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)

Gan, Han Ming, Tan, Mun Hua, Austin, Christopher M., Sherman, Craig D.H., Wong, Yen Ting, Strugnell, Jan, Gervis, Mark, McPherson, Luke, and Miller, Adam D. (2019) 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). Frontiers in Genetics, 10. 889.

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Abstract

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). 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" (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 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).

Item ID: 61736
Item Type: Article (Research - C1)
ISSN: 1664-8021
Keywords: Abalone, Haliotis, Heat shock protein 70, Heterozygosity, Hybrid assembly, Oxford Nanopore
Copyright Information: Copyright © 2019 Gan, Tan, Austin, Sherman, Wong, Strugnell, Gervis, McPherson and Miller. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Funders: Deakin University (DU)
Projects and Grants: DU SEBE-RGS_2018- 0509.3132531.01
Date Deposited: 05 Feb 2020 03:01
FoR Codes: 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060408 Genomics @ 100%
SEO Codes: 83 ANIMAL PRODUCTION AND ANIMAL PRIMARY PRODUCTS > 8301 Fisheries - Aquaculture > 830103 Aquaculture Molluscs (excl. Oysters) @ 100%
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