Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

De novo transcriptome assembly of the tree swallow (Tachycineta bicolor): tissue-specific expression profiles and positive selection analysis

ABSTRACT: Tree swallows (Tachycineta bicolor) are one of the most commonly studied wild birds in North America. They have advanced numerous research areas, including life history, physiology, and organismal responses to global change; however, molecular resources are scarce. Thus, we generated a transcriptome for the tree swallow using six tissues (brain, blood, ovary, spleen, liver, and muscle) collected from breeding females. We de novo assembled 207,747 transcripts, which we aligned to 14,717 protein-coding genes. We then characterized tissue-specific expression profiles and applied this transcriptome to two fundamental questions in evolutionary biology and endocrinology. First, we analyzed 3,015 single-copy orthologs and identified 46 genes under positive selection in the tree swallow lineage, including those with putative links to adaptations in this species. Second, we analyzed tissue-specific expression patterns of genes involved in sex steroidogenesis and processing. Enzymes capable of synthesizing these behaviorally relevant hormones were largely limited to the ovary, whereas steroid binding genes were found in nearly all other tissues, highlighting the potential for local regulation of sex steroid-mediated traits. These analyses provide new insights into potential sources of phenotypic variation in a free-living female bird, and in doing so, further advance the utility of this system for biologists across disciplines.

ORGANISM(S): Tachycineta bicolor

PROVIDER: GSE126210 | GEO | 2019/11/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

How experimental competition changes ovarian gene activity in free living birds: implications for steroidogenesis, maternal effects, and beyond

Project description:The ovary plays an important role in mediating both a female’s response to her own social environment and communicating it to her developing offspring. However, we know little about the underlying genomic mechanisms that facilitate social responsiveness in the ovary. This issue is further complicated by mixed support linking female competition to ovarian production of testosterone, the often-evoked mechanism mediating both social aggression and maternal effects. Here, we experimentally generated social competition among wild, cavity-nesting female birds (tree swallows, Tachycineta bicolor). After territorial settlement, we reduced the availability of key breeding resources (i.e., nest boxes), generating heightened competition; within 24hr we reversed the manipulation, causing aggressive interactions to subside. We measured transcriptomic responses in the ovary during the peak of competition and 48hr after it ended, along with date-matched controls. Network analyses indicated that competing females experienced an immediate and temporary decrease in the expression of genes involved in the early stages of steroidogenesis; however, two days after competition had ended, there was a marked increase in the expression of genes involved in the final stages of sex steroid biosynthesis, including HSD17B1. In addition, ovaries that had been socially primed also displayed altered activity in gene networks related to the cell cycle, muscle performance, and extracellular matrix organization, which collectively point to social effects on future reproduction. Altogether, these findings show how the social environment shapes ovarian processes associated with both social behavior and adaptive transgenerational plasticity.

2021-10-03 | GSE184993 | GEO

Expression profiling of in vitro Poplar roots during early interaction with the ectomycorrhizal fungus Laccaria bicolor

Project description:The early phase of the interaction between tree roots and ectomycorrhizal (ECM) fungi, prior to symbiosis establishment, is accompanied by a stimulation of lateral root (LR) development. We set out to identify gene networks that regulate LR development during the early signal exchanges between Populus tremula x Populus alba (hereafter called poplar) and the ECM fungus Laccaria bicolor. A sandwich culture system was developed in order to bring plant and fungus into an indirect contact, which permits signal molecule exchange and LR stimulation (emergence after 4-5 days of contact) but prohibits root colonization. A NimbleGen full genome poplar oligo-array was used to investigate transcript profiles at three days of indirect poplar/L. bicolor contact, referring to the time point of LR initiation in response to the fungus.

2009-11-01 | GSE16662 | GEO

Gene expression changes in Meliniomyces bicolor- Vaccinium myrtillus mycorrhizal roots compared to Meliniomyces bicolor free-living mycelium

Project description:Illumina HiSeq technology was used to generate mRNA profiles from Meliniomyces bicolor mycorrhizal roots compared to free-living mycelium . Mycorrhizal roots and control mycelium were harvested after 113 days and used for RNA extraction. Reads of 150bp were generated and aligned to Meliniomyces bicolor transcripts (https://genome.jgi.doe.gov/Melbi2/Melbi2.home.html) using CLC Genomics Workbench 8.

2018-01-01 | GSE107845 | GEO

Mycorrhizal Metabolome: L. bicolor :: P. trichocapra

Project description:Mycorrhizae, symbiotic interactions between soil fungi and tree roots, are ubiquitous in terrestrial ecosystems. The fungi contribute phosphorous, nitrogen and mobilized nutrients from organic matter in the soil and in return the fungus receives photosynthetically-derived carbohydrates. This union of plant and fungal metabolisms is the mycorrhizal metabolome. Understanding this symbiotic relationship at a molecular level provides important contributions to the understanding of forest ecosystems and global carbon cycling. We generated next generation short-read transcriptomic sequencing data from fully-formed ectomycorrhizae between Laccaria bicolor and aspen (Populus tremuloides) roots. The transcriptomic data was used to identify statistically significantly expressed gene models using a bootstrap-style approach, and these expressed genes were mapped to specific metabolic pathways. Integration of expressed genes that code for metabolic enzymes and the set of expressed membrane transporters generates a predictive model of the ectomycorrhizal metabolome. Results indicate the specific compounds glycine, glutamate, and allantoin are synthesized by L. bicolor and that these compounds or their metabolites may be used for the benefit of aspen in exchange for the photosynthetically-derived sugars fructose and glucose.The analysis illustrates an approach to generate testable biological hypotheses to investigate the complex molecular interactions that drive ectomycorrhizal symbiosis. These models are consistent with experimental environmental data and provide insight into the molecular exchange processes for organisms in this complex ecosystem. The method used here for predicting metabolomic models of mycorrhizal systems from deep RNA sequencing data can be generalized and is broadly applicable to transcriptomic data derived from complex systems. Fully formed L.bicolor::P.trichocapra mycorrhizae in duplicate

2011-03-25 | E-GEOD-28157 | biostudies-arrayexpress

Gene expression of Laccaria bicolor S238N free-living mycelium grown on different media

Project description:Transcript profiles of Laccaria bicolor S238N mycelium on various media were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, department of energy) Laccaria bicolor genome sequence version 1. One goal was to evaluate the effect of nutrient deprivation on the transcriptome of Laccaria bicolor.

2012-03-01 | GSE35556 | GEO

RNA-seq of Basidiomycete fungi Laccaria bicolor

Project description:We performed whole transcriptome sequencing of L. bicolor mycelium cultivated under normal and elevated vitamin C conditions.

2022-01-16 | GSE185548 | GEO

Sorghum bicolor and Setaria viridis PARE-seq

Project description:Parallel Analysis of RNA Ends (PARE) sequencing reads were generated to validate putative microRNAs and identify cleavage sites in Sorghum bicolor and Setaria viridis.

2020-05-19 | GSE150798 | GEO

Tissue specific expression data in Sorghum bicolor BTx623

Project description:This study used with RNA-Seq to examine the tissue specific expression data within sorghum plants for improving the Sorghum bicolor gene annotation. We examined the RNA from tissues (spikelet, seed and stem) in Sorghum bicolor (BTx623).Total RNAs form each tissues were extracted using SDS/phenol method followed by LiCl purification

2015-03-11 | E-MTAB-4273 | biostudies-arrayexpress

Transcriptome analyses of the Laccaria bicolor-Populus trichocarpa mycorrhiza development

Project description:Illumina GAIIx technology was used to generate mRNA profiles from the ectomycorrhizal fungi Laccaria bicolor colonizing roots of Populus trichocarpa. Samples were taken after two, four and 12 weeks of contact in order to identify mycorrhiza-regulated transcripts. 37bp reads were generated and aligned to the Populus trichocarpa (http://www.phytozome.net/poplar.php) and the Laccaria bicolor (http://genome.jgi-psf.org/Lacbi2/Lacbi2.home.html) reference genomes using CLC Genomics Workbench 6.

2014-02-08 | GSE54789 | GEO

Laccaria bicolor gene expression in different tissues and with different host trees

Project description:Laccaria bicolor transcript profiles of different tissues and mycorrhizal root tips from different host trees were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, department of energy) Laccaria bicolor genome sequence version 1. One goal was to compare gene expression profiles from ectomycorrhizal root tips with different host plants.

2011-12-15 | GSE32559 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data