Transcriptome-derived SNP markers for population assignment of sandfish, Holothuria (Metriatyla) scabra

Ordoñez, June F.; Ravago-Gotanco, Rachel

doi:10.1016/j.aquaculture.2023.740261

Cited by 3 publications

(4 citation statements)

References 92 publications

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“…Tissues were preserved in 96% ethanol or salt-saturated DMSO buffer and maintained under refrigeration (4°C) until DNA extraction at the Marine Science Institute, University of the Philippines at Diliman, Manila, the Philippines. Total genomic DNA was extracted using a Qiagen DNEasy Blood and Tissue kit (Qiagen, Valencia, California, USA) as per Ordoñez and Ravago-Gotanco (2024), quality-checked and quantified using agarose gel electrophoresis and Qubit 2.0 Fluorometer (ThermoFisher Scientific, Wilmington, USA), respectively, before being submitted for DArTseq ™ genotyping to Diversity Arrays Technology Ltd (DArT PL), in Canberra, Australia.…”

Section: Sample Collection and Tissue Samplingmentioning

confidence: 99%

“…Assessment of a suitable nextgeneration sequencing approach (DArTseq) for sandfish was reported by Lal et al (2021), and used to investigate population genomic diversity and structure in Fiji (Brown et al, 2022) and the Philippines (this study). Genome-wide SNPs were also employed to examine loss of genetic diversity in hatchery-produced sandfish (Brown et al, 2024), examine growth rate variability (Ordoñez et al, 2021) and assign populations of origin for traceability studies (Ordoñez and Ravago-Gotanco, 2024).…”

Section: Implications For Fishery and Restocking Management In The Ph...mentioning

confidence: 99%

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Complex patterns of genetic structure in the sea cucumber Holothuria (Metriatyla) scabra from the Philippines: implications for aquaculture and fishery management

Lal,

Macahig,

Juinio-Meñez

et al. 2024

Front. Mar. Sci.

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The sandfish Holothuria (Metriatyla) scabra, is a high-value tropical sea cucumber harvested from wild stocks for over four centuries in multi-species fisheries across its Indo-Pacific distribution, for the global bêche-de-mer (BDM) trade. Within Southeast Asia, the Philippines is an important centre of the BDM trade, however overharvesting and largely open fishery management have resulted in declining catch volumes. Sandfish mariculture has been developed to supplement BDM supply and assist restocking efforts; however, it is heavily reliant on wild populations for broodstock supply. Consequently, to inform fishery, mariculture, germplasm and translocation management policies for both wild and captive resources, a high-resolution genomic audit of 16 wild sandfish populations was conducted, employing a proven genotyping-by-sequencing approach for this species (DArTseq). Genomic data (8,266 selectively-neutral and 117 putatively-adaptive SNPs) were used to assess fine-scale genetic structure, diversity, relatedness, population connectivity and local adaptation at both broad (biogeographic region) and local (within-biogeographic region) scales. An independent hydrodynamic particle dispersal model was also used to assess population connectivity. The overall pattern of population differentiation at the country level for H. scabra in the Philippines is complex, with nine genetic stocks and respective management units delineated across 5 biogeographic regions: (1) Celebes Sea, (2) North and (3) South Philippine Seas, (4) South China and Internal Seas and (5) Sulu Sea. Genetic connectivity is highest within proximate marine biogeographic regions (mean Fst=0.016), with greater separation evident between geographically distant sites (Fst range=0.041–0.045). Signatures of local adaptation were detected among six biogeographic regions, with genetic bottlenecks at 5 sites, particularly within historically heavily-exploited locations in the western and central Philippines. Genetic structure is influenced by geographic distance, larval dispersal capacity, species-specific larval development and settlement attributes, variable ocean current-mediated gene flow, source and sink location geography and habitat heterogeneity across the archipelago. Data reported here will inform accurate and sustainable fishery regulation, conservation of genetic diversity, direct broodstock sourcing for mariculture and guide restocking interventions across the Philippines.

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Section: Sample Collection and Tissue Samplingmentioning

confidence: 99%

Section: Implications For Fishery and Restocking Management In The Ph...mentioning

confidence: 99%

Complex patterns of genetic structure in the sea cucumber Holothuria (Metriatyla) scabra from the Philippines: implications for aquaculture and fishery management

Lal,

Macahig,

Juinio-Meñez

et al. 2024

Front. Mar. Sci.

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show abstract

Section: Sample Collection and Tissue Samplingmentioning

confidence: 99%

Section: Implications For Fishery and Restocking Management In The Ph...mentioning

confidence: 99%

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Genetic variation mining of the Chinese mitten crab (Eriocheir sinensis) based on transcriptome data from public databases

Xu,

Yu,

Feng

et al. 2024

Briefings in Functional Genomics

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At present, public databases house an extensive repository of transcriptome data, with the volume continuing to grow at an accelerated pace. Utilizing these data effectively is a shared interest within the scientific community. In this study, we introduced a novel strategy that harnesses SNPs and InDels identified from transcriptome data, combined with sample metadata from databases, to effectively screen for molecular markers correlated with traits. We utilized 228 transcriptome datasets of Eriocheir sinensis from the NCBI database and employed the Genome Analysis Toolkit software to identify 96 388 SNPs and 20 645 InDels. Employing the genome-wide association study analysis, in conjunction with the gender information from databases, we identified 3456 sex-biased SNPs and 639 sex-biased InDels. The KOG and KEGG annotations of the sex-biased SNPs and InDels revealed that these genes were primarily involved in the metabolic processes of E. sinensis. Combined with SnpEff annotation and PCR experimental validation, a highly sex-biased SNP located in the Kelch domain containing 4 (Klhdc4) gene, CHR67-6415071, was found to alter the splicing sites of Klhdc4, generating two splice variants, Klhdc4_a and Klhdc4_b. Additionally, Klhdc4 exhibited robust expression across the ovaries, testes, and accessory glands. The sex-biased SNPs and InDels identified in this study are conducive to the development of unisexual cultivation methods for E. sinensis, and the alternative splicing event caused by the sex-biased SNP in Klhdc4 may serve as a potential mechanism for sex regulation in E. sinensis. The analysis strategy employed in this study represents a new direction for the rational exploitation and utilization of transcriptome data in public databases.

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Transcriptome-derived SNP markers for population assignment of sandfish, Holothuria (Metriatyla) scabra

Cited by 3 publications

References 92 publications

Complex patterns of genetic structure in the sea cucumber Holothuria (Metriatyla) scabra from the Philippines: implications for aquaculture and fishery management

Complex patterns of genetic structure in the sea cucumber Holothuria (Metriatyla) scabra from the Philippines: implications for aquaculture and fishery management

DataSheet_2.csv

Genetic variation mining of the Chinese mitten crab (Eriocheir sinensis) based on transcriptome data from public databases

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