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.
- These occurred at either side of the Wessel Islands and were termed (3.
- Three candidate adaptive SNPs were identified as occurring within known genes and gene ontology was well described for the sex peptide receptor gene..
- 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0.
- 2 School of Science and Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, Queensland 4556, Australia.
- Full list of author information is available at the end of the article.
- Under- standing the genetics of natural populations also pro- vides potential benefits for improving aquaculture and biosecurity practices as many adaptive traits in the wild are important production traits, such as.
- The use of these technologies in the detection of fine- scale structure and signatures of selection are important for determining management units, particularly in popu- lations that may otherwise appear homogenous in their distribution [10]..
- This is true for the tropical oyster Crassostrea corteziensis in the Gulf of California where allozyme analyses revealed a single panmictic popula- tion, possessing high genetic diversity [19].
- echinata are planktonic and devel- opment occurs over approximately 21 days in the hatch- ery, after which metamorphosis and settlement takes place [29].
- To achieve the genetic conservation of oyster stocks in the face of devel- oping aquaculture efforts, a sound knowledge of popula- tion genetic structure is essential.
- Mitochondrial COI data.
- Bowen had the lowest number of alleles, with 27,585 (neutral) and 28 (candidate adaptive), and an allelic richness of 0.972 (neutral) and 0.892 (candidate adaptive) (Table 4).
- Table 2 Pairwise ϕ ST estimates of haplotype frequency between each of the 10 Saccostrea echinata populations (below diagonal and corresponding P-values of ϕ ST estimates (above diagonal).
- Pairwise estimates that were not significant occurred between some of the Northern Territory populations, indicating greater homogeneity between these populations..
- The alignment of the 31 candidate sequences to the complete black-lip rock oyster transcriptome resulted in 19 hits.
- (1) SNP 2350 is situated in the gene Kmt5a, which is.
- (2) SNP 18035 is situated in the gene FAXC that may play a role in neural, axonal develop- ment.
- Table 3 Number of SNPs retained after each filtering step for the black-lip rock oyster, Saccostrea echinata.
- 70% of the samples samples).
- 50% of the locations H OBS <.
- Table 5 Pairwise F ST estimates between each of the 10 Saccostrea echinata populations based on 27,896 putatively neutral SNPs (below diagonal and corresponding P-values of F ST estimates (above diagonal).
- Genetic confirmation of the geographic range of S.
- A recent review of the diversity and evolution of oysters (both temperate and tropical species) with a focus on molecular studies by Guo et al.
- In the current study, analyses of mitochondrial COI data showed high haplo- type and nucleotide diversities (excluding the Bowen loca- tion), that are similar to those reported for other molluscs, such as the oyster C.
- a summary of published haplotype and nucleotide diver- sity estimates by Goodall-Copestake et al.
- High diversity estimates in wild populations, as reported in the current study, are a positive attribute for hatchery-based aquaculture and support the development of selective breeding programs [6, 10]..
- It is also probable that the Bowen population is close to the edge of the species range and many taxa show a general decline in genetic diversity towards range margins.
- Greater differentiation of nuclear SNP markers, compared with mitochondrial COI markers, was similarly reported by Varney et al.
- [50] in a population genetic inves- tigation of the eastern oyster, C.
- virginica, in the Gulf of Mexico.
- In the current study, the SNP analyses clearly showed that the S.
- Within the Northern Territory, Australia, low but sig- nificant differentiation was observed among some of the sample locations and DAPC analyses identified two gen- etic clusters in this region (here termed ‘west’ and ‘east’)..
- between the west and east clusters in the Northern Territory, which was further confirmed by the detection of two migrant individuals at Mooroongga, which is part of the west cluster, that were genetically most similar to the Nhulunbuy sample location, which is part of the east cluster.
- Both the structure shown in the DAPC analyses and a significant positive correlation between genetic and geographic distance support isolation by distance occurring in sampled S.
- These two clusters occur either side of the Wessel Islands, a chain of small islands extending 120 km northeast from the Napier Peninsula (Fig.
- Furthermore, this island chain would have been a land barrier around seven thousand years ago, when sea levels were lower, which may be reflected in the genetic clusters identified [58]..
- The dominant near-surface current circulation patterns and location of the Arafura Basin (indicated by the lined polygon) are illustrated (adapted from Schiller [56] and Geoscience Australia [57]).
- the sea cucumber, Holothuria scabra, in northern Australia, Gardner et al.
- [59] reported the same genetic clusters either side of the Wessel Islands.
- currents on the west side carry larvae westward and on the ‘east’ side a circular current in the Gulf may entrain larvae, restricting the passive dispersal of H.
- Gardner et al.
- [59] also proposed that the Arafura Basin, situated west of the Wessel Islands (Fig.
- The congruence between the findings of Gardner et al..
- such investigations may include a multi-species phylogeographic study of the region [52].
- In the current study neutral and candidate adaptive SNPs were analysed separately and together (when appropri- ate), and no major conflicts between resulting data sets were detected.
- In the current study of S.
- echinata, three candidate adaptive SNPs were successfully identified as belonging to known genes, and gene ontology was well described for the SPR gene.
- Further research is required to better understand the role of the SPR gene in relation to seascape genomics of S.
- Within the Northern Territory, Australia where most of the sample locations in this study occur, and where S.
- A 594 bp fragment of the mitochondrial COI gene was amplified using the polymerase chain reaction (PCR) protocol.
- Tajima’s D and Fu’s Fs neutrality tests were per- formed in the program ARLEQUIN .
- echi- nata from previous studies (n were ob- tained from GenBank and also included in the network analyses.
- Double-digest restriction site-associated DNA (ddRAD) libraries were constructed following a protocol modified from Peterson et al.
- In the population module of STACKS, and following consecutive filtering steps, SNPs were retained in at least 70% of the individuals and 50% of the locations, had a minor allele frequency of at least 10%, and heterozygos- ity <.
- Details of the number of SNPs kept after each filtering step are provided in Table 3.
- This was done to increase the accuracy of the assign- ment test, as they are moderately accurate.
- In a given genotype, when the observed frequency of any allele was zero (a missing al- lele), the frequency of this allele was replaced by a fixed value of 0.005 as recommended by Paetkau et al.
- The Cornuet et al.
- [84] algorithm, with a statistical threshold calculated separately for every population based on an alpha-value of 0.05, was used [82].
- 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, anno- tated transcriptome of the black-lip rock oyster, referred to as Saccostrea lineage J by McDougall [36].
- A minimal E-value threshold of and the highest ‘Grade’ (a weighted score for the hit comprised of the E-value, the.
- (ZIP 12536 kb) Additional file 5: This file includes a list of identifying numbers and sequences for the 31 candidate adaptive SNPs.
- SJN carried out all tissue collections, participated in the investigation design and conceptualisation, performed data analyses, drafted the manuscript and provided project funding.
- PCS developed the broad project concept, participated in the investigation design, provided supervisory support, advice on tropical oyster biology and ecology, and edited the manuscript.
- JMS participated in design and conceptualisation of the project, provided statistical advice and technical input on investigation design, assisted with data analyses and interpretation, provided supervisory support and edited the manuscript.
- This study was conducted within the Australian Northern Territory Government “ Tropical Rock Oyster Aboriginal Economic Development Program ” that was administered by the Darwin Aquaculture Centre, Department of Primary Industry and Resources of the Northern Territory Government.
- The Program scientist (Samantha Nowland) is the first author of this paper and was involved in all aspects of the research.
- design of the study and collection, analysis, and interpretation of data and in writing the manuscript..
- 4 Australian Centre for Pacific Islands Research and School of Science and Engineering, University of the Sunshine Coast, Maroochydore, Queensland 4556, Australia..
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