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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)

Publication

Date: 25th September 2019 | Source: Frontiers in Genetics

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

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. Many abalone fisheries have collapsed in recent decades due to overexploitation, environmental change, and disease, with a number of target species now listed as endangered or considered “species of concern”.

To keep up with global demand and to counter disease and environmental stress, effective management of wild stock and farmed abalone is vital to ensure maximized productivity, sustainability, and biosecurity of the industry. To date, population and quantitative genetic research have contributed genomic resources to assist H. rubra fisheries management and conservation; however, a fully assembled and annotated genome sequence for this species is still unavailable.

In this study, we generated the first Nanopore long read data (∼ 30× coverage) for the blacklip abalone and applied the hybrid meta-assembly approach to assemble its genome.

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