Coral reefs are under threat worldwide due to anthropogenic change. Particular threats are climate change that causes coral bleaching, and ocean acidification that can interfere with calcification. In order to mitigate these threats, it is crucial to understand how they affect the corals at a molecular level. As coral species are known to differ in their susceptibility to these threats, insights into the molecular basis of resilience to climate change can be obtained by comparison of whole genome sequences.
However, the high repeat content and polymorphism of coral genomes present a formidable barrier to genome assembly. The repeat content of coral genomes is around 30-40%. These regions are usually hard to resolve using short-read sequencing. Moreover, the heterozygosity rate of 1-2% is about 10 times higher than that of mammals. Such high levels of polymorphism complicated with repeat structure usually result in extremely fragmented contigs with both haplotypes present in the final assembly.
A number of excellent assemblies of Acropora cora genomes exist. We aim to leverage these assemblies to conduct a reference-guided assembly of A. hyacinthus, for which we have Illumina paired-end short reads at a coverage of ~100X. The project will be to developt a general reference-guided assembly pipeline, and test it on this data set. The development of this pipeline can help accelarate genome assembly for other highly heterozygous genomes using short-read data.