Pocillopora and Cladocopium gene expression levels and Cladocopium SNPs

Pocillopora holobiont gene expression levels

This 2nd version contains the genes expression levels of Pocillopora and its Cladocopium photosymbiont for 253 Pocillopora coral colonies collected around 32 islands in the framework of Tara Pacific expedition. 

Pocillopora_MetaT_32islands_ReadCount.tsv : Pocillopora raw read counts

Pocillopora_MetaT_32islands_TPM.tsv : Pocillopora normalized read counts

CladocopiumC1_MetaT_32islands_ReadCount.tsv : Cladocopium raw read counts

CladocopiumC1_MetaT_32islands_TPM.tsv : Cladocopium normalized read counts

Methods: Pocillopora fragments from 253 colonies were processed to extract then sequence RNA. Metatranscriptomic reads (Illumina-generated 150-bp, paired-end) were separately aligned to predicted coding sequences (CDS) of the Pocillopora meandrina coral host reference genome, the CDS of the Cladocopium goreaui genome, and a Durusdinium transcriptome using Burrows–Wheeler Transform Aligner (BWA-mem, v0.7.15) with the default settings. Host- and symbiont-mapped reads were then sorted and processed using SAMtools v1.10.282 to generate respective bam files. A read was considered a host contig if its sequence aligned to the P. meandrina predicted coding sequence with ≥ 95% of sequence identity and with ≥ 50% of the sequence aligned. Reads aligned to Cladocopium goreaui coding sequences with a cutoff of ≥ 98% of sequence identity over ≥ 80% of the read length were retained as symbiont reads. Reads were further filtered to remove those in which more than 75% of the read length was low complexity or less than 30% was high complexity. Read counts were normalized as transcript per million (TPM).