Phylgenomics of Pooideae
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB73591 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR12834610_1.fastq.gz | Fastqsanger.gz | |||
| ERR12834610_2.fastq.gz | Fastqsanger.gz | |||
| ERR12834611_1.fastq.gz | Fastqsanger.gz | |||
| ERR12834611_2.fastq.gz | Fastqsanger.gz | |||
| ERR12834612_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 16 |
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Project description:Successive Evolutionary Steps Drove Pooideae Grasses from Tropical to Temperate Regions
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Project description:To investigate the evolution of cold response in Pooideae, five species spanning early to later diverging lineages were sampled before and after subjecting them to a drop in temperature (17C to 6C), shorter days (12 to 8 hours of light) and less intensive light. Short-term response was sampled in the afternoon 8 hours after drop in temperature but 24 hours after the respective control sample to control for diurnal rhythm. Long-term response was sampled after 4 and 9 weeks in the morning directly after lights were turned on with a respective control sample also taken in the morning on the day before the temperature drop.
2016-12-12 | E-MTAB-5300 | biostudies-arrayexpress
Project description:Gene expression under short day vernalization in Pooideae
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Project description:Streptococcus suis is an important zoonotic pathogen that can cause meningitis and sepsis in both pigs and humans. In this study,we evaluated the genetic difference of 40 Streptococcus suis strains belonging to various sequence types by comparative genomic hybridization to identify genes associated with the variation in pathogenicity using NimbleGen’s tilling microarray platform. Application of Comparative Phylogenomics to Identify Genetic Differences Relating to Pathogenicity of Streptococcus suis
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Project description:14-3-3 proteins are involved in a number of developmental processes in plants, largely acting through the control of transcription factor localization within the cytoplasm or nucleus. The temperate Pooideae grass 14-3-3 gene GF14h in particular was previously found to be co-expressed with flowering activators in the vernalization pathway, leading to the hypotheses that its protein product is involved in vernalization responsive flowering and/or cold acclimation. To test predictions of these non-exclusive hypotheses, and to assess functional conservation broadly across angiosperms, we generated CRISPR lines of GF14h in Brachypodium distachyon (Pooideae) and compared their mutant phenotypes with those of the co-orthologous Arabidopsis thaliana (Brassicaceae) grf9 T-DNA mutant. Contrary to our first prediction, we found that rather than promoting flowering as part of the vernalization pathway, both BdGF14h and AtGRF9 repress flowering under different conditions. Our data also support a conserved role for GF14h/GRF9 genes in the promotion of growth at the expense of abiotic stress resilience. We discuss these results in the light of crop improvement and climate change.
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Project description:Temperate Pooideae are a large clade of economically important grasses distributed in some of the Earth's coldest and driest terrestrial environments. Previous studies have inferred that Pooideae diversified from their tropical ancestors in a cold montane habitat, suggesting that above-freezing cold (chilling) tolerance evolved early in the subfamily. By contrast, drought tolerance is hypothesized to have evolved multiple times independently in response to global aridification that occurred after the split of Pooideae tribes. To independently test predictions of the chilling-before-drought hypothesis in Pooideae, we assessed conservation of whole plant and gene expression traits in response to chilling vs. drought. We demonstrated that both trait responses are more similar across tribes in cold as compared to drought, suggesting that chilling responses evolved before, and drought responses after, tribe diversification. Moreover, we found significantly more overlap between drought and chilling responsive genes within a species than between drought responsive genes across species, providing evidence that chilling tolerance genes acted as precursors for the novel acquisition of increased drought tolerance multiple times independently, partially through the cooption of chilling responsive genes.
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Project description:Abstract Agrostis is one of the most diverse genera of the Poaceae, including ca. 198 species, principally distributed in cold and temperate regions of the world, but also found in the high mountains of the tropics. We present a revision based on morphoanatomical evidence, for the biogeographic region known as Megamexico 3 (i.e., Mexico including the desert areas of southern USA and the Central America territory, to northern Nicaragua). We include taxonomic descriptions and an identification key for the found taxa, maps with the known geographical distribution of the species, and figures with the morphoanatomical characteristics, elevation and phenology. Agrostis is represented in the study zone by 20 species, of which four are endemic and three are introduced. Most records of the genus are distributed in the mountains, above 1500 m a.s.l., in open areas of temperate forests, with conifers and Quercus. Specimens with spikelets occur year round, but most records occur during the wet season, in the months of July to October. We propose a preliminary conservation assessment for each species in the study zone, according to the International Union for Conservation of Nature categories: one with Deficient Data (DD), six as Endangered (EN), two as Vulnerable (VU), and 11 as Least Concern (LC).
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Project description:Molecular phylogenomics investigates evolutionary relationships based on genomic data. However, despite genomic sequence conservation, changes in protein interactions can occur relatively rapidly and may cause strong functional diversification. To investigate such functional evolution, we here combine phylogenomics with interaction proteomics. We develop this concept by investigating the molecular evolution of the shelterin complex, which protects telomeres, across 16 vertebrate species from zebrafish to humans covering 450 million years of evolution. Our phylointeractomics screen discovers previously unknown telomere-associated proteins and reveals how homologous proteins undergo functional evolution. For instance, we show that TERF1 evolved as a telomere-binding protein in the common stem lineage of marsupial and placental mammals. Phylointeractomics is a versatile and scalable approach to investigate evolutionary changes in protein function and thus can provide experimental evidence for phylogenomic relationships.
2017-02-15 | PXD005517 | Pride