Project description:Illumina HiSeq technology was used to generate mRNA profiles from Suillus luteus ectomycorrhizal roots compared to free-living mycelium . Mycorrhizal roots were harvested after 40 days, pooled and used for RNA extraction. Reads of 2X100bp were generated and aligned to Suillus luteus (http://genome.jgi-psf.org/Suilu1/Suilu1.home.html) using CLC Genomics Workbench 6. mRNA profiles from Suillus luteus ectomycorrhizal roots and free-living mycelium were generated by paired-end (2x100bp) Illumina HiSeq2000 sequencing. Two biological replicates were sequenced for mycorrhizal and mycelium samples.
Project description:Using standard morphometric methods and gene expression profiling with a DNA microarray, we explored the impacts of high CO2 conditions on development of the sea urchin, Lytechinus pictus, a pelagic larvae that forms a calcium carbonate endoskeleton. Larvae were raised from fertilization to pluteus stage in seawater with elevated CO2 conditions based upon IPCC emissions scenarios B1 (540ppm CO2) and A1FI (970ppm CO2). Larval L. pictus were cultured in seawater treated with three different concentrations of CO2. We aerated water in culture chambers with air that had been mixed to different CO2 concentrations chosen from IPCC predictions of future atmospheric CO2 levels (28). The B1 scenario, one of the most optimistic, predicts a stabilization of atmospheric CO2 levels at ~540 ppm by 2100, and the A1F1 scenario, which, reflecting a more “business as usual” scenario, predicts atmospheric CO2 levels of ~970 ppm by 2100. Compressed air (~380 ppm CO2) was used as a control condition. The culture chambers were 20 L buckets medified to allow aeration bubbles of the experimental gas to mix with and gently stir the culture water without contacting the larvae. Replacement seawater (0.35 μm filtered) was added at a constant rate of 0.5 L hr-1. Water pH of each chamber was monitored daily using a Radiometer Analytical PHM240 pH meter. Adult L. pictus were maintained in flowing seawater at ambient temperature (~15-18 ºC) and fed kelp until use. Spawning was induced by coelomic injection of 0.5 M KCl, and eggs were collected in 0.35 μm-filtered seawater. Eggs from 5 females were combined in approximately equal concentrations. Sperm from a single male was collected in the same way, diluted with filtered seawater and added to the egg mixture; thus, all the larvae are half-siblings. Immediately following fertilization, embryos were split into 12 culture chambers providing four replicates of the three CO2 treatments. At the 48 hour time point, a sample of 40,000 larvae was removed from each of the 8 cultures in the 380 and 970 ppm treatments and stored in1 mL Trizol at -80 ºC for later RNA analysis. The larval cDNA samples from each treatment were competitively hybridized on each microarray following a balanced incomplete block design (BIBD) with respect to the assignment of treatments to arrays. In this way, differential expression between all pairs of treatments is estimated with equal precision. Although dye swaps of technical replicates were not used, treatment and dye effects are orthogonal to one another, i.e. treatment effects can be estimated independently of dye effects.