Data from: Reef-specific patterns of gene expression plasticity in eastern oysters (Crassostrea virginica)

Understanding the interaction between phenotypic plasticity and evolutionary processes is important for predicting a species' response to changing environment. Strong recurrent selection each generation may be an important process in highly fecund species with broad dispersal and extensive early mortality. We tested whether selection was associated with spatial divergence in gene expression plasticity for osmoregulation in the eastern oyster (Crassostrea virginica). We collected adult oysters from high and low salinity reefs within a single estuary and after 9 weeks of acclimation at 10 and 30 salinity, measured gene expression in 24 oysters using next-generation RNA sequencing technology. The oysters had significantly different expression (DE) in response to salinity treatments for 7936 (18.9%) transcripts overall, with planned contrasts showing 8× more DE in oysters from the high-salinity reef and 15× more DE between reefs when tested at 10 salinity. The reef-by-treatment interaction was also genomically pervasive (5858 DE transcripts, 13.9%). Inter-reef F ST for transcript SNPs averaged 0.0025 with the top 1% between 0.29 and 0.73. Transcripts containing "outlier" SNPs were significantly enriched for osmoregulatory genes and showed patterns of variation consistent with selection on the low-salinity reef. Both phenotypic plasticity and recurrent selection seem to be important factors determining the realized niche of oysters within estuaries.FASTA Sequences for the Annotated Reference Transcriptome of the Eastern OysterThe FASTA file consists of the annotated reference transcriptome cDNA sequences used to map sample reads. The reference transciprtome was generated by collapsing two previously published transcriptomes (Eierman and Hare 2014, Zhang et al. 2014) using Cd-hit-est (Li and Godzik 2006) as described in the publication (Eierman and Hare 2015).Eierman_Hare_2015_JOH_Transcriptome_Sequences.fastaAnnotation File for the Annotated Reference Transcriptome of the Eastern OysterThe Excel file provides the annotation information, including original source transcriptome, for each contig in the reference transcriptome. The ReadMe files describes the content of each Excel file column.Eierman_Hare_2015_JOH_Transcriptome_Annotation.xlsxFiltered, mapped RNA-seq reads from eastern oysters in merged bam fileThe file is a merged bam file. It contains the reads that mapped to the annotated reference transcriptome for all 24 sample oysters. The ReadMe file indicates that source population and treatment salinity for each sample oyster.All_samples_JOH_Eierman_Hare.ba