An Annotated Genome for Haliotis rufescens (Red Abalone) and Resequenced Green, Pink, Pinto, Black, and White Abalone Species.

Arun S Seetharam,Catherine M Purcell,Andrew J Severin,Rick E Masonbrink,Sara E Boles,John R Hyde,Marta Barluenga,Andrew Whitehead

doi:10.1093/gbe/evz006

Abstract

Abalone are one of the few marine taxa where aquaculture production dominates the global market as a result of increasing demand and declining natural stocks from overexploitation and disease. To better understand abalone biology, aid in conservation efforts for endangered abalone species, and gain insight into sustainable aquaculture, we created a draft genome of the red abalone (Haliotis rufescens). The approach to this genome draft included initial assembly using raw Illumina and PacBio sequencing data with MaSuRCA, before scaffolding using sequencing data generated from Chicago library preparations with HiRise2. This assembly approach resulted in 8,371 scaffolds and total length of 1.498 Gb; the N50 was 1.895 Mb, and the longest scaffold was 13.2 Mb. Gene models were predicted, using MAKER2, from RNA-Seq data and all related expressed sequence tags and proteins from NCBI; this resulted in 57,785 genes with an average length of 8,255 bp. In addition, single nucleotide polymorphisms were called on Illumina short-sequencing reads from five other eastern Pacific abalone species: the green (H. fulgens), pink (H. corrugata), pinto (H. kamtschatkana), black (H. cracherodii), and white (H. sorenseni) abalone. Phylogenetic relationships largely follow patterns detected by previous studies based on 1,784,991 high-quality single nucleotide polymorphisms. Among the six abalone species examined, the endangered white abalone appears to harbor the lowest levels of heterozygosity. This draft genome assembly and the sequencing data provide a foundation for genome-enabled aquaculture improvement for red abalone, and for genome-guided conservation efforts for the other five species and, in particular, for the endangered white and black abalone.

Highlights

362 metric tons of farmed abalone are produced annually in the United States (Cook 2016)
Single nucleotide polymorphisms were called on Illumina short-sequencing reads from five other eastern Pacific abalone species: the green (H. fulgens), pink (H. corrugata), pinto (H. kamtschatkana), black (H. cracherodii), and white (H. sorenseni) abalone
Phylogenetic relationships largely follow patterns detected by previous studies based on 1,784,991 high-quality single nucleotide polymorphisms

Summary

Introduction

362 metric tons of farmed abalone are produced annually in the United States (Cook 2016). Green (H. fulgens) and pink abalone (H. corrugata) have more southern distributions and are of greater interest for aquaculture production in Mexico, where they can be grown at warmer water temperatures (McBride and Conte 1996; Allsopp et al 2011) Ranges for these two species extend from Point Conception, CA to the southern portion of Baja California (National Marine Fisheries Service 2008). Genetic information and techniques such as Marker Assisted Selection can rapidly improve broodstock selection, characterize variation (both beneficial and detrimental), and provide methods to directly improve the value, efficiency, and production in a target species (van der Merwe et al 2011; Rhode et al 2012) These tools and techniques may become especially important as aquaculture efforts seek to maintain sustainability in the face of changing ocean conditions. We report a high-quality reference genome assembly and annotation for red abalone, including an examination of genome-wide single nucleotide polymorphism (SNP) variation for five related abalone species native to the Pacific coast of North America: the green, pink, pinto, black, and white abalone

Materials and Methods

Results and Discussion

Conclusion

Literature Cited