Transciptional response to acute thermal stress in Chinook salmon
ABSTRACT: Thermal stress is a serious and growing challenge facing Chinook salmon (Oncorhynchus tshawytscha) living in the southern portion of their native range. River alterations have increased the likelihood that juveniles will be exposed to warm water temperatures during their freshwater life stage, which can negatively impact survival, growth, and development and poses a threat to dwindling salmon populations. In order to better understand how acute thermal stress affects the biology of salmon, we performed a transcriptional analysis of gill tissue from unacclimated Chinook juveniles exposed to short periods at water temperatures ranging from ideal to potentially lethal. Reverse transcribed RNA libraries were sequenced on the Illumina HiSeq2000 platform and a de novo reference transcriptome was created. Differentially expressed transcripts were annotated using Blast2GO and relevant gene clusters were identified. Fifty-five fish were randomly assigned to one of five treatment groups and were allowed to acclimate at 12 degrees C in the experimental chambers overnight. Treatments consisted of a three-hour water bath at 15 degrees C, 18 degrees C, 21 degrees C or 25 degrees C degrees, followed by one hour of recovery at 12 degrees C. The experimental chambers were moved to water baths held at a constant temperature, facilitating very rapid change in the temperature experienced by the fish. Controls were handled identically to the other four treatment groups, but remained at 12 degrees C. Three replicates were performed on consecutive days. RNA from the 11 individuals in each treatment group were proportionally pooled and used to create 15 illumina libraries.
Project description:Southern California (USA) populations of the intertidal marine snail Chlorostoma (formerly Tegula) funebralis are generally exposed to higher air and water temperatures than northern California populations. Previous studies have shown that southern populations are more tolerant of heat stress than northern populations. To assess the potential role of gene regulation in these regional differences, we examined transcriptome responses to thermal stress in two southern and two northern populations of C. funebralis. Snails from the four populations were acclimated to a common lab environment, exposed to a heat stress representative of natural low tide conditions, and then analyzed using RNA-Seq to characterize changes in gene expression associated with stress and differences in expression across geographic regions. Changes in expression following stress were dominated by genes involved in apoptosis, the inflammatory response, response to mis and unfolded proteins, and ubiquitination of proteins. Heat shock proteins (Hsps) were up-regulated in both northern and southern populations. However, while the magnitude of the response was significantly greater in northern populations for the majority of Hsp70s, the southern populations showed a greater up-regulation for roughly half of the Hsp40s, which are co-chaperones for Hsp70s. Differential expression analysis of the control versus treatment genes in the northern and southern populations respectively revealed that 56 genes, many involved in the inflammation and immune response, responded to heat stress only in the northern populations. Moreover, several of the molecular chaperones and antioxidant genes that were not differentially expressed in the southern populations instead showed higher constitutive expression under control conditions compared to the northern populations. The expression levels of some of these constitutive genes such as superoxide dismutase were also found to positively correlate with survival following heat stress. This suggests that expression of these genes has evolved a degree of “frontloading” that may contribute to the higher thermal tolerance of southern populations. mRNA profiles of northern and southern California heat-stressed and control C. funebralis were generated by 100bp paired end sequencing, in duplicate, using Illumina HiSeq2000.
Project description:Plant growth promoting bacteria (PGPB) might be an alternative to increase nitrogenous use efficiency (NUE) in important crops such wheat. Azospirillum brasilense is one of the most promising PGPB and wheat roots colonized by Azospirillum brasilense is a good model to investigate the molecular basis of plant-PGPB interaction including improvement in plant-NUE promoted by PGPB. An RNA-seq transcriptional analysis of Triticum aestivum roots was carried out in two independent samples (biological replicates) of each treatment (PGPB-colonized or non-inoculated), yielding a total of 4 sequencing libraries, which were designated CWR1 and CWR2 libraries (colonized roots) and N-IWR1 and N-IWR2 (non-inoculated roots).
Project description:Mammals differ more than hundred fold in maximum lifespan, which can be altered in either direction during evolution, but the molecular basis for natural changes in longevity is not understood. Divergent evolution of mammals also led to extensive changes in gene expression within and between lineages. To understand the relationship between lifespan and variation in gene expression, we carried out RNA-seq-based gene expression analyses of liver, kidney and brain of 33 diverse species of mammals. Our analysis uncovered parallel evolution of gene expression and lifespan, as well as the associated life history traits, and identified the processes and pathways involved. These findings provide direct insights into how Nature reversibly adjusts lifespan and other traits during adaptive radiation of lineages. RNA-seq gene expression profiling in normal liver, kidney and brain of 33 mammalian species.
Project description:Spatial regulation analysis across multiple condition comparisons revealed distinct patterns of gene expression. We combined these transcriptome data with spatial CNS data to produce the spatio-transcripto map of the ganglia chain. The Hirudo Medicinalis set of transcripts generated here provides a resource for gene discovery and gene regulation within the nervous system. In addition, the strategy for de novo assembly of transcriptome data presented here may be helpful in other similar transcriptome studies. Examination of 3 different ganglia in 3 different leeches.
Project description:In this study, we performed de novo transcriptome assembly for L. japonica, representing transcripts from nine different tissues. A total of 22Gbps clean RNA-seq reads from nine tissues of L. japonica were used, resulting in 243,185 unigenes, with 99,938 unigenes annotated based on homology search using blastx against NCBI-nr protein database. Unsupervised principal component analysis and correlation studies using transcripts expression data from all nine tissues of L. japonica showed relationships between tissues explaining their association at different developmental stages. Homologs for all genes associated with chlorogenic acid, luteolin, and secoiridoid biosynthesis pathways were identified in the L. japonica transcriptome assembly. Expression of unigenes associated with chlorogenic acid were enriched in stem and leaf-2, unigenes from luteolin were enriched in stem and flowers, while unigenes from secoiridoid metabolic pathways were enriched in leaf-1 and shoot apex. Our results showed that different tissues of L. japonica are enriched with sets of unigenes associated with a specific pharmaceutically important metabolic pathways, and therefore, possess unique medicinal properties. Present study will serve as a resource for future attempts for functional characterization of enzyme coding genes within key metabolic processes. De novo transcriptome assembly and characterization, and transcriptome profiling for nine tissues of Lonicera japonica
Project description:Here, we performed deep transcriptome sequencing for the aerial-tissues and the roots of S. japonica, generating over 2 billion raw reads with an average length of 101 nt by using an Illumina paired-end sequencing by HiSeq2000 platform. Using a combined approach of three popular assemblers, de novo transcriptome assembly for S. japonica was obtained, yielding in 81,729 unigenes with an average length as 884bps and N50-value as 1,452bps, with 46,963 unigenes being annotated based on the sequence similarity against NCBI-nr protein database. Transcriptome profiling of the aerial-tissues and the roots of Swertia japonica
Project description:Here, we develop a systems-level approach leveraging powerful next generation sequencing, proteomics and phenotypic studies to rapidly obtain an integrated view of lignocellulose degradation in the earliest free living fungi RNA-seq of Piromyces grown on Glucose, Cellulose, Cellulobiose, Avicel, Filter paper, and time-course of transient glucose pulse (catabolite repression). N>=2