Abstract
Aquaculture is a growing industry globally; however, genomic resources are lacking for the aquaculture farming industry. The Greenshell™ Mussel (GSM) is an endemic species of economic importance to the New Zealand aquaculture industry and is currently the largest aquaculture export by both volume and value. The development of a mussel hatchery has enabled establishment of breeding program for GSM, reducing the industry’s reliance on sources of wild mussels. Current breeding approaches rely on the accurate recording of pedigrees to select mating pairs and destructive methods to record phenotypes.
The advent of Next Generation Sequencing, lower sequencing costs and new genotyping technologies such as Genotyping-By-Sequencing (GBS) have resulted in the development of genomic tools for industries where the cost was previously prohibitive. Here, we have developed a genomic toolbox for GSM to enable the implementation of genomic tools for applications including parentage assignment, genomic selection, estimating relatedness between individuals and genome wide association studies. In order to do this, we have assembled a draft de novo genome using a combination of Illumina short-read sequencing, Illumina TruSeq Synthetic Long Reads and a de novo transcriptome assembly. Bivalve mollusc genomes have features that increase the difficulty of de novo assemblies, including significant levels of heterozygosity and high levels of repeats. Therefore, a range of genome assembly methods were tested to generate a high quality, 1.1Gb genome assembly for the GSM. This assembly will provide a foundation for further research into this economically and culturally important species for both breeding purposes and conservation efforts.
An additional advantage of whole genome sequencing was that high depth coverage of the GSM mitochondrial genome was obtained, enabling assembly into a complete contig and clarity of the relationship of GSM to other Perna species and species from the Mytilidae family. Furthermore, the mitogenome enabled insight into unique features of bivalve mitochondrial inheritance patterns and the identification of a putative truncated atp8 gene that was previously thought to be absent in Mytilid mitogenomes.
The nuclear genome assembly was utilised to develop a high throughput GBS platform for use as a cost effective tool for GSM breeding. In order to develop this, three enzyme combinations were tested along with five GBS SNP calling pipelines, including two de novo methods and two reference based methods, to identify an optimal, high-throughput, cost effective GBS method. Furthermore, the effects of different filtering pipelines were tested on biologically relevant outcomes, utilising breeding populations to assess the accuracy of genomic parentage assignment and validate the pipeline to ensure quality for implementation in industry.