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31 results for “ecological transcriptomics”
The utility of reptile blood transcriptomes in molecular ecology
<p>Reptiles and other non-mammalian vertebrates have transcriptionally active nucleated red blood cells. If blood transcriptomes can provide quantitative data to address questions relevant to molecular ecology, this could circumvent the need to euthanize animals to assay tissues. This would allow longitudinal sampling of animals' responses to treatments, as well as sampling of protected taxa. We developed and annotated blood transcriptomes from six reptile species. We found on average 25,000 proteins are being transcribed in the blood, and there is a CORE group of 9,282 orthogroups that are found in at least four of six species. In comparison to liver transcriptomes from the same taxa, approximately two-thirds of the orthogroups were found in both blood and liver; and a similar percentage of ecologically relevant gene groups (insulin and insulin-like signaling, electron transport chain, oxidative stress, glucocorticoid receptors) were found transcribed in both blood and liver. As a resource, we provide a user-friendly database of gene ids identified in each blood transcriptome. Although, on average 37% of reads mapped to hemoglobin, importantly, the majority of non-hemoglobin transcripts had sufficient depth (e.g., 97% at >10 reads) to be included in differential gene expression analysis. Thus, we demonstrate that RNAseq blood transcriptomes from a very small blood sample (<10 ul) is a minimally invasive option in non-mammalian vertebrates for quantifying expression of a large number of ecologically relevant genes longitudinally and in protected populations.</p>
Data from: Genomic and transcriptomic analyses reveal polygenic architecture for ecologically-important functional traits in aspen (Populus tremuloides Michx.)
<p>Intraspecific genetic variation in foundation species such as aspen (<em>Populus</em> <em>tremuloides</em> Michx.) shapes their impact on forest structure and function. Identifying genes underlying ecologically important traits is key to understanding that impact. Previous studies, using single-locus genome-wide association (GWA) analyses to identify candidate genes, have identified fewer genes than anticipated for highly heritable quantitative traits. Mounting evidence suggests that polygenic control of quantitative traits is largely responsible for this "missing heritability" phenomenon. Our research characterized the genetic architecture of 30 ecologically important traits using a common garden of aspen through genomic and transcriptomic analyses. A multilocus association model revealed that most traits displayed a highly polygenic architecture, with most variation explained by loci with small effects (likely below the detection levels of single-locus GWA methods). Consistent with a polygenic architecture, our single-locus GWA analyses found only 38 significant SNPs in 22 genes across 15 traits. Next, we used differential expression analysis on a subset of aspen genets with divergent concentrations of salicinoid phenolic glycosides (key defense traits). This complementary method to traditional GWA discovered 1,243 differentially expressed genes for a polygenic trait. Soft clustering analysis revealed three gene clusters (241 candidate genes) involved in secondary metabolite biosynthesis and regulation. Our work reveals that ecologically important traits governing higher-order community- and ecosystem-level attributes of a foundation forest tree species have complex underlying genetic structures and will require methods beyond traditional GWA analyses to unravel.</p>
The utility of reptile blood transcriptomes in molecular ecology
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Data from: Genomic and transcriptomic analyses reveal polygenic architecture for ecologically-important functional traits in aspen (Populus tremuloides Michx.)
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Data from: Characterization of the transcriptome and gene expression of four different tissues in the ecologically relevant sea urchin Arbacia lixula using RNA-seq
The sea urchin Arbacia lixula is a keystone species in Mediterranean ecosystems that drive landscape changes in littoral communities. However, genomic information available for the whole order Arbacioida is very limited. Using RNA-seq techniques, we have characterized the transcriptome of four different tissue types in A. lixula: the 'somatic' tissues (coelomocytes and digestive tissue) and the 'reproductive' tissues (ovary and testis), from two replicated cDNA libraries for each sample. Additionally, we performed a de novo assembly to build the 'reference' transcriptome, pooling reads of the four tissues, to analyse the differential expression (DE) in pairwise comparisons between tissues. The complete de novo assembly yielded 186 084 transcripts, with a sequence size limit of 100 nt, being 31% of them spliced isoforms. Approximately 21% of the transcripts had blast hits against proteins of metazoans (E < 10−5), being less than 2.2% functionally annotated. Between coelomocytes and digestive, 30 794 transcripts showed DE (~11.8% of them with blast hit), and 19 567 transcripts did so between testis and ovary (~28.5% of them with blast hit). Major GO-term categories upregulated in somatic tissues were those related to muscle contraction and energy generation in digestive, and lipid metabolism associated with immune response in coelomocytes. Between reproductive tissues, the major upregulated GO categories were related to energy generation in testis, and negative regulation of nucleotide metabolism in ovary. We particularly screened for a collection of target genes in each tissue because of their relevance for further studies on evolution and adaptation of echinoids.
Data from: The plover neurotranscriptome assembly: transcriptomic analysis in an ecological model species without a reference genome
We assembled a de novo transcriptome of short-read Illumina RNA-Seq data generated from telencephalon and diencephalon tissue samples from the Kentish plover, Charadrius alexandrinus. This is a species of considerable interest in behavioural ecology for its highly variable mating system and parental behaviour, but it lacks genomic resources and is evolutionarily distant from the few available avian draft genome sequences. We assembled and identified over 21 000 transcript contigs with significant expression in our samples, showing high homology to exonic sequences in avian draft genomes. From these, we identified >31 000 high-quality SNPs and > 2500 simple sequence repeats (SSRs). We also analysed expression patterns in our data to identify potential candidate genes related to differences in male and female behaviour, identifying over 200 nonoverlapping putative autosomal transcripts that show significant expression differences between males and females. Gene ontology analysis revealed that female-biased transcripts were significantly enriched for cerebral functions related to learning, cognition and memory, and male-biased transcripts were mostly enriched for terms related to neural function such as neuron projection and synapses. This data set provides one of the first de novo transcriptome assemblies from non-normalized short-read next-generation data and outlines an effective strategy for measuring sequence and expression variability simultaneously without the aid of a reference genome.
Data from: Comparative ecological transcriptomics and the contribution of gene expression to the evolutionary potential of a threatened fish
Understanding whether small populations with low genetic diversity can respond to rapid environmental change via phenotypic plasticity is an outstanding research question in biology. RNA sequencing (RNA-seq) has recently provided the opportunity to examine variation in gene expression, a surrogate for phenotypic variation, in non-model species. We used a comparative RNA-seq approach to assess expression variation within and among adaptively divergent populations of a threatened freshwater fish, Nannoperca australis, found across a steep hydroclimatic gradient in the Murray-Darling Basin, Australia. These populations evolved under contrasting selective environments (e.g. dry/hot lowland; wet/cold upland) and represent opposite ends of the species' spectrum of genetic diversity and population size. We tested the hypothesis that environmental variation among isolated populations has driven the evolution of divergent expression at ecologically important genes using differential expression (DE) analysis and an ANOVA-based comparative phylogenetic expression variance and evolution model framework based on 27,425 de novo assembled transcripts. Additionally, we tested whether gene expression variance within-populations was correlated with levels of standing genetic diversity. We identified 290 DE candidate transcripts, 33 transcripts with evidence for high expression plasticity, and 50 candidates for divergent selection on gene expression after accounting for phylogenetic structure. Variance in gene expression appeared unrelated to levels of genetic diversity. Functional annotation of the candidate transcripts revealed variation in water quality is an important factor influencing expression variation for N. australis. Our findings suggest that gene expression variation can contribute to the evolutionary potential of small populations.
Data from: Transcriptomics and in vivo tests reveal novel mechanisms underlying endocrine disruption in an ecological sentinel, Nucella lapillus
Anthropogenic endocrine disruptors now contaminate all environments globally, with concomitant deleterious effects across diverse taxa. While most studies on endocrine disruption (ED) have focused on vertebrates, the superimposition of male sexual characteristics in the female dogwhelk, Nucella lapillus (imposex), caused by organotins, provides one of the most clearcut ecological examples of anthropogenically induced ED in aquatic ecosystems. To identify the underpinning mechanisms of imposex for this 'nonmodel' species, we combined Roche 454 pyrosequencing with custom oligoarray fabrication inexpensively to both generate gene models and identify those responding to chronic tributyltin (TBT) treatment. The results supported the involvement of steroid, neuroendocrine peptide hormone dysfunction and retinoid mechanisms, but suggested additionally the involvement of putative peroxisome proliferator–activated receptor (PPAR) pathways. Application of rosiglitazone, a well-known vertebrate PPARγ ligand, to dogwhelks induced imposex in the absence of TBT. Thus, while TBT-induced imposex is linked to the induction of many genes and has a complex phenotype, it is likely also to be driven by PPAR-responsive pathways, hitherto not described in invertebrates. Our findings provide further evidence for a common signalling pathway between invertebrate and vertebrate species that has previously been overlooked in the study of endocrine disruption.
Data from: De novo assembly of the transcriptome of an invasive snail and its multiple ecological applications
Studying how invasive species respond to environmental stress at the molecular level can help us assess their impact and predict their range expansion. Development of markers of genetic polymorphism can help us reconstruct their invasive route. However, to conduct such studies requires the presence of substantial amount of genomic resources. This study aimed to generate and characterize genomic resources using high throughput transcriptome sequencing for Pomacea canaliculata, a non-model gastropod indigenous to Argentina that has invaded Asia, Hawaii and southern United States. De novo assembly of the transcriptome resulted in 128,436 unigenes with an average length of 419 bp (range: 150 to 8,556 bp). Many of the unigenes (2,439) contained transposable elements, showing the existence of a source of genetic variability in response to stressful conditions. A total of 3,196 microsatellites were detected in the transcriptome; among 20 of the randomly tested microsatellites, 10 were validated to exhibit polymorphism. A total of 15,412 single-nucleotide polymorphisms (SNPs) were detected in the ORFs. LC-MS/MS analysis of the proteome of juveniles revealed 878 proteins, of which many are stress-related. This study has demonstrated the great potential of high throughput DNA sequencing for rapid development of genomic resources for a non-model organism. Such resources can facilitate various molecular ecological studies, such as stress physiology and range expansion.
Data from: Transcriptome characterization and screening of molecular markers in ecologically important Himalayan species (Rhododendron arboreum)
Rhododendron arboreum is an ecologically prominent species, which also lends commercial and medicinal benefits in the form of palatable juices and useful herbal drugs. Local abundance and survival of the species under a highly fluctuating climate make it an ideal model for genetic structure and functional analysis. However, a lack of genomic data has hampered additional research. In the present study, cDNA libraries from floral and foliar tissues of the species were sequenced to provide a foundation for understanding the functional aspects of the genome and to construct an enriched repository that will promote genomics studies in the genera. Illumina's platform facilitated the generation of ∼100 million high-quality paired-end reads. De novo assembly, clustering, and filtering out of shorter transcripts predicted 113 167 non-redundant transcripts with an average length of 1164.6 bases. Of these, 71 961 transcripts were categorized based on functional annotations in the Gene Ontology database, whereby 5710 were grouped into 141 pathways and 23 746 encoded for different transcription factors. Transcriptome screening further identified 35 419 microsatellite regions, of which, 43 polymorphic loci were characterized on 30 genotypes. Seven hundred and nineteen transcripts had 811 high-quality single-nucleotide polymorphic variants with a minimum coverage of 10, a total score of 20, and SNP% of 50.
Data from: The plover neurotranscriptome assembly: transcriptomic analysis in an ecological model species without a reference genome
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Data from: Characterization of the transcriptome and gene expression of four different tissues in the ecologically relevant sea urchin Arbacia lixula using RNA-seq
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Data from: Transcriptome characterization and screening of molecular markers in ecologically important Himalayan species (Rhododendron arboreum)
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Data from: "De novo transcriptome assembly and polymorphism detection in ecological important widely distributed Neotropical toads from the Rhinella marina species complex (Anura: Bufonidade)" in Genomic Resources Notes Accepted 1 August 2014-30 September 2014
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Data from: Comparative ecological transcriptomics and the contribution of gene expression to the evolutionary potential of a threatened fish
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Data from: Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations
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Data from: De novo assembly of the transcriptome of an invasive snail and its multiple ecological applications
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Data from: Transcriptomics and in vivo tests reveal novel mechanisms underlying endocrine disruption in an ecological sentinel, Nucella lapillus
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Data from: Transcriptome sequencing and microarray development for the woodrat (Neotoma spp.): custom genetic tools for exploring herbivore ecology
Massively parallel sequencing has enabled the creation of novel, in-depth genetic tools for nonmodel, ecologically important organisms. We present the de novo transcriptome sequencing, analysis and microarray development for a vertebrate herbivore, the woodrat (Neotoma spp.). This genus is of ecological and evolutionary interest, especially with respect to ingestion and hepatic metabolism of potentially toxic plant secondary compounds. We generated a liver transcriptome of the desert woodrat (Neotoma lepida) using the Roche 454 platform. The assembled contigs were well annotated using rodent references (99.7% annotation), and biotransformation function was reflected in the gene ontology. The transcriptome was used to develop a custom microarray (eArray, Agilent). We tested the microarray with three experiments: one across species with similar habitat (thus, dietary) niches, one across species with different habitat niches and one across populations within a species. The resulting one-colour arrays had high technical and biological quality. Probes designed from the woodrat transcriptome performed significantly better than functionally similar probes from the Norway rat (Rattus norvegicus). There were a multitude of expression differences across the woodrat treatments, many of which related to biotransformation processes and activities. The pattern and function of the differences indicate shared ecological pressures, and not merely phylogenetic distance, play an important role in shaping gene expression profiles of woodrat species and populations. The quality and functionality of the woodrat transcriptome and custom microarray suggest these tools will be valuable for expanding the scope of herbivore biology, as well as the exploration of conceptual topics in ecology.
Data from: Transcriptome resources for the perennial sunflower Helianthus maximiliani obtained from ecologically divergent populations
Next generation sequencing (NGS) technologies provide a rapid means to generate genomic resources for species exhibiting interesting ecological and evolutionary variation but for which such resources are scant or nonexistent. In the current report, we utilize 454 pyrosequencing to obtain transcriptome information for multiple individuals and tissue types from geographically disparate and ecologically differentiated populations of the perennial sunflower species Helianthus maximiliani. A total of 850,275 raw reads were obtained averaging 355 bp in length. Reads were assembled, post processing, into 16,681 unique contigs with an N50 of 898 bp and a total length of 13.6 Mb. A majority (67%) of these contigs were annotated based on comparison to the Arabidopsis thaliana genome (TAIR10). Contigs were identified that exhibit high similarity to genes associated with natural variation in flowering time and freezing tolerance in other plant species and will facilitate future studies aimed at elucidating the molecular basis of clinal life history variation and adaptive differentiation in H. maximiliani. Large numbers of gene-associated simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) also were identified that can be deployed in mapping and population genomic analyses.
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Allen Brain Atlas
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OpenNeuro
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