Comparative De Novo transcriptome analysis of the Australian black-lip and Sydney rock oysters reveals expansion of repetitive elements in Saccostrea genomes

McDougall, Carmel

doi:10.1371/journal.pone.0206417

Cited by 4 publications

(2 citation statements)

References 51 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Results from the mitochondrial COI analyses, are consistent with those of McDougall [36], and the observational data of Thomson [26], in that they support a broad tropical Indo-Pacific distribution of S. echinata ; from at least Taketomi Island in Japan, to Noumea in New Caledonia, and across northern Australia; from Cone Bay in Western Australia, to Bowen in Queensland. Few studies have employed genetic data to assist in investigating the distribution of tropical oyster species within the Indo-Pacific region.…”

Section: Discussionsupporting

confidence: 84%

“…The basic local alignment search tool (BLAST) function, incorporated in Geneious 11.1.5, was used to BLAST the 31 candidate adaptive SNPs against the complete, annotated transcriptome of the black-lip rock oyster, referred to as Saccostrea lineage J by McDougall [36]. A minimal E-value threshold of 1 × 10 − 6 and the highest ‘Grade’ (a weighted score for the hit comprised of the E-value, the pairwise identity, and the coverage) for each hit were applied to the analyses.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Mitochondrial and nuclear genetic analyses of the tropical black-lip rock oyster (Saccostrea echinata) reveals population subdivision and informs sustainable aquaculture development

et al. 2019

View full text Add to dashboard Cite

Background The black-lip rock oyster (Saccostrea echinata) has considerable potential for aquaculture throughout the tropics. Previous attempts to farm S. echinata failed due to an insufficient supply of wild spat; however, the prospect of hatchery-based aquaculture has stimulated renewed interest, and small-scale farming is underway across northern Australia and in New Caledonia. The absence of knowledge surrounding the population genetic structure of this species has raised concerns about the genetic impacts of this emerging aquaculture industry. This study is the first to examine population genetics of S. echinata and employs both mitochondrial cytochrome c oxidase subunit I gene (COI) and single nucleotide polymorphism (SNP) markers. Results The mitochondrial COI data set included 273 sequences of 594 base pair length, which comprised 74 haplotypes. The SNP data set included 27,887 filtered SNPs for 272 oysters and of these 31 SNPs were identified as candidate adaptive loci. Data from the mitochondrial COI analyses, supports a broad tropical Indo-Pacific distribution of S. echinata, and showed high haplotype and nucleotide diversities (0.887–1.000 and 0.005–0.008, respectively). Mitochondrial COI analyses also revealed a ‘star-like’ haplotype network, and significant and negative neutrality tests (Tajima’s D = − 2.030, Fu’s Fs = − 25.638, P < 0.001) support a recent population expansion after a bottleneck. The SNP analyses showed significant levels of population subdivision and four genetic clusters were identified: (1) the Noumea (New Caledonia) sample location; (2) the Bowen (north Queensland, Australia) sample location, and remaining sample locations in the Northern Territory, Australia (n = 8) were differentiated into two genetic clusters. These occurred at either side of the Wessel Islands and were termed (3) ‘west’ and (4) ‘east’ clusters, and two migrant individuals were detected between them. The SNP data showed a significant positive correlation between genetic and geographic distance (Mantel test, P < 0.001, R2 = 0.798) and supported isolation by distance. Three candidate adaptive SNPs were identified as occurring within known genes and gene ontology was well described for the sex peptide receptor gene. Conclusions Data supports the existence of genetically distinct populations of S. echinata, suggesting that management of wild and farmed stocks should be based upon multiple management units. This research has made information on population genetic structure and connectivity available for a new aquaculture species.

show abstract

Section: Discussionsupporting

confidence: 84%

Section: Methodsmentioning

confidence: 99%

Mitochondrial and nuclear genetic analyses of the tropical black-lip rock oyster (Saccostrea echinata) reveals population subdivision and informs sustainable aquaculture development

et al. 2019

View full text Add to dashboard Cite

show abstract

Evaluating spawning induction methods for the tropical black-lip rock oyster, Saccostrea echinata

Nowland

O’Connor

Elizur

et al. 2021

Aquaculture Reports

View full text Add to dashboard Cite

Numerical investigation of the restored oyster reef flow field with the lattice Boltzmann method

Wu,

Yin,

Wang

et al. 2024

Physics of Fluids

View full text Add to dashboard Cite

Oyster reefs play a dual role in the ecological and economic sustainability of global estuarine resources. Due to human activity and climate change, the prevalence of cosmopolitan oyster reefs has noticeably declined in recent decades, triggering a global restoration movement. However, the hydrodynamic functions of oyster reefs during and after restoration, particularly the impacts of growth and morphology on the flow field, remain poorly understood. This study employs the lattice Boltzmann method coupled with large-eddy simulation to simulate unidirectional flow around restored oyster reef models using the open-source Palabos library. It examines the effects of unidirectional flow velocity and reef morphology on hydrodynamic characteristics. The research analyzes spatial and temporal variations in velocity, vorticity, and turbulence structure around the reef. The findings indicated significant flow field differences between the initially restored reefs and those post-restoration. The dimensionless wake region scale parameters of the initially restored reefs exhibit hysteresis effects, generating larger turbulence during the post-recruitment stage than in the initial stage. Areas of high turbulence in the wake are associated with above-canopy flow, bypass flow, and within-canopy flow. The presence of gaps and branches in the reef leads to complex turbulence structures and irregular vortex shedding in the reef's wake at the post-recruitment stage. These results are valuable for assessing oyster reef resilience and planning effective restoration interventions.

show abstract

Comparative De Novo transcriptome analysis of the Australian black-lip and Sydney rock oysters reveals expansion of repetitive elements in Saccostrea genomes

Cited by 4 publications

References 51 publications

Mitochondrial and nuclear genetic analyses of the tropical black-lip rock oyster (Saccostrea echinata) reveals population subdivision and informs sustainable aquaculture development

Mitochondrial and nuclear genetic analyses of the tropical black-lip rock oyster (Saccostrea echinata) reveals population subdivision and informs sustainable aquaculture development

Evaluating spawning induction methods for the tropical black-lip rock oyster, Saccostrea echinata

Numerical investigation of the restored oyster reef flow field with the lattice Boltzmann method

Contact Info

Product

Resources

About