Population genetics of the coralAcropora millepora: Towards a genomic predictor of bleaching

Abstract

Although reef-building corals are rapidly declining worldwide, responses to bleaching vary both within and among species. Because these inter-individual differences are partly heritable, they should in principle be predictable from genomic data. Towards that goal, we generated a chromosome-scale genome assembly for the coral Acropora millepora. We then obtained whole genome sequences for 237 phenotyped samples collected at 12 reefs distributed along the Great Barrier Reef, among which we inferred very little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin. We further used 213 of the samples to conduct a genome-wide association study of visual bleaching score, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for the use of genomics-based approaches in conservation strategies.

Signatures of selection in the coral holobiont reveal complex adaptations to inshore environments driven by Holocene climate change

“…The high completeness of our long-read assembly allowed us to resolve a substantially larger proportion of interspersed repeats (41.65%) compared with published acroporid assemblies from short reads ( A. digitifera 36 : (30.15%), A. millepora 37 (31.58%), A. tenuis 32 (34.32%). The only other available coral genome with comparable repeat resolution is a recently released long-read assembly for A. millepora 38 which identified a very similar proportion (40.69%) of interspersed repeats to our A. tenuis assembly. This increased ability to resolve repeats is reflected in a substantially increased proportion of unclassified elements in long-read assemblies (20.8% A. tenuis ; 21.2% A. millepora ) compared with short read assemblies (16.4% A. digitifera ; 16.5% A. millepora ), but the overall composition of known repeat classes was remarkably similar between Acropora genomes (Supp Figure S1).…”

“…As an additional check on the accuracy of our A. tenuis assembly we compared its high-level genomic organisation with that of its congeneric, A. millepora for which a chromosome-scale linkage map is available 38 . As expected given their small evolutionary distance (15Mya 32 ), macrosynteny analysis between the two Acropora genomes revealed a high degree of collinearity and limited rearrangements between linkage groups (an example is shown with arrows in Figure 1A).…”

Meta-analysis of the General Coral Stress Response:Acroporacorals show opposing responses depending on stress intensity

“…Reads were mapped to an annotated draft reference genome for Acorpora millepora that can currently available on the Przeworski laboratory website (Fuller et al 2018). The reference genome was generated using a combination of PacBio reads and Illumina paired-end reads with 10X Chromium barcodes and anchored into chromosomes with linkage mapping data from two previous studies (Wang et al 2009;Dixon et al 2015).…”

Benchmarking DNA Methylation Assays for Marine Invertebrates

“…Raw reads were trimmed and quality filtered using cutadapt simultaneously trimming low-quality bases from the 3' end (-q 20) and removing reads below 30 bp in length (-m 30) (Martin 2011). Trimmed reads were mapped to the A. millepora reference genome (Fuller et al 2019) with bowtie2 using the --local argument (Langmead and Salzberg 2012). Alignments were sorted and indexed using samtools (Li et al 2009), and PCR duplicates were removed using MarkDuplicates from Picard Toolkit (Broad Institute 2019).…”