Best Foot Forward: Nanopore Long Reads, Hybrid Meta-Assembly, and Haplotig Purging Optimizes the First Genome Assembly for the Southern Hemisphere Blacklip Abalone (Haliotis rubra).

Han Ming Gan,Yen Ting Wong,Jan Strugnell,Mun Hua Tan,Mark Gervis,Luke Mcpherson,Craig D H Sherman,Adam D Miller,Christopher M Austin

doi:10.3389/fgene.2019.00889

Han Ming Gan, Yen Ting Wong + Show 7 more

Open Access

https://doi.org/10.3389/fgene.2019.00889

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Journal: Frontiers in Genetics	Publication Date: Sep 25, 2019
Citations: 21	License type: CC BY 4.0

Affiliation: Deakin University, James Cook University

Abstract

Marine molluscs of the family Haliotidae, commonly referred to as abalone, are a group of benthic reef targeted by commercial fisheries in 11 countries, forming an important global industry worth approximately US $180 million (Gordon and Cook, 2013). Many abalone fisheries have collapsed in recent decades due to overexploitation, environmental change, and disease, with a number of target now listed as endangered or considered species of concern (Hauck and Sweijd, 1999; Leiva and Castilla, 2002; Gruenthal and Burton, 2005; Kashiwada and Taniguchi, 2007). The world's largest thriving abalone fisheries persist in southern Australia which is currently home to a thriving and rapidly growing aquaculture industry making up approximately 10% of Australia's export market. In this region, the abalone Haliotis rubra (Figure 1A) was targeted in five states extending from Western Australia to southern New South Wales and Tasmania with a net value of US $79 million (Mundy et al., 2014).

Highlights

Marine molluscs of the family Haliotidae, commonly referred to as abalone, are a group of benthic reef species targeted by commercial fisheries in 11 countries, forming an important global industry worth approximately US $180 million (Gordon and Cook, 2013)
The abalone species Haliotis rubra (Figure 1A) was targeted in five states extending from Western Australia to southern New South Wales and Tasmania with a net value of US $79 million (Mundy et al, 2014)
Using the k-mer approach based on 291.7 Gb of Illumina short read data, the H. rubra haploid genome size was predicted to be between 1.24 to 1.31 Gb with moderate-high heterozygosity of 1.27 to 1.44% (Supplemental Table 2)

Summary

Introduction

Marine molluscs of the family Haliotidae, commonly referred to as abalone, are a group of benthic reef species targeted by commercial fisheries in 11 countries, forming an important global industry worth approximately US $180 million (Gordon and Cook, 2013). Population and quantitative genetic research have contributed genomic resources to assist H. rubra fisheries management and conservation (Baranski et al, 2008; Miller et al, 2016; Kijas et al, 2019); a fully assembled and annotated genome sequence for this species is still unavailable.

Results

Conclusion