A long-reads based de-novo assembly of Magallana bilineata for improved tropical oyster aquaculture

Matthew A Campbell; Luke W Silver; Nirooparaj Balachandran; Erandi Pathirana; Cara Jeffrey; Monal Lal; Wayne A O'Connor; Carolyn J Hogg; Joy A Becker

doi:10.1093/g3journal/jkaf242

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A long-reads based de-novo assembly of Magallana bilineata for improved tropical oyster aquaculture

Journal article

Open access

Peer reviewed

A long-reads based de-novo assembly of Magallana bilineata for improved tropical oyster aquaculture

Matthew A Campbell, Luke W Silver, Nirooparaj Balachandran, Erandi Pathirana, Cara Jeffrey, Monal Lal, Wayne A O'Connor, Carolyn J Hogg and Joy A Becker

G3: Genes, Genomes, Genetics, Vol.15(12), pp.1-10

2025

DOI: https://doi.org/10.1093/g3journal/jkaf242

PMCID: PMC12693617

PMID: 41109684

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Abstract

Genome Assembly

Translocations

Crassostrea; Fiji

Sri Lanka

Computational Scaffolding

Introduced Species

Indian Backwater Oyster

Magallana; Marine Policy

Black Scar Oyster

True oysters, molluscs in the family Ostreidae, are important species in fisheries and aquaculture. As such, genome enabled research can improve these industries and the conservation of these species. The tropical rock oyster Magallana bilineata (known as the black scar oyster or Indian backwater oyster) is naturally distributed in the tropical Indo-Pacific Ocean excluding Australia and is intensively cultured in India and the Philippines. It is also an aquaculture species in Sri Lanka with potential for much greater cultivation. We present the first reference genome for M. bilineata sourced from a Sri Lankan individual along with genetic variants that can be used in tool development for questions of molecular ecology and evolution as well as applications in breeding and commercial applications. Long-read PacBio data from a single M. bilineata were assembled following the Vertebrate Genomes Project workflow on the Galaxy Australia platform. A primary assembly composed of 105 contigs that is 551.94 Mbp in size was produced. The assembly N50 is 13.42 Mb and has a BUSCO completeness score of 98.1%. As collection and transport conditions challenged transcriptomic as well as scaffolding data generation, these approaches were undertaken computationally. Genetic variants in the form of SNPs from 90 individuals representing three naturally occurring populations in Sri Lanka and a fourth introduced population in Fiji was generated through DArTseq and a set of 3,115 SNPs produced after filtering. Combined we present the first known genome assembly and the first genome-wide SNP data from M. bilineata, both of which have diverse applications for conservation and aquaculture.

Details

Title: A long-reads based de-novo assembly of Magallana bilineata for improved tropical oyster aquaculture
Authors: Matthew A Campbell (Corresponding Author) - The University of Sydney
Luke W Silver - The University of Sydney
Nirooparaj Balachandran - National Aquatic Resources Research and Development Agency
Erandi Pathirana - University of Sri Jayewardenepura
Cara Jeffrey - The University of Sydney
Monal Lal - University of the Sunshine Coast, Queensland, School of Science, Technology and Engineering
Wayne A O'Connor - New South Wales Department of Primary Industries
Carolyn J Hogg - The University of Sydney
Joy A Becker - The University of Sydney
Publication details: G3: Genes, Genomes, Genetics, Vol.15(12), pp.1-10
Publisher: Oxford University Press
Date published: 2025
DOI: 10.1093/g3journal/jkaf242
ISSN: 2160-1836
PMID: 41109684; PMC12693617
Copyright note: © The Author(s) 2025. Published by Oxford University Press on behalf of The Genetics Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Data Availability: Genotypes are provided as Supplemental File S1 in VCF format. The reference genome and raw sequence data for assembly are available under NCBI BioProject PRJNA1181550 with the genome reported in this manuscript version JBLMKS010000000. Raw DArTseq data are available under NCBI BioProject PRJNA1181550. Full annotation output from MAKER and computationally scaffolded genomes available at https://doi.org/10.25387/g3.29095958.
Grant note: The ‘Sustainable marine Aquaculture Development for Sri Lanka’ project was funded through an ‘Australian High Commission, Sri Lanka and Maldives Knowledge and Linkages for an Inclusive Economy’ grant. Salary support for MC was provided by a Charles Gilbert Heydon Travelling Fellowship gifted to The University of Sydney and for LS from the NCRIS funded Australian BioCommons and The University of Sydney.
Organisation Unit: Australian Centre for Pacific Islands Research; School of Science, Technology and Engineering
Language: English
Record Identifier: 991173177502621
Output Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Web Of Science research areas: Genetics & Heredity

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