mistergroot/apal_acer_genomes: Acropora palmata and A. cervicornis resource release v1.0.0

Initial Release of Acropora palmata and Acropora cervicornis genome assemblies, genetic maps, gene predictions, and functional annotations.

Here, we make available the code and genomic resources described in Locatelli et al., 2023. These files describe the genomic resources for Florida Acropora palmata sampled at Horseshoe Reef (genet HS1, STAGdb ID HG0004) and Acropora cervicornis sampled from Grassy Key (genet M5, STAGdb ID HG0005). All tissue samples were generously provided by the Coral Restoration Foundation™ (CRF).

In jupyter_notebooks/, we provide code for Acropora cervicornis (prefix Acervicornis in all files) genome assembly, gene prediction, and functional annotation in FunAnnotate. We additionally provide code for Acropora palmata (prefix Apalmata in all files) and Acropora cervicornis linkage map generation using LepWrap. Further, we provide code for some figure generation, whole genome alignments and dotplots, and phylogenetically significant gene family expansion analyses (CAFE5).

In resources/, we provide chromosome-level genome assemblies (.fa.gz), gene predictions (.gff3.gz), functional annotations (.annotations.txt.gz), masks for repetitive content (.repeatmask.bed.gz), and PLINK-formatted male, female, and sex-average genetic maps (.map) for Acropora cervicornis and Acropora palmata. Please keep in mind that the assemblies and annotations for each species were generated in slightly different ways, as described in the manuscript. So not all files are identically formatted.