Journal Articles - UP - MSI
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- Transcriptome analysis of growth variation in early juvenile stage sandfish Holothuria scabraOrdoñez, 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.).
- Associated effects of shading on the behavior, growth, and survival of Stichopus cf. horrens juvenilesRioja, Rose Angeli; Palomar-Abesamis, Nadia; Juinio–Meñez, Marie Antonette (Springer Science and Business Media LLC, 2021-07-07)Stichopus cf. horrens is an emergent culture species. It is known to be nocturnal and negatively phototactic; hence, determining its behavioral and growth responses to different light regimes is essential in optimizing culture protocols. This study examined the interactive effects of shading and relative food availability on the feeding pattern, absolute growth rates, and survival of juvenile S. cf. horrens. Six-month-old juveniles (4.27 to 19.41 g) were reared in replicate aquaria with three different shading treatments (covered, exposed, and half-covered aquaria) under ambient light conditions for 30 days. Juveniles in the exposed treatment with high microalgal biomass (13.44 ± 4.57 mg/g) had the highest growth rates (0.10 ± 0.05 g/day) but also the highest mortality (50%). In contrast, juveniles in the covered treatment had the lowest growth (−0.07 ± 0.03 g/day) but the highest survival (100%). Growth rates in the half-covered treatment were comparable with the exposed, and survival was higher than in the covered treatment. These indicate a trade-off between growth associated with more food and mortality risks due to light-induced stress. Juveniles in the half-covered treatment showed a significant preference to stay in the shaded portion whenever they were inactive during the day, suggesting avoidance to high light intensities (4726.51 ± 1582.43 Lux). Results of this study suggest that careful calibration of light intensities in nursery systems may help enhance juvenile growth. For indoor systems that may have limited space or surfaces for microalgal growth, cultured benthic diatom can be added to the partially covered tanks to increase the food available for the juveniles.
- Sargassum sp. juice as an early juvenile supplemental feed for Stichopus cf. horrensIbañez, Glaiza; Cabanayan-Soy, Rona; Baure, Jerwin; Juinio-Meñez, Marie Antonette (Springer, 2022-09-28)The development of an efficient and low-cost feed is important to reduce the production and maintenance costs of microalgae. In this study, two experiments were conducted to evaluate the feasibility of using Sargassum sp. juice (SARG) to boost the growth and survival of post-settled Stichopus cf. horrens juveniles. Experiment 1 tested whether SARG improves growth compared with live microalgae diets, Chaetoceros calcitrans (Cc), combined Cc and Navicula ramosissima (Nr), and an unfed treatment. Experiment 2 determined the best SARG concentration—high feeding regime (HFR; 1 mL ind−1), medium (MFR; 0.5 mL ind−1), or low (LFR; 0.25 ml ind−1), relative to live microalgae Chaetoceros muelleri (CM). Juveniles in both experiments were reared for 30 days. In Experiment 1, the average daily growth rate (DGRL) of juveniles in SARG (0.04 ± 0.01 cm d−1) was the highest although not significantly different from Cc and Cc + Nr, but was significantly higher than the control. In Experiment 2, DGRL at day 14 in HFR (− 0.02 ± 0.02 cm d−1) was significantly lower than LFR (0.01 ± 0.01 cm d−1) and MFR (0.02 ± 0.02 cm d−1). Survival was higher in all SARG treatments compared with CM, while a significant decrease in feeding activity was observed in HFR by day 30. Results indicate that concentrations of 0.25–0.5 mL SARG per juvenile can boost growth and be an alternate diet for post-settled juveniles during early rearing. However, SARG alone is not sufficient to maintain growth beyond 3 weeks. With SARG feed supplementation and water quality management, the scaling-up of juvenile production of this emergent culture species can be accelerated.Our sincere gratitude to Mr. Tirso Catbagan and Mr. Garry Bucol for their assistance in the set-up of the experiments. We also thank Ms. Rose Angeli Rioja and Ms. JayR Gorospe for providing inputs to improve this paper. We also thank the Sea cucumber Research Team and the staff of the University of the Philippines—Marine Science Institute, Bolinao Marine Laboratory for their support and assistance during the conduct of the study.
- Transcriptome-derived SNP markers for population assignment of sandfish, Holothuria (Metriatyla) scabraOrdoñez, June F.; Ravago-Gotanco, Rachel (Elsevier, 2024-01-30)The sandfish, Holothuria scabra is a commercially important fishery and aquaculture species contributing to the high-value sea cucumber industry. Overexploited across many areas throughout its distributional range, natural populations are considered in decline. Accurate genetic assignment to population of origin is becoming increasingly important for genetics-based marine fisheries management and monitoring, especially for species experiencing depletion of natural stocks and decline in fisheries productivity due to overfishing and illegal, unreported, and unregulated (IUU) fishing. Initiatives for genetics-based applications on economically important seafood such as H. scabra have been limited by the lack of comprehensive genome or transcriptome resources. The present study developed and evaluated the use of gene-associated single nucleotide polymorphism (SNP) markers to assign sandfish to three locations in the Philippines, in the proximity of existing and emerging hatchery production centers. In silico SNP discovery pipeline using pooled RNA-Seq libraries and medium-throughput genotyping approach generated a dataset comprising 115 individuals genotyped at 88 SNPs. Population assignment using machine-learning analysis and Bayesian approach revealed that the 88 transcriptome-derived SNPs allowed the assignment of sandfish individuals to population of origin, with an overall assignment accuracy of >80%. The novel SNPs developed could find their utility in facilitating the development of geographic traceability tools applicable in the context of sandfish aquaculture, fisheries management and conservation.
- Metamorphic success and production cost of Holothuria scabra reared on microalgae concentrates compared with live microalgaeGarpa, Tomilyn Jan; Caasi, Olivier Josh C.; Juinio–Meñez, Marie Antonette (Bureau of Fisheries and Aquatic Resources, 2024-03-07)The production of live microalgae poses challenges for the expansion of sandfish hatcheries, hindered by high costs and limited technical resources. In relation to this, the use of three imported commercial concentrates (Instant Algae®) - TW1200 (Thalassiosira weisflogii), TISO1800 (Isochrysis sp.), and Shellfish1800 (mixed diatom) - were compared with live Chaetoceros calcitrans (CC). The diet efficacy was evaluated based on larval development, growth, and survival to late auricularia (LA) with hyaline spheres (HS), and the number of post-settled juveniles. Larvae reared with TW did not progress beyond LA, while those fed CC exhibited earlier LA development, larger sizes (1028.43 ± 19.38 µm), and significantly more post–settled juveniles (9,268 ± 2,183.79) compared to SHELL and TISO. Although TISO larvae reached a larger size during LA (855.7 ± 62.67 µm), SHELL resulted in a higher number of post-settled juveniles. The better performance of CC and SHELL may be attributed to their higher carbohydrate content. Despite SHELL and TISO having lower juvenile yields and longer feeding durations, the estimated cost per juvenile using SHELL, TISO, and CC were PHP 2.00, PHP 11.77, and PHP 0.52, respectively. Results showed that microalgae concentrates are not a cost-effective option under the studied conditions. The potential use of microalgae concentrates as supplemental feeds and further research to develop the use of local microalgae concentrates to sandfish larval culture are discussed.This study was funded by Australian Centre for International Agricultural Research (ACIAR) through the project FIS/2016/122 “Increasing technical skills supporting community-based sea cucumber production in Vietnam and the Philippines” and administrative support from the Marine Environment and Resources Foundation (MERF), Inc. We would also like to thank the Bolinao Marine Laboratory of the University of the Philippines Marine Science Institute for the use of facilities and equipment. We are grateful to our collaborators, Jon Altamirano and Roselyn Noran, and SEAFDEC AQD for guidance on the methods used for preparation and protocols of microalgae concentrate feeding regimen. Special thanks to JayR Gorospe for comments on the earlier draft and Jerwin Baure for copyediting this manuscript. The assistance of Mr. Tirso Catbagan in the culture of larvae and maintenance of the experimental tanks was invaluable during the experiment.
- Pseudocryptic diversity and species boundaries in the sea cucumber Stichopus cf. horrens (Echinodermata: Stichopodidae) revealed by mitochondrial and microsatellite markersLizano, Apollo Marco D.; Kim, Kenneth M.; Juinio-Meñez, Marie Antonette; Ravago-Gotanco, Rachel (Nature Research, 2024)Morphologically cryptic and pseudo-cryptic species pose a challenge to taxonomic identification and assessments of species diversity and distributions. Such is the case for the sea cucumber Stichopus horrens, commonly confused with Stichopus monotuberculatus. Here, we used mitochondrial cytochrome oxidase subunit I (COI) and microsatellite markers to examine genetic diversity in Stichopus cf. horrens throughout the Philippine archipelago, to aid species identification and clarify species boundaries. Phylogenetic analysis reveals two recently diverged COI lineages (Clade A and Clade B; c. 1.35–2.54 Mya) corresponding to sequence records for specimens identified as S. monotuberculatus and S. horrens, respectively. Microsatellite markers reveal two significantly differentiated genotype clusters broadly concordant with COI lineages (Cluster 1, Cluster 2). A small proportion of individuals were identified as later-generation hybrids indicating limited contemporary gene flow between genotype clusters, thus confirming species boundaries. Morphological differences in papillae distribution and form are observed for the two species, however tack-like spicules from the dorsal papillae are not a reliable diagnostic character. An additional putative cryptic species was detected within Clade B-Cluster 2 specimens warranting further examination. We propose that these lineages revealed by COI and genotype data be referred to as Stichopus cf. horrens species complex. © The Author(s) 2024.