Pocillopora and Cladocopium Gene Expression Levels and SNPs from Tara Pacific

102 Pocillopora coral colonies from the Tara Pacific expedition provide metatranscriptomic data for host and symbiont gene expression. The dataset includes raw and normalized read counts for Pocillopora and its Cladocopium photosymbiont, plus single nucleotide polymorphism (SNP) data for Cladocopium from 82 samples. It was produced by Eric Armstrong of the Centre National de la Recherche Scientifique.

Use Cases

• Analyze differential gene expression between coral host and symbiont based on read count data.
• Study population structure and genetic variation within Cladocopium symbionts based on SNP distributions.
• Investigate holobiont responses to environmental stress using metatranscriptomic profiles.
• Benchmark alignment and variant calling methods for non-model marine organisms.

Strengths

• Includes data from 102 distinct coral colonies, providing a substantial sample size.
• Offers both raw read counts and normalized TPM values for gene expression analysis.
• Contains paired host (Pocillopora) and symbiont (Cladocopium) data from the same samples.
• Provides filtered SNP data with alternative allele frequencies for 82 samples.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Last update date is unknown; freshness unverified.

Provenance

Source

Centre National de la Recherche Scientifique

Collection Method

RNA extracted from coral fragments and sequenced. Reads aligned to reference genomes (Pocillopora meandrina, Cladocopium goreaui) using BWA-mem. Variants called with GATK.

Geography

Samples collected during the Tara Pacific expedition; specific locations not stated.