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PROVIDER: PRJNA580023 | ENA |
REPOSITORIES: ENA
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Project description:Although the importance of host plant chemistry in plant-insect interactions is widely accepted, the genetic basis of adaptation to host plants is poorly understood. Here, we investigate transcriptional changes associated with a host plant shift in Drosophila mettleri. While D. mettleri is distributed mainly throughout the Sonoran Desert where it specializes on columnar cacti (Carnegiea gigantea and Pachycereus pringleii), a population on Santa Catalina Island has shifted to coastal prickly pear cactus (Opuntia littoralis). We compared gene expression of larvae from the Sonoran Desert and Santa Catalina Island when reared on saguaro (C. gigantea), coastal prickly pear, and laboratory food. Consistent with expectations based on the complexity and toxicity of cactus relative to laboratory food, within population comparisons between larvae reared on these food sources revealed transcriptional differences in detoxification and other metabolic pathways. The majority of transcriptional differences between populations on the cactus hosts were independent of the rearing environment, and included a disproportionate number of genes involved in processes relevant to host plant adaptation (e.g. detoxification, central metabolism, and chemosensory pathways). Comparisons of transcriptional reaction norms between the two populations revealed extensive shared plasticity that likely allowed colonization of coastal prickly pear on Santa Catalina Island. We also found that while plasticity may have facilitated subsequent adaptive divergence in gene expression between populations, the majority of genes that differed in expression on the novel host were not transcriptionally plastic in the presumed ancestral state.
2015-09-03 | GSE71110 | GEO
Project description:Although the importance of host plant chemistry in plant-insect interactions is widely accepted, the genetic basis of adaptation to host plants is poorly understood. Here, we investigate transcriptional changes associated with a host plant shift in Drosophila mettleri. While D. mettleri is distributed mainly throughout the Sonoran Desert where it specializes on columnar cacti (Carnegiea gigantea and Pachycereus pringleii), a population on Santa Catalina Island has shifted to coastal prickly pear cactus (Opuntia littoralis). We compared gene expression of larvae from the Sonoran Desert and Santa Catalina Island when reared on saguaro (C. gigantea), coastal prickly pear, and laboratory food. Consistent with expectations based on the complexity and toxicity of cactus relative to laboratory food, within population comparisons between larvae reared on these food sources revealed transcriptional differences in detoxification and other metabolic pathways. The majority of transcriptional differences between populations on the cactus hosts were independent of the rearing environment, and included a disproportionate number of genes involved in processes relevant to host plant adaptation (e.g. detoxification, central metabolism, and chemosensory pathways). Comparisons of transcriptional reaction norms between the two populations revealed extensive shared plasticity that likely allowed colonization of coastal prickly pear on Santa Catalina Island. We also found that while plasticity may have facilitated subsequent adaptive divergence in gene expression between populations, the majority of genes that differed in expression on the novel host were not transcriptionally plastic in the presumed ancestral state. mRNA profiles of third instar larvae from two different populations reared on three food types was sequenced on two lanes of an Illumina HiSeq 2000 Please note that the de novo assembly gives names to transcripts with the following convention: compXXX_cX_seqX. The first two identifiers (compXX_cX) are equivalent to a gene while the 'seq' identifier might refer to different isoforms or splice variants, etc. Therefore, for example, a gene might be comp123_c0, and this could have multiple sequences corresponding to different isoforms or splice variants. Since the analysis was carried out at the gene level, the program internally merged the multiple sequences together for each gene to generate the count matrix (AllGenesint.counts.matrix.txt) (i.e. it only includes comp123_c0), while the file from the assembly (i.e. Trinity.fasta) also include the individual sequences with the 'seq' identifier.
2015-09-03 | E-GEOD-71110 | biostudies-arrayexpress
Project description:Gray fox (Urocyon cinereoargenteus) and island fox (Urocyon littoralis) Raw sequence reads
| PRJNA478450 | ENA
Project description:ChIP-Seq study in human MCF7 and HEPG2 cells using antibodies against CTCF (Millipore, 07-729), STAG1 (abcam, ab4457), RAD21 (abcam, ab992), ERa (santa cruz, sc-543), CEBPa (santa cruz, sc-9314) ArrayExpress Release Date: 2010-05-12 Publication Title: A CTCF-independent role for cohesin in tissue-specific transcription Publication Author List: Dominic Schmidt, Petra C. Schwalie, Caryn S. Ross-Innes, Antoni Hurtado, Gordon D. Brown, Jason S. Carroll, Paul Flicek and Duncan T. Odom Person Roles: submitter Person Last Name: Schwalie Person First Name: Petra Catalina Person Email: schwalie@ebi.ac.uk Person Address: Person Affiliation: EBI
2011-02-05 | GSE25021 | GEO
Project description:Local adaptation can play a fundamental role in the isolation of populations. While less well-studied than differentiation in sequence variation, changes in transcriptional variation during speciation also are fundamental to the evolutionary process. Drosophila mojavensis offers an unprecedented opportunity to examine the role of transcriptional differentiation in local adaptation. Drosophila mojavensis is a cactophilic fly composed of four ecologically distinct subspecies that inhabit the deserts of western North America. Each of the four subspecies utilizes necrotic tissue of different cactus host species characterized by distinct chemical profiles. The subspecies in Baja California, Mexico uses Stenocereus gummosus (Agria), in mainland Sonora it uses S. thurberi (Organ Pipe), in the Mojave Desert the host is Ferocactus cylindraceus (Red Barrel) and in Santa Catalina Island, USA, Opuntia littoralis (Prickly Pear) is the host. In this chapter we examine how the adaptation to the different environmental conditions across the four subspecies have shaped their transcriptional profiles. Using complete D. mojavensis genome microarrays we examined the transcriptome of third instar larvae from all four subspecies reared in standard laboratory media free of necrotic cactus-derived compounds. This experimental strategy focused on differences between constitutively expressed genes and not genes induced by necrotic cactus-derived compounds. The subspecies exhibited significant differential expression of genes that likely underlie the adaptation to different cactus hosts, such as detoxification genes (Glutathione S-transferases, Cytochrome P450s and UDP-Glycosyltransferases) and chemosensory genes (Odorant Receptors, Gustatory Receptors and Odorant Binding Proteins). Dataset from Matzkin, L. M. and Markow, T.A. Transcriptional differentiation across the four cactus host races of Drosophila mojavensis. In Speciation: Natural Processes, Genetics and Biodiversity. Edited by Michalak, P. Nova Science Publishers, Inc.
2015-01-01 | GSE41155 | GEO