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Freshwater sediment metagenome

ABSTRACT: The genetic basis of the species-specificity and morphological diversity of magnetotactic bacteria

PROVIDER: PRJNA657227 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR30797584_1.fastq.gz	Fastqsanger.gz
	SRR30797584_2.fastq.gz	Fastqsanger.gz

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sediment metagenome

Project description:Magnetotactic Bacteria Metagenome Project (MagMeta)

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Assessing the remarkable morphological diversity and transcriptomic basis of leaf shape in Ipomoea batatas (sweetpotato)

Project description:Leaf shape is a spectacularly diverse trait that influences various aspects of plant physiology, and is even correlated with crop yield and quality in multiple species. However, only a few genetic dissections of leaf shape have been accomplished at a species-wide level. Here, we perform an initial characterization of leaf shape variation in Ipomoea batatas, the sweetpotato, at multiple scales of analysis. We use a transcriptomic survey to identify gene expression changes associated with two commonly studied leaf shape traits--circularity and aspect ratio using 19 individuals (accession) of sweetpotato. We comprehensively describe the remarkable morphological diversity in leaf shape in sweetpotato, and identify 147 differentially regulated genes associated with circularity and aspect ratio, providing an initial set of hypotheses regarding the genetic basis of leaf shape in this species.

2019-08-31 | GSE128065 | GEO

uncultured magnetotactic bacterium

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hourglass

Project description:The observation that animal morphology tends to be conserved during the embryonic phylotypic period led to the proposition that embryogenesis diverges more extensively early and late than in the middle, known as the hourglass model. This pattern of conservation is thought to reflect a major constraint on the evolution of animal body plans. Despite a wealth of morphological data confirming that there is often remarkable divergence in the early and late embryos of species from the same phylum, it is not yet known to what extent gene expression evolution, which plays a central role in the elaboration of different animal forms, underpins the morphological hourglass. Here we address this question using species-specific microarrays designed from six sequenced Drosophila species. Although it is generally appreciated that gene expression divergence plays a key role in the evolution of morphological diversity, no studies to date have addressed the extent to which expression divergence underpins the hourglass pattern at the genome-wide level. We test the molecular basis of the hourglass model of developmental evolution using gene expression data from six Drosophila species with sequenced genomes (D. ananassae, D. melanogaster, D. persimilis, D. pseudoobscura, D. simulans, and D. virilis) thereby enabling unambiguous quantitative comparisons across orthologous genes for a set of species separated by up to 40 million years. Gene expression levels were measured for 3019 genes, known to be expressed during embryonic development from RNA in situ data, at 2 hour intervals for the majority of embryogenesis using a microarray time-course with three biological replicates per species and four species-specific probes per gene.

2011-02-18 | E-MTAB-404 | biostudies-arrayexpress

freshwater sediment metagenome

Project description:environmental bacteria Raw sequence reads

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Identification of Iron-Inducible Genes in Magnetospirillum magneticum AMB-1 Non-Magnetic Mutant

Project description:Iron is limiting in the environment, bacteria respond to this deprivation by activating genes required for bacterial iron homeostasis. Transcriptional regulation in response to iron in Gram-negative bacteria is largely mediated by the ferric uptake regulator protein Fur, which in the presence of iron binds to a specific sequence in the promoter regions of genes under its control and acts as a repressor. Here we describe comparative global gene expression analysis using DNA microarray based on the whole genome sequence of the magnetotactic bacterium Magnetospirillum magneticum AMB-1 was conducted between wild type strain and a non-magnetic NMA61 mutant strain, generated by mini-Tn5 transposon mutagenesis which is incapable of assimilating iron to cytoplasm. No induction of the fur genes in NMA61 mutant strain was considered to be due to low intracellular iron concentration. In the iron-replete condition, among 4492 genes, 434 genes were down-regulated and 527 genes were up-regulated in the wild type strain. Among 434 genes down-regulated, 299 genes were not down-regulated in NMA61 mutant strain, indicating these genes are candidates of Fur-regulated. Keywords: Iron, magnetotactic bacteria

2007-07-07 | GSE5832 | GEO

freshwater sediment metagenome

Project description:Microbal diversity in sediments

| PRJNA319784 | ENA