Data & script for "Host genetics structure prokaryotic and Symbiodiniaceae assemblages and their co-variation in sympatric fire coral species"

This dataset contains the data and analysis scripts associated with the manuscript 'Host genetics and local environment jointly shape fire coral holobionts in sympatric Millepora species' . Symbiodiniaceae and prokaryotic assemblages were characterized in three sympatric fire coral species (Millepora cf. exaesa, M. tenera, and M. cf. platyphylla) across three adjacent reef habitats on Réunion Island (inner reef flat, outer reef flat, mid reef slope). Raw sequencing data (mt16S host sequences & 16S and ITS2 amplicon sequences) are available on NCBI under BioProject PRJNA1527031. This repository includes: 1) R scripts for all statistical analyses, 2) phyloseq objects for Symbiodiniaceae (ITS2) and prokaryotic (16S rRNA) communities, and 3) intermediate supplementary tables. SuppTable1_metadata.csv -> complete metadata file SuppTable2_microsatellite_millepora.xlsx -> Multilocus Genotype (MLG) dataset and clone discrimination Phylogenetic tree from mt16S sequencing data millepora_phylotree.Rmd -> R script to reproduce the Fig. S1 millepora_mt16S_phylogeny.contree -> maximum likelihood tree millepora_mt16S_alignment_51.aln -> sequence alignment of the 51 samples Symbiodiniaceae assemblages (ITS2 metabarcoding) millepora_ITS2.Rmd ps.its2 -> phyloseq object with ITS2 sequence data SuppTable3_its2_seq_filt.csv -> raw abundance data of DIVs SuppTable4_its2_type_filt.csv -> raw abundance data of ITS2 type profiles Prokaryotic assemblages (16S metabarcoding) millepora_16S.Rmd ps.16S -> phyloseq object with ASV sequence data SuppTable5_asv_table_seq.csv -> raw abundance data of ASVs ITS2 x 16S Data integration millepora_codispersion.Rmd -> R script for microbiome dispersion, requires intermediate data generated in millepora_ITS2.Rmd (section 4.2) & millepora_16S.Rmd (section 3.2) millepora_covariation.Rmd -> R script for microbiome co-variation using DIABLO