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Series GSE144422 Query DataSets for GSE144422
Status Public on Feb 19, 2020
Title An Initial Comparative Genomic Autopsy of Wasting Disease in Sea Stars
Organism Pisaster ochraceus
Experiment type Expression profiling by high throughput sequencing
Summary Beginning in 2013, sea stars throughout the Eastern North Pacific were decimated by wasting disease, also known as ‘asteroid idiopathic wasting syndrome’ (AIWS) due to its elusive etiology. The geographic extent and taxonomic scale of AIWS meant events leading up to the outbreak were heterogeneous, multifaceted, and oftentimes unobserved; progression from morbidity to death was rapid, leaving few tell-tale symptoms. Here we take a forensic genomic approach to discover candidate genes that may help explain sea star wasting syndrome. We report the first genome and annotation for P. ochraceus, along with differential gene expression (DGE) analyses in four size classes, three tissue types, and in symptomatic and asymptomatic individuals. We integrate nucleotide polymorphisms associated with survivors of the wasting disease outbreak, DGE associated with temperature treatments in P. ochraceus, and DGE associated with wasting in another asteroid Pycnopodia helianthoides. In P. ochraceus, we find DGE across all tissues, among size classes, and between asymptomatic and symptomatic individuals; the strongest wasting-associated DGE signal is in pyloric caecum. We also find previously identified outlier loci co-occur with differentially expressed genes. In cross-species comparisons of symptomatic and asymptomatic individuals, consistent responses distinguish genes associated with invertebrate innate immunity and chemical defense, consistent with context-dependent stress responses, defensive apoptosis, and tissue degradation. Our analyses thus highlight genomic constituents that may link suspected environmental drivers (elevated temperature) with intrinsic differences among individuals (age/size, alleles associated with susceptibility) that elicit organismal responses (e.g. coelomocyte proliferation) and manifest as sea star wasting mass mortality.
 
Overall design Tissue biopsies - of tube feet, pyloric caecum, and dermis - were taken from 17 individuals: 15 collected at McClures Beach and two from Lifeboat House in Point Reyes National Seashore (SI Appendix, Table S1) on the 19th and 21st August 2017, respectively, and preserved in RNAlater® in the field. A DGE analysis was first conducted to evaluate differential expression between tissue types. Subsequent analyses were conducted separately for each tissue type to assess differential expression between size classes and between symptomatic and asymptomatic individuals. Each size class (i.e. small, medium, large, or x-large) was compared to the mean of all other size classes. An additional analysis was conducted comparing just the small individuals directly to the x-large individuals to reveal potential DGE that might be masked by variation in intermediate size classes. Genes were filtered at a minimum threshold of mean 1 count per million (CPM). Significance was assessed at a false discovery rate (FDR) < 0.01 (unless otherwise noted).
 
Contributor(s) Ruiz-Ramos DV, Schiebelhut LM, Hoff KJ, Wares JP, Dawson MN
Citation(s) 32069379
Submission date Jan 28, 2020
Last update date Feb 19, 2020
Contact name Lauren Schiebelhut
E-mail(s) lschiebelhut@ucmerced.edu, lschiebelhut@gmail.com
Organization name University of California, Merced
Street address 5200 N. Lake Rd.
City Merced
State/province CA
ZIP/Postal code 95343
Country USA
 
Platforms (1)
GPL28087 Illumina HiSeq 4000 (Pisaster ochraceus)
Samples (50)
GSM4287881 M0D055219G_A_B1_DE_SM_NF_CCM
GSM4287882 M0D055219G_A_B1_TF_SM_NF_CCM
GSM4287883 M0D055219G_A_B3_PC_SM_NF_CCM
Relations
BioProject PRJNA603587
SRA SRP245672

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE144422_RAW.tar 3.1 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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