Evidence map›Paper›PMID 41109684›Full record

ArticleG3 (Bethesda, Md.)2025

A long-read-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

Abstract read
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In one paragraph

Article in G3 (Bethesda, Md.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Matthew A CampbellSchool of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia.ORCID 0000-0002-5826-0329
Luke W SilverSchool of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia.ORCID 0000-0002-1718-5756
Nirooparaj BalachandranNational Aquaculture Development Authority, Ministry of Fisheries and Aquatic Resources Development, Kilinochchi 44000, Sri Lanka.
Erandi PathiranaFaculty of Urban and Aquatic Bioresources, The University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka.ORCID 0000-0002-1795-5423
Cara JeffreySchool of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia.ORCID 0000-0001-7370-4752
Monal LalSchool of Science, Technology & Engineering, University of the Sunshine Coast, Sunshine Coast, QLD 4556, Australia.ORCID 0000-0002-8545-2887
Wayne A O'ConnorNew South Wales Department of Primary Industries and Rural Development, Port Stephens Fisheries Institute, Taylors Beach, NSW 2316, Australia.ORCID 0000-0002-0972-4668
Carolyn J HoggSchool of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia.ORCID 0000-0002-6328-398X
Joy A BeckerSchool of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia.ORCID 0000-0003-4749-4004

Funding

Australian High Commission, Sri Lanka and Maldives Knowledge and Linkages for an Inclusive EconomyCharles Gilbert Heydon TravellingThe University of Sydney
6 · The paper itself

Abstract

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 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.

Indexed as

AquacultureOstreidaeAnimalsGenomeGenomicsMolecular Sequence AnnotationPolymorphism, Single Nucleotideblack scar oystercomputational scaffoldingFijigenome assemblyIndian backwater oysterintroduced speciesmarine policySri Lankatranslocations

Identifiers

PMID41109684
PMCPMC12693617

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LicenceCC BY
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.