions and genes contrasting full apomictic, facultative and sexual genotypes using the methylation sensitive technique MCSeEd. The distribution of the differentially methylated positions over the genes shows a peak around the start and stop codon boundaries, hence regulating gene expression mainly through the incorporation of methyl groups on these positions. The main pathways being regulated were ubiquitin and auxins. The methylation pathway itself was also found to be self-regulated since ROS1 and ROS4, the main demethylating genes were found differentially methylated among the different genotypes. Even more, this work allowed us to detect genes regulated by methylation that were previously found differentially expressed in the comparisons between apomictic and sexual genotypes.</p>
From tetraploid to diploid, a pangenomic approach to identify genes lost during synthetic diploidization of Eragrostis curvula
<p><strong>Introduction:</strong> In <em>Eragrostis curvula</em>, commonly known as weeping lovegrass, a synthetic diploidization event of the facultative apomictic tetraploid Tanganyika INTA cv. originated from the sexual diploid Victoria cv. Apomixis is an asexual reproduction by seeds in which the progeny is genetically identical to the maternal plant.</p> <p><strong>Methods:</strong> To assess the genomic changes related to ploidy and to the reproductive mode occurring during diploidization, a mapping approach was followed to obtain the first <em>E. curvula</em> pangenome assembly. In this way, gDNA of Tanganyika INTA was extracted and sequenced in 2x250 Illumina pair-end reads and mapped against the Victoria genome assembly. The unmapped reads were used for variant calling, while the mapped reads were assembled using Masurca software.</p> <p><strong>Results:</strong> The length of the assembly was 28,982,419 bp distributed in 18,032 contigs, and the variable genes annotated in these contigs rendered 3,952 gene models. Functional annotation of the genes showed that the reproductive pathway was differentially enriched. PCR amplification in gDNA and cDNA of Tanganyika INTA and Victoria was conducted to validate the presence/absence variation in five genes related to reproduction and ploidy. The polyploid nature of the Tanganyika INTA genome was also evaluated through the variant calling analysis showing the single nucleotide polymorphism (SNP) coverage and allele frequency distribution with a segmental allotetraploid pairing behavior.</p>
Santa Rita Experimental Range site, station Pasture 12B at Santa Rita Experimental Range, study of plant cover of Eragrostis curvula (weeping lovegrass) in units of percent on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Santa Rita Experimental Range (SRE) contains plant cover of Eragrostis curvula (weeping lovegrass) measurements in percent units and were aggregated to a yearly timescale.
Santa Rita Experimental Range site, station Pasture 12B at Santa Rita Experimental Range, study of plant density of Eragrostis curvula var. conferta in units of numberPerMeterSquared on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Santa Rita Experimental Range (SRE) contains plant density of Eragrostis curvula var. conferta measurements in numberPerMeterSquared units and were aggregated to a yearly timescale.
Santa Rita Experimental Range site, station Pasture 2S at Santa Rita Experimental Range, study of plant cover of Eragrostis curvula (weeping lovegrass) in units of percent on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Santa Rita Experimental Range (SRE) contains plant cover of Eragrostis curvula (weeping lovegrass) measurements in percent units and were aggregated to a yearly timescale.
Santa Rita Experimental Range site, station Pasture 2S at Santa Rita Experimental Range, study of plant density of Eragrostis curvula var. conferta in units of numberPerMeterSquared on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Santa Rita Experimental Range (SRE) contains plant density of Eragrostis curvula var. conferta measurements in numberPerMeterSquared units and were aggregated to a yearly timescale.
Santa Rita Experimental Range site, station Santa Rita Experimental Range pastures where the mesquite were killed and the pastures were burned: pasture 2S, study of plant cover of Eragrostis curvula (weeping lovegrass) in units of percent on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Santa Rita Experimental Range (SRE) contains plant cover of Eragrostis curvula (weeping lovegrass) measurements in percent units and were aggregated to a yearly timescale.
Santa Rita Experimental Range site, station Santa Rita Experimental Range pastures where the mesquite were killed and the pastures were burned: pasture 2S, study of plant density of Eragrostis curvula var. conferta in units of numberPerMeterSquared on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Santa Rita Experimental Range (SRE) contains plant density of Eragrostis curvula var. conferta measurements in numberPerMeterSquared units and were aggregated to a yearly timescale.
Santa Rita Experimental Range site, station Santa Rita Experimental Range pastures where the existing mesquite were killed and the pastures were grazed: pastures 3, 5N, 5S, 6B and 12B, study of plant cover of Eragrostis curvula (weeping lovegrass) in units of percent on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Santa Rita Experimental Range (SRE) contains plant cover of Eragrostis curvula (weeping lovegrass) measurements in percent units and were aggregated to a yearly timescale.
A combined transcriptome - miRNAome approach revealed that a kinesin gene is differentially targeted by a novel miRNA in an apomictic genotype of Eragrostis curvula
<p>Weeping lovegrass (<em>Eragrostis curvula</em> [Shrad.] Nees) is a perennial grass typically established in semi-arid regions, with good adaptability to dry conditions and sandy soils. This polymorphic complex includes both sexual and apomictic cytotypes, with different ploidy levels (2x-8x). Diploids are known to be sexual, while most polyploids are facultative apomicts, and full apomicts have also been reported. Plant breeding studies throughout the years have focused on achieving the introgression of apomixis into species of agricultural relevance, but, given the complexity of the trait, a deeper understanding of the molecular basis of regulatory mechanisms of apomixis is still required. Apomixis is thought to be associated with silencing or disruption of the sexual pathway, and studies have shown it is influenced by epigenetic mechanisms. In a previous study, we explored the role of miRNA-mRNA interactions using two contrasting <em>E. curvula</em> phenotypes. Here, the sexual OTA-S, the facultative Don Walter and the obligate apomictic Tanganyika cDNA and sRNA libraries were inquired, searching for miRNA discovery and miRNA expression regulation of genes related to the reproductive mode. This allowed for the characterization of seven miRNAs and the validation of their miRNA-target interactions. Interestingly, a <em>kinesin</em> gene was found to be repressed in the apomictic cultivar Tanganyika, targeted by a novel miRNA that was found to be overexpressed in this genotype, suggestive of an involvement in the reproductive mode expression. Our work provided additional evidence of the contribution of the epigenetic regulation of the apomictic pathway.</p>
Eragrostis curvula (Schrad.) Nees (BR0000010426548)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Eragrostis curvula (Schrad.) Nees (BR0000012185948)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Eragrostis curvula (Schrad.) Nees (BR0000011521860)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Eragrostis curvula (Schrad.) Nees (BR0000005386161)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Eragrostis curvula (Schrad.) Nees (BR0000011521594)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Eragrostis curvula (Schrad.) Nees (BR0000011519270)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Eragrostis curvula (Schrad.) Nees (BR0000005386246)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Eragrostis curvula (Schrad.) Nees (BR0000011521693)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
Eragrostis curvula (Schrad.) Nees (BR0000010426616)
Belgium Herbarium image of <a href="https://www.plantentuinmeise.be">Meise Botanic Garden</a>.
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