danielyao12 / pachyseris

Electronic notebook for "Morphological stasis masks ecologically divergent coral species on tropical reefs" (Current Biology, 2021)

"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.