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Journal Articles - UP - MSI

Permanent URI for this collectionhttps://repository.unesco.gov.ph/handle/123456789/50

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Author: search.filters.author.Ravago-Gotanco, RachelGeographic name: search.filters.geographicname.Philippines

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    Transcriptome analysis of growth variation in early juvenile stage sandfish Holothuria scabra
    Ordoñez, June Feliciano F.; Galindez, Gihanna Gaye S.T.; Gulay, Karina Therese; Ravago-Gotanco, Rachel (Elsevier, 2021-12)
    The sandfish Holothuria scabra is a high-value tropical sea cucumber species representing a major mariculture prospect across the Indo-Pacific. Advancements in culture technology, rearing, and processing present options for augmenting capture production, stock restoration, and sustainable livelihood activities from hatchery-produced sandfish. Further improvements in mariculture production may be gained from the application of genomic technologies to improve performance traits such as growth. In this study, we performed de novo transcriptome assembly and characterization of fast- and slow-growing juvenile H. scabra from three Philippine populations. Analyses revealed 66 unigenes that were consistently differentially regulated in fast-growing sandfish and found to be associated with immune response and metabolism. Further, we identified microsatellite and single nucleotide polymorphism markers potentially associated with fast growth. These findings provide insight on potential genomic determinants underlying growth regulation in early juvenile sandfish which will be useful for further functional studies.
    The authors are grateful to the following individuals and institutions for providing samples and facilitating their collection: D. Ticao of (Finfish Hatcheries, Inc.); Dr. M.A. Juinio-Menez, ˜ J.R. Gorospe, C. Edullantes, B. Rodriguez, A. Rioja, T. Catbagan, and G. Peralta of Bolinao Marine Laboratory, University of the Philippines Marine Science Institute; and E. Tech (Palawan Aquaculture Corp.).
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    Zooxanthellae diversity and coral-symbiont associations in the Philippine archipelago: specificity and adaptability across thermal gradients
    Torres, Andrew F.; Valino, Darryl Anthony M.; Ravago-Gotanco, Rachel (Frontiers Media SA, 2021-10-20)
    Prolonged thermal stress and high levels of solar irradiance can disrupt the coral-algal symbiosis and cause bleaching and lowered overall fitness that lead to the likely death of the cnidarian host. Adaptive bleaching and acclimatization of corals, which posits bleaching as an opportunity for the coral host to switch its currently susceptible endosymbionts to more stress-tolerant taxa, offers hope for survival of reefs amid rapidly warming oceans. In this study, we explored the diversity and distribution of coral-zooxanthellae associations in the context of geospatial patterns of sea surface temperature (SST) and thermal anomalies across the Philippine archipelago. Thermal clusters based on annual sea surface temperature means and each site’s frequency of exposure to heat stress were described using three-decade (1985–2018) remotely sensed data. Haphazard sampling of 628 coral fragments was conducted in 14 reef sites over 3 years (2015–2018). Using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprinting and sequencing of the zooxanthellae ITS2 region, we characterized endosymbiont diversity within four reef-building coral families across archipelagic thermal regimes. Consistency in dominant Symbiodiniaceae taxon was observed in Acropora spp., Porites spp., and Heliopora coerulea. In contrast, the family Pocilloporidae (Pocillopora spp., Seriatopora spp., and Stylophora pistillata) exhibited biogeographic variability in zooxanthellae composition, concordant with inferred occurrences of sustained thermal stress. Multivariate analyses identify two broad Pocilloporidae clusters that correspond with mean SST ranges and frequency of exposure to bleaching-level thermal stress which are largely supported by ANOSIM. Differences in zooxanthellae assemblages may reflect host-specific responses to ecological or environmental gradients across biogeographic regions. Such patterns of variability provide insight and support for the adaptability and potential resilience of coral communities in geographically and oceanographically complex regions, especially amidst the increasing severity of global and local-scale stressors.
    This paper is dedicated to the late Ronald D. Villanueva whose contribution to the project during its inception has been invaluable. The authors thank Patrick R. Pata and the reviewers LE and RC-T for their helpful comments and suggestions, and acknowledge Hazel O. Arceo, Cesar L. Villanoy, and Maria Lourdes San Diego-McGlone for their support of this study. Eileen Peñaflor and Mariana Soppa shared key knowledge in processing satellite products. Mikhael Tañedo, Romer Albino, Emmeline Jamodiong, David Siquioco, Lovely Heyres, Rhea Luciano, Joey Cabasan, Frederico Sabban, Geminne Manzano, Clairecynth Yu, Joyce Velos, Joseph Garcia, Robert Casauay, Maryjune Cabiguin, Macy A onuevo-Arcega, Ariel Loja, Jerome Genilan, Amabelle Go, Jamie Dichaves, Elaine Saniel, and Miledel Quibilan assisted with field collections. Supporting hard coral data were provided by the DOST-PCAARRD NACRE Program and the DENR-BMB WPS and SECURE Philippine Rise Projects. This is MSI contribution number 486.
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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, Monal M.; Macahig, Deo A. S.; Juinio-Meñez, Marie A.; Altamirano, Jon P.; Noran-Baylon, Roselyn; de la Torre-de la Cruz, Margarita; Villamor, Janine L.; Gacura, Jonh Rey L.; Uy, Wilfredo H.; Mira-Honghong, Hanzel; Southgate, Paul C.; Ravago-Gotanco, Rachel (Frontiers Media SA, 2024-06-04)
    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.