Signatures of selection in the stickleback transcriptome.
Ontology highlight
ABSTRACT: Total RNA was extracted from liver tissues of lab-reared threespine stickleback. The dataset combines transcripts common to two experiments: first generation fish originating from the Baltic Sea near Helsinki (Finland) bred using a paternal half-sib design (E-MTAB-3098), and second generation fish originating from three different Fennoscandian populations bred from a full-sib design. Annotated R scripts defining the normalization procedures are available as additional files (see http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-3099). Additional files also include a metadata file (matrix.df.csv) to facilitate construction of design matrices used by the snm package.
Project description:Total RNA was extracted from liver tissues of lab-reared threespine stickleback. First generation fish originating from the Baltic Sea near Helsinki (Finland) were bred using a paternal half-sib design. At 6 months individuals were randomly assigned to either a treatment or control group: the temperature of treated fish (T) was raised 1oC per hour over the course of 6h to a final temperature of 23oC, then maintained for 1h at final temperature; control (C) fish were maintained at 17oC under similar holding conditions. Immediately following experimental (or sham) treatment, fish were euthanized by anaesthetic overdose. Liver tissues were immediately dissected and flash frozen in liquid nitrogen for subsequent RNA extraction. Annotated R scripts defining the normalization procedures are available as additional files (see http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-3098). Additional files also include a targets file to assist with reading raw data into R (Targs.txt), and a metadata file (matrix.df.csv) to facilitate construction of design matrices used by the M-bsnmM-b package.
Project description:This study compares the transcriptomes of wild and domesticated Atlantic salmon strains and their transcriptional response to acute stress. Microarray interrogations consisted of 48 hybridizations; 4 crosses (pure wild; Figgjo x Figgjo, pure domesticated; Mowi x Mowi and their reciprocal hybrids; Figgjo x Mowi, Mowi x Figgjo) x 2 conditions (stress and control) x 6 biological replicates and employed a custom 44k oligonucleotide microarray design.
Project description:This study compares the transcriptomes of wild (Figgjo) and domesticated (Mowi) Atlantic salmon embryos, employing a custom 44k oligonucleotide microarray to identify gene pathways perturbed between wild and domesticated strains and with the aid of heir reciprocal hybrids, to examine the heritability of differentially expressed genes.
Project description:Local adaptation and its underlying molecular basis has long been a key focus in evolutionary biology. There has recently been increased interest in the evolutionary role of plasticity and the molecular mechanisms underlying local adaptation. Using transcriptome analysis, we assessed differences in gene expression profiles for three brown trout (Salmo trutta) populations, one resident and two anadromous, experiencing different temperature regimes in the wild. The study was based on an F2 generation raised in a common garden setting. A previous study of the F1 generation revealed different reaction norms and significantly higher QST than FST among populations for two early life-history traits. In the present study we investigated if similar reaction norm patterns were present at the transcriptome level. Eggs from the three populations were incubated at two temperatures (5 and 8 degrees C) representing conditions encountered in the local environments. Global gene expression for fry at the stage of first feeding was analysed using a 32k cDNA microarray. The results revealed differences in gene expression between populations and temperatures and population M-CM-^W temperature interactions, the latter indicating locally adapted reaction norms. Moreover, the reaction norms paralleled those observed previously at early life-history traits. We were able to identify 90 cDNA clones among the genes with an interaction effect that were differently expressed between the ecologically divergent populations. These included genes involved in immune- and stress response. We observed less plasticity in the resident as compared to the anadromous populations, possibly reflecting that the degree of environmental heterogeneity encountered by individuals throughout their life cycle will select for variable level of phenotypic plasticity at the transcriptome level. Our study demonstrates the usefulness of transcriptome approaches to identify genes with different temperature reaction norms. The responses observed suggest that populations may vary in their susceptibility to climate change. Brown trout populations from three rivers in Denmark were studied: the Karup (KAR), Norring Moellebaek (NOR) and Lilleaa Rivers (LIL). These rivers experience different temperature regimes during the period lasting from egg incubation until fry emergence. During the autumn of 2004 and the winter of 2004/2005, adults from the three populations were collected by electro fishing. The fish were stripped for milt and eggs to establish an F1 generation. In autumn/winter 2008/2009, mature F1s were used to establish F2 offspring for each of the three populations. For KAR and LIL, 20 full-sib families were established, whereas for NOR, 15 full-sib families were established. Eggs from each full sib family were divided into two pools that were incubated at 5 and 8M-BM-!C in separate hatching troughs. At the time of first feeding (ca. 750-780 day-degrees), 10 individuals from each family and temperature were collected and transferred to separate tubes containing RNAlater (QIAGEN, Hilden, Germany). A 32K cDNA microarray developed for salmonids by cGRASP was used for the analyses. Ten families were randomly selected from each population. From each family two individuals were analyzed for each temperature (5 and 8oC, respectively), amounting to a total of 120 individuals. Of the two individuals from each temperature treatment within a family, one was labeled with CY5 and the other with CY3. For each family there were two comparisons of individuals representing different temperatures, but with dyes swapped between comparisons.
Project description:Wood stiffness is the most important wood quality trait of forest trees for structural timber production. We investigated genes differentially transcribed in radiate pine trees with distinct wood stiffness using bulked segregant analysis (BSA) and cDNA microarrays. Transcript accumulation in earlywood (EW) and latewood (LW) of high (HS) and low stiffness (LS) trees in two progeny trials was compared. Radiata pine trees used for microarray experiment were selected from two progeny trials planted at Flynn and Kromelite, Australia. Based on the IML-based MOE measurement, five families with highest and lowest MOE each were selected from each trial, which represented two segregant populations with contrasting wood stiffness. Two individuals from each selected family were further sampled. Developing xylem tissues of selected trees in Flynn trial were sampled in spring (October) and autumn (April), representing earlywood (EW) and latewood (LW) of juvenile aged trees, respectively. Collection of xylem tissues from Kromelite trial was arranged in summer (late November) when latewood (LW) was formed. The xylem tissues were scraped at breast height with a sharp chisel after the bark was removed. In Flynn trial EW and LW tissues were collected from the same sampled trees on opposite sides of the trunk. Transcript accumulation was compared in trees with highest (HS) and lowest stiffness (LS) using xylem samples from Flynn collected in spring (EW) and autumn (LW), as well as Kromelite in summer (LW), respectively. Bulked segregant analysis (BSA) was used for the experiment design. Total RNA samples extracted from the five trees with HS were pooled at equal amount, and compared to the bulked five individuals with LS. This pooling strategy can partly minimize the genetic variation among different genotypes. Dye swaps were applied in each biological replicate.
Project description:Liver transcriptomes of Atlantic salmon families with contrasting flesh n-3 LC-PUFA profiles, and all fed the same 100% vegetable oil replacement diet, were compared by microarray analysis (Agilent oligoarray platform). The objective was to identify gene pathways and molecular mechanisms which might explain differences in flesh n-3 LC-PUFA content, independent of total lipid deposition, when salmon families are fed the same LC-PUFA deficient diet. A factorial design was chosen in which families containing higher and lower n-3 LC-PUFA relative levels were compared at similar total lipid percentages in flesh.
Project description:Embryonic temperature modulates muscle fibre number in adult zebrafish: genome-wide changes in microRNA and mRNA expression and predicted miRNA-mRNA regulatory networks involved in the transition from hyperplastic to hypertrophic growth phenotypes.
Project description:Liver tissue from three-spine stickleback individuals from 3 populations were tested on arrays to determine array suitability for transcriptomics experiments.
Project description:Microarray experiments were used to determine the global changes in microRNA and mRNA expression associated with the transition from the myotube producing phenotype (M+, 10-12 mm total length) to the hypertrophic growth phenotype (M-, 28-31 mm total length) in fish reared at 26-27oC over the whole life-cycle. 26 down-regulated and 31up-regulated miRNAs were identified in the M- phenotype together with 43 down-regulated and 69 up-regulated mRNAs.
Project description:Anopheles gambiae isofemale families from Tororo, Uganda were assayed for resistance to lambda-cyhalothrin (1.5hr exposure). Resistant families were compared to susceptible families. A portion of each family was exposed to 0.05% lambda-cyhalothrin in order to determine the family phenotype. The families used for the array were of known phenotype but were themselves unexposed.