A Genomic Toolbox (genome, transcriptome and GBS) for the New Zealand Greenshell™ Mussel (Perna canaliculus)

Aquaculture is a growing industry globally, but a lack of genomic resources limits effective genetic selection in this sector. The Greenshell™ Mussel (GSM) is an endemic mollusc of economic importance for the New Zealand aquaculture industry. The GSM breeding program requires a panel of single nucleotide polymorphism (SNP) markers for assessment of genetic diversity and differentiation, parentage assignment, inbreeding estimation, genomic selection and genome wide association studies. However, mussels are highly heterozygous species, which reduces the accuracy of identifying SNPs without a reference genome. There are currently only 10 mollusca genomes publically available; only two are for mussel species and these are only partially assembled. We have tested and defined an optimal pipeline to assemble a draft genome of GSM using a combination of Illumina short reads and Illumina TruSeq Synthetic Long-Reads. This assembly is a massive improvement on currently available genomes for mussels (77% partial CEGMA genes compared with 43% in the published Mytilus galloprovincialis assembly). In addition, we have assembled the GSM transcriptome and used this to further scaffold our genome assembly. This is the first genome assembly for the Perna genus and the first transcriptome for GSM. The genome has been utilized to develop an optimised Genotyping-by-Sequencing (GBS) pipeline to enable and enhance the productivity of GSM and potentially other species.