"Morphological stasis masks ecologically divergent coral species on tropical reefs"

Bongaerts P, Cooke I, Ying H, Wels D, Haan den S, Hernandez-Agreda, Brunner C, Dove S, Englebert N, Eyal G, Forêt S, Grinblat M, Hay KB, Harii S, Hayward DC, Lin Y, Mihaljević M, Moya A, Muir P, Sinniger F, Smallhorn-West P, Torda G, Ragan MA, van Oppen MJH, Hoegh-Guldberg O (2021) Morphological stasis masks ecologically divergent coral species on tropical reefs. Current Biology https://doi.org/10.1016/j.cub.2021.03.028

A - Genome assembly and annotation (PacBio)

Pachyseris speciosa genome (v0.12) - Genome scaffolds and gene models, also available through: http://pspe.reefgenomics.org/. Genomic DNA was extracted from the sperm of a P. speciosa colony belonging to the "green" lineage (accession code PRJNA686482).

Raw sequence data - reference genome (ENA) - Raw PacBio and Illumina sequence data used for the genome assembly (accession code PRJEB23386).

B - Reduced-representation sequencing (nextRAD)

NextRAD electronic notebook - Details the processing and analyses of the Pachyseris speciosa reduced representation (nextRAD) genome sequencing data.

Raw sequence data - nextRAD (NCBI SRA) - Raw Illumina sequence data (fastq format) for the 501 coral colonies succesfully sequenced in this study (accession code PRJNA701715).

RADseq script library (GitHub) - Separate github repository with generic Python scripts used throughout the nextRAD electronic notebook.

C - Whole-genome resequencing (WGS)

WGS electronic notebook (by Ira Cooke) - Details the processing and analyses of the Pachyseris speciosa whole-genome resequencing data.

Raw sequence data - whole-genome resequencing (NCBI SRA) - Raw Illumina sequence data (fastq format) for the whole genomes of 20 coral colonies sequenced in this study (accession code PRJNA686482).

Whole-genome resequencing coverage summary - Sequencing coverage estimates from samtools depth based on the entire genome.

D - Diagnostic PCR assay (CAPS)

CAPS electronic notebook - Details the development of the cleaved amplified polymorphic sequence (CAPS) markers from the nextRAD data, and subsequent scoring of the CAPS genotyping data.

E - Phenotypic and microbial characterization

Phenotype data - Morphology, physiology and reproductive data files.

Raw 16S amplicon sequencing data (NCBI SRA) - Raw Illumina sequence data (fastq format) for the microbial communities sequenced in Hernandez-Agreda et al. (2016) (accession code PRJNA328211).

F - Statistical analyses

Statistical analyses - Tables with outcomes of univariate/multivariate statistics.

Additional resources

Fieldwork Photos - Several photos of the fieldwork associated with this study.