DNA Barcoding and Diversity Analysis of 19 Economically Important Philippine Sea Cucumbers (Holothuroidea)

Ma. Neda Alcudia-Catalma1§, Maria Genaleen Q. Diaz2, Roberta N. Garcia1,
Pablo P. Ocampo2, Antonio C. Laurena1, and Evelyn Mae Tecson-Mendoza1*

1Institute of Plant Breeding, College of Agriculture and Food Science
2Institute of Biological Sciences, College of Arts and Sciences
University of the Philippines Los Baños, College 4031 Laguna, Philippines
§Silk/Silkworm Genomics Project, Research and Development Division
Philippine Textile Research Institute, Department of Science and Technology
Bicutan 1631 Taguig City, Philippines

*Corresponding Author: This email address is being protected from spambots. You need JavaScript enabled to view it.




This study established the DNA barcodes of 19 economically important Philippine sea cucumbers belonging to Class Holothuroidea under Phylum Echinodermata using the cytochrome c oxidase I (COI) gene. These include sea cucumbers from the Family Holothuriidae under Order Aspidochirotida: Bohadschia marmorata, B. koellikeri, B. vitiensis, B. argus, Bohadschia sp. 1, Actinopyga echinites, A. lecanora, Holothuria scabra, H. fuscogilva, H. atra, H. impatiens, and H. albiventer; from the Family Stichopodiidae under Order Aspidochirotida: Stichopus horrens, S. monotuberculatus, S. vastus, S. hermanni, S. chloronotus, and Thelenota ananas; and from the Family Phyllophoriidae under Order Dendochirotida was Neocucumis proteus. Based on Kimura-2 pairwise (K2P) distances, low genetic variation within species of 0.005–0.018 was observed except for several species such as S. chloronotus, H. albiventer, A. echinites, and H. scabra – which had 0.057, 0.181, 0.207, and 0.215 within-species genetic variations, respectively. On the other hand, variation between species within a genus was 0.123 for Bohadschia, 0.18 for Actinopyga, 0.19 for Holothuria, and 0.071 for Stichopus. Phylogenetic tree using neighbor-joining analysis showed monophyletic clades for the genera Bohadschia, Actinopyga, Stichopus, Thelenota, and Neocucumis while paraphyletic clade was formed for the genus Holothuria. COI DNA sequences and barcodes were established for the first time for Neocucumis proteus and Holothuria albiventer.



The sea cucumber is an aquatic marine invertebrate that belongs to Class Holothuroidea, Phylum Echinodermata. It is globally traded because its dried product – commonly known as “balat,” “bat,” “gamat,” or “trepang” in Asia and “bêche-de-mer” in France – is used as an exotic Asian cuisine and source of natural products. The dried sea cucumbers command high price in the international market with retail price ranging from USD 15–385/kg and are exported to Hong Kong, China, Japan, South Korea, Singapore, and the US (Purcell 2014). The sea cucumber is also explored for biomedical research, and for medicinal and therapeutic properties due to the presence of high valued bioactive compounds (Bordbar et al. 2011). . . . read more



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