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Journal Articles - UP - MSI

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

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    Update of seagrass cover and species diversity in Southern Viet Nam using remote sensing data and molecular analyses
    Nguyen, Xuan-Vy; Lau, Va-Khin; Nguyen-Nhat, Nhu-Thuy; Nguyen, Trung-Hieu; Phan, Kim-Hoang; Dao, Viet-Ha; Ho-Dinh, Duan; Hayashizaki, Ken-ichi; Fortes, Miguel D.; Papenbrock, Jutta (Elsevier, 2021-05)
    Along with coral reefs and mangroves, seagrass meadows are being threatened globally Southeast Asia is considered within the area of seagrasses’ cradle of diversity. However, information on the current status of seagrass beds from Southern Viet Nam is limited due to lack of reliable data about seagrass species occurring in the Southeast Asian region. One factor is the difficulty of unambiguous species identification. For example, the leaf morphological characteristics of Halophila ovalis and closely related species are overlapping which leads to misidentifications. In this study, the latest satellite Landsat 8 OLI and SENTINEL-2B image analyses were applied to determine the distribution of seagrass beds in Southern Viet Nam. Detailed morphological and genetic marker analyses were used to determine and update the species composition. The present study together with literature reviews indicate that the total area of seagrass beds from Southern Viet Nam are 10,832.1 ha. 2562 ha (or 19.1%) of seagrass coverage has been lost. The seagrass beds at Phu Quoc Island are the largest with 7579 ha. The occurrence of Halophila major is updated for almost all off-shore islands and open-water areas.
    We are deeply indebted to all staff of the Department of Marine Botany, Center for Oceanographic Data, GIS and Remote Sensing, Institute of Oceanography (ION), Viet Nam, for their support, generously providing many valuable suggestions. We thank the VAST Key lab on Food and Environmental Safety (Central Viet Nam) for the ability to use their equipment. We would like to thank the three anonymous reviewers for their suggestions, comments, and editing. We also thank to JSPS Core-toCore Program CREPSUM.JPJSCCB20200009. This work was supported by Vietnam Academy of Science and Technology, grant code VAST04.01/20-21.
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    Sequence variation in the ribosomal DNA internal transcribed spacer of Tridacna crocea
    Yu, Eizadora T.; Juinio-Meñez, Ma. Antonette; Monje, Virginia D. (Springer, 2000-11-01)
    DNA-based genetic markers are needed to augment existing allozyme markers in the assessment of genetic diversity of wild giant clam populations. The dearth of polymorphic mitochondrial DNA regions amplified from known universal polymerase chain reaction (PCR) primers has led us to search other regions of the genome for viable sources of DNA polymorphism. We have designed tridacnid-specific PCR primers for the amplification of internal transcribed spacer regions. Sequences of the first internal transcribed spacer segment (ITS-1) revealed very high polymorphism, showing 29% variation arising from base substitutions alone. Preliminary restriction analysis of the ITS regions using 8 restriction enzymes revealed cryptic changes in the DNA sequence. These mutations are promising as marker tools for differentiating geographically separated populations. Such variation in the ITS region can possibly be used for population genetic analysis.
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    Transcriptome-derived SNP markers for population assignment of sandfish, Holothuria (Metriatyla) scabra
    Ordoñez, 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.