Mimulus guttatus rhizosphere microbiome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA451377 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7054590_1.fastq.gz | Fastqsanger.gz | |||
| SRR7054590_2.fastq.gz | Fastqsanger.gz | |||
| SRR7054600_1.fastq.gz | Fastqsanger.gz | |||
| SRR7054600_2.fastq.gz | Fastqsanger.gz | |||
| SRR7054610_1.fastq.gz | Fastqsanger.gz |
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Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Mimulus guttatus tissues (including leaves, flowers and roots). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study. Small RNA libraries were derived from leaves, flowers and roots of Mimulus guttatus, strain âIM62â. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank John Willis for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.
2011-05-09 | E-GEOD-28971 | biostudies-arrayexpress
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Mimulus guttatus tissues (including leaves, flowers and roots). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.
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Project description:Background: The soil environment is responsible for sustaining most terrestrial plant life on earth, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere and how it responds to agricultural management such as crop rotations and soil tillage will be vital for improving global food production. Methods: The rhizosphere soils of wheat and chickpea growing under + and - decaying root were collected for metagenomics sequencing. A gene catalogue was established by de novo assembling metagenomic sequencing. Genes abundance was compared between bulk soil and rhizosphere soils under different treatments. Conclusions: The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the microbiome from decaying root in determining the metagenome of developing root systems, which is fundamental to plant growth, since roots preferentially inhabit previous root channels. Modifications in root microbial function through soil management, can ultimately govern plant health, productivity and food security.
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Project description:The action of natural selection across heterogeneous natural landscapes drives local adaptation and the formation of plant ecotypes, the precursors to new species. Plant ecotypes typically differ greatly in morphology, physiology, and development, yet we have a poor understanding of the underlying genetic basis of this divergence. Despite their importance, studies of the molecular underpinnings of ecotypic divergence through developmental stages are rare. In this study, we compared gene expression at different developmental time points between two locally adapted populations derived from the coastal perennial and inland annual ecotypes of the yellow monkeyflower, Mimulus guttatus. We conducted gene co-expression network analyses to identify putative genetic and molecular mechanisms driving ecotypic divergence and evaluated gene ontology enrichment. Overall, we found significant global expression differences between the ecotypes and among developmental stages. We also found evidence to support the hypothesis that interacting hormone pathways, especially the gibberellin and jasmonic acid pathways, may play a key role in annual versus perennial ecotype divergence. Further, genes within known chromosomal inversions were more likely to be differentially expressed than genes in colinear regions, but only in leaves and not for floral buds. Collectively, our results reinforce our existing hypotheses about how ecotype formation has occurred in this system through shifts in hormone biosynthesis/signaling and help advance our understanding of the evolution of annuality versus perenniality in plants.
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Project description:Here we identify and characterize a spontaneous mutant allele that disrupts the initiation and specification of the ovule integument in Mimulus nudatus. The mutant phenotype is characterized by the early arrest of the ovule integument or alternatively, the delayed development of a carpel-like structure in place of the integument. Additionally, medusa mutant ovule primordia fail to develop female gametophytic structures. Morphological analyses indicate that a nucellar domain is specified within the ovule and a megaspore-like cell is often specified, but that cell aborts before generating the female gametophyte. We mapped the position of the mutation to a location on Chromosome1. Mapping revealed a primary candidate gene that was a member of a family of MADS-domain containing transcription factors with sequence similarity to the Arabidopsis BEL1 gene (At5G41410) and is an orthologue of the Mimulus guttatus gene MgTOL.A0789.1. Analysis of the sequence of the Mimulus nudatus homolog (referred hereafter as MnBEL1) locus, revealed the insertion of a mitochondrial DNA genomic fragment within the MnBEL1 locus that segregated with the medusa mutant phenotype. The mitochondrial insertion sequence is predicted to disrupt the coding sequence of MnBEL1. RNA expression analysis revealed dramatically reduced levels of the expression of the MnBEL1 in gynoecia from medusa mutant plants relative to wild type sisters. RNA seq analysis revealed that the medusa mutant seedpods failed to express MnBEL1 at wildtype levels. RNA sequence data comparisons between wildtype and medusa mutant seedpods also identified a set of genes, that are expressed in wildtype seedpods, but that are expressed at very low levels or that are not detected in the medusa seed pods. Homologues of many of these genes have been previously shown to be strongly expressed in female gametophyte in Arabidopsis. This RNA seq analysis further indicates a strong developmental disruption and identifies sets of genes with expected roles in female gametophyte development in Mimulus species for further investigation. Our evidence strongly suggests that MnBEL1 is a true functional orthologue of AtBEL1. To the best of our knowledge, these studies provide the first mutational analysis of a BEL1 orthologue outside of Arabidopsis and indicate the functional conservation of this gene between Mimulus and Arabidopsis. This work also presents the first identification of a mutational event in Mimulus that is linked to an insertion of a mitochondrial sequence in the nuclear genome.
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