Eudromia elegans
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA10813 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18820603_1.fastq.gz | Fastqsanger.gz | |||
| SRR18820603_2.fastq.gz | Fastqsanger.gz | |||
| SRR21907600_1.fastq.gz | Fastqsanger.gz | |||
| SRR21907600_2.fastq.gz | Fastqsanger.gz |
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Project description:<p>Residues from ancient artifacts can help identify which plant species were used for their psychoactive properties, providing important information regarding the deep-time co-evolutionary relationship between plants and humans. However, relying on the presence or absence of one or several biomarkers has limited the ability to confidently connect residues to particular plants. We describe a comprehensive metabolomics-based approach that can distinguish closely related species and provide greater confidence in species use determinations. An approximately 1430-year-old pipe from central Washington State not only contained nicotine, but also had strong evidence for the smoking of <em>Nicotiana quadrivalvis</em> and <em>Rhus glabra</em>, as opposed to several other species in this pre-contact pipe. Analysis of a post-contact pipe suggested use of different plants, including the introduced trade tobacco, <em>Nicotiana rustica</em>. Ancient residue metabolomics provides a new frontier in archaeo-chemistry, with greater precision to investigate the evolution of drug use and similar plant-human co-evolutionary dynamics.</p>
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Project description:Changes in gene expression are thought to underlie many of the phenotypic differences between species. However, large-scale analyses of gene expression evolution were until recently prevented by technological limitations. Here we report the sequencing of polyadenylated RNA from six organs across ten species that represent all major mammalian lineages (placentals, marsupials and monotremes) and birds (the evolutionary outgroup), with the goal of understanding the dynamics of mammalian transcriptome evolution. We show that the rate of gene expression evolution varies among organs, lineages and chromosomes, owing to differences in selective pressures: transcriptome change was slow in nervous tissues and rapid in testes, slower in rodents than in apes and monotremes, and rapid for the X chromosome right after its formation. Although gene expression evolution in mammals was strongly shaped by purifying selection, we identify numerous potentially selectively driven expression switches, which occurred at different rates across lineages and tissues and which probably contributed to the specific organ biology of various mammals. Our transcriptome data provide a valuable resource for functional and evolutionary analyses of mammalian genomes. To study mammalian transcriptome evolution at high resolution, we generated RNA-Seq data (∼3.2 billion Illumina Genome Analyser IIx reads of 76 base pairs) for the polyadenylated RNA fraction of brain (cerebral cortex or whole brain without cerebellum), cerebellum, heart, kidney, liver and testis (usually from one male and one female per somatic tissue and two males for testis) from nine mammalian species: placental mammals (great apes, including humans; rhesus macaque; mouse), marsupials (gray short-tailed opossum) and monotremes (platypus). Corresponding data (∼0.3 billion reads) were generated for a bird (red jungle fowl, a non-domesticated chicken) and used as an evolutionary outgroup.
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Project description:The purpose of this microarray experiment was to validate the Del-Mar 14K Chicken Integrated Systems Microarray for different chicken tissues and to determine the utility of this chicken cDNA microarray for other closely related and more distant avian species. The Del-Mar 14 K array was constructed from cDNAs amplified from EST clones sequenced from five normalized chicken cDNA libraries derived from neuroendocrine (5,929), abdominal fat (4,800), liver (2,635), skeletal muscle (2,398), reproductive tract (2,008), 387 long (70mer) oligonucleotides and 72 quality control spots. The array contains 17,770 cDNA clones, where protein matches were found by BlastX analysis for 68% of chicken contigs and 46% of singleton sequences represented on the array. A reference RNA design was used for the hybridization of total RNA from four chicken tissues (liver, abdominal fat, breast muscle and hypothalamus) and the cross-species hybridization (CSH) of total RNA from tissue from birds representing four orders of the Class Aves [Galliformes (chicken, Coturnix quail and domestic turkey), Anseriformes (Peking duck), Falconiformes (American kestrel) and Passeriformes (American tree sparrow)]. A reference RNA pool was made from an equal amount of high-quality total RNA extracted from chicken liver, abdominal fat, breast muscle and hypothalamus. Each of the 43 microarrays was co-hybridized with Cy3-labeled cDNA targets from one of the avian tissue samples and Cy5-labled cDNA targets from the reference chicken RNA pool. Loess-normalized data were used to determine the number of cDNAs expressed in chicken tissues and the number of genes (cDNAs) detectable by cross-hybridization with various avian tissue samples. The Cy5-labeled reference samples were used to determine the coefficient of variation across the 43 microarrays. This study shows a remarkably high level of cross hybridization of Cy3-labeled cDNA targets from a wide range of avian species to the Del-Mar 14K microarray, where 38 to 62% of the cDNA probes on the chicken array (genes) were detectable. Keywords: Transcriptional profiling, Del-Mar 14K Chicken Integrated Systems Microarray validation, multi-tissues, cross-species hybridization, class Aves
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