Towards a genomic predictor of bleaching in the coral Acropora millepora (NESP TWQ 4.4, AIMS)

This dataset is the genome assembly of the staghorn coral Acropora millepora. Tissue samples were collected along the Central Great Barrier Reef during the 2017 mass bleaching event. Tissue was collected from a range of individual exhibiting both bleaching and non-bleaching phenotypes. A range of phenotypic analysis were conducted and linked to the genomic sequencing data provided here. The A.millepora genome (Scaffold N50 =1.23 Mb) draft assembly was constructed from a combination of PacBio and Illumina paired-end reads with 10X Genomics barcodes.

Methods:

The de novo genome assembly of A. millepora was constructed by using a combination of PacBio reads and Illumina paired-end reads with 10X Genomics Chromium barcodes. Sequencing was performed by the New York Genome Center and Cold Spring Harbor Laboratory. PacBio only assemblies using the software Canu and Falcon and used the 10X barcodes and paired-end reads for scaffolding and error correction. The high–molecular weight DNA used for the assembly was extracted from an adult specimen, which also contained symbiont DNA. To remove potential symbiont contigs from the coral genome assembly, we additionally generated paired-end reads from two pools of aposymbiotic larvae and mapped these reads to our draft assembly. Using an unsupervised clustering approach, we identified and removed assembled contigs that appeared to be derived from the symbiont and masked regions of the assembly with no reads from the larvae. To assemble chromosome-scale scaffolds, we used previously published linkage maps inferred from SNP and restriction site–associated DNA sequencing (RAD-seq) markers to linearly arrange contigs. Previously published transcriptome data were used to predict gene models and annotate the resulting assembly. 

Further information can be found on the published article and supplementary materials: Fuller ZL, Mocellin VJL, Morris LA, Cantin N, Shepherd J, Sarre L, Peng J, Liao Y, Pickrell J, Andolfatto P, Matz M, Bay LK, Przeworski M (2020) Population genetics of the coral Acropora millepora: Toward genomic prediction of bleaching. Science 369:268
DOI: 10.1126/science.aba4674

Format:

Genome Assembly
Scaffold N50: 19.84 Mb (Contig N50: 1.08 Mb); Average length: 556.6 kb; Total length: 475.4 mb; # of scaffolds: 854; # of gene models: 28,188

Amil.v2.00.chrs.fasta: Fasta file of assembly
Amil.all.maker.noseq.gff: Gff3 (all features: gene, TE, tRNA)
Amil.coding.gff3: Gff3 file (coding genes)
Amil.repeat.gff: Gff (repeats)
Amil.all.maker.proteins.fasta: Predicted Protein file
Amil.all.maker.transcripts.fasta: Predicted transcripts file 
Amillepora_trinotate_annotation_report.xls: Functional annotation result by Trinotate
Amillepora_euk.emapper.annotations: Functional annotation result by eggnog-mapper
Amil.repeat.consensi.fasta: Repeat families identified by RepeatModeler
BUSCO.result: BUSCO analysis result

References:

Fuller ZL, Mocellin VJL, Morris LA, Cantin N, Shepherd J, Sarre L, Peng J, Liao Y, Pickrell J, Andolfatto P, Matz M, Bay LK, Przeworski M (2020) Population genetics of the coral Acropora millepora: Toward genomic prediction of bleaching. Science 369:268 DOI: 10.1126/science.aba4674

Data Location:

This dataset is filed in the eAtlas enduring data repository at: data\custodian\2018-2021-NESP-TWQ-4\4.4_Traits-of-corals-that-survived

Organization: Australian Ocean Data Network