Species identification and molecular phylogenetics of processed sea cucumbers from Malaysian market based on 12s mitochondrial rRNA gene

Extensive processing of sea cucumber causes body deformation of the marine organism, hence causing difficulties in species identification of processed sea cucumbers. Due to the copresence of cases of unlabelled or mislabelled sea cucumber products in Malaysian markets and worldwide, a study was conducted to determine the species identities of processed sea cucumbers from selected Malaysian markets using non-protein-coding 12S mitochondrial rRNA gene. Phylogenetic analyses based on the distance-based Neighbour Joining method, and the character-based methods i.e. the Maximum Parsimony method, Maximum Likelihood method, and the Bayesian Analysis method of 81 ingroup sequences representing 63 processed sea cucumber specimens, 13 fresh and processed reference samples for species identification, and five fresh additional specimens from Teluk Nipah Beach, Pangkor Archipelago and Manukan Island, Sabah suggested the presence of three main clusters i.e. a gamat family cluster consisting of family Stichopodidae (Stichopus horrens, Stichopus vastus, and Thelenota anax) and two clusters of timun laut family comprising family Holothuriidae (Holothuria (Mertensiothuria) leucospilota, Holothuria (Metriatyla)scabra, Holothuria (Metriatyla) lessoni, Holothuria (Halodeima) atra, and Holothuria (Halodeima) edulis) and family Caudinidae (Acaudina molpadioides). The outcomes of this study also highlighted the availability of 40 new 12S mitochondrial rRNA gene sequences deposited in the GenBank that can be utilised by the enforcement agencies to monitor and overcome the issues of species substitution and product mislabelling of processed sea cucumber products in Malaysian markets

Species identification of processed sea cucumbers from Malaysian market based on concatenated gene sequences of mitochondrial rRNA genes

Species identification of sea cucumbers that have undergone body deformation due to extensive food processing e.g. beche-de-mer is difficult especially with the copresence of cases of unlabelled or mislabelled sea cucumber-based products in the markets. Therefore, a study was done to determine the species identities of processed sea cucumbers from selected Malaysian markets using concatenated gene sequences of non-protein-coding 12S and 16S mitochondrial rRNA genes. Phylogenetic analyses based on the distance-based Neighbour Joining method, and the character-based methods i.e. the Maximum Parsimony method, Maximum Likelihood method, and the Bayesian Analysis method of 47 ingroup sequences representing 37 processed sea cucumber specimens, 6 reference samples, and 4 additional specimens suggested the presence of 3 main clusters i.e. gamat family consisting of genus Stichopus and genus Thelenota; and timun laut family comprising family Holothuriidae. A number of 3 gamat species i.e. Stichopus horrens, Stichopus vastus, and Thelenota anax were recorded. Meanwhile, the specimens of Holothuria (Halodeima) atra, Holothuria (Halodeima) edulis, Holothuria (Metriatyla) lessoni, Holothuria (Mertensiothuria) leucospilota, and Holothuria (Metriatyla) scabra were the 5 timun laut species that grouped under the family Holothuriidae. The outcomes of this study can be utilised by the enforcement agencies to monitor and overcome the issues of species substitution and product mislabelling of processed sea cucumber products in Malaysian markets

Phylogenetic relationships within the genus holothuria inferred from 16s mitochondiral rRNA gene sequences

This study aimed to resolve the taxonomic status of a morphologically undetermined sea cucumber species of order Apodida from Malaysia (GenBank accession no.: FJ223867) using partial 16S mitochondrial rRNA gene sequences and subsequently to determine the validity of morphological taxonomy of Holothuria species into its current subgenera. The undetermined species clustered with all taxa of Holothuria in previous study. Phylogenetic analyses using maximum parsimony and Bayesian methods suggest that the undetermined species was genetically closer to Holothuria (Lessonothuria) pardalis and Holothuria (Acanthotrapeza) coluber; and its position in both phylogenetic trees further suggests its status as a Holothuria taxon. Subgenera of Holothuria, Merthensiothuria and Metriatyla are monophyletic with strong bootstrap supports and posterior probabilities of clades, thus strengthening their morphological taxonomies. Nonetheless, the non-monophyly of subgenera of Halodeima, Microthele and Platyperona suggests a requirement for their taxonomic revisions using integrative taxonomy. The status of Holothuria (Halodeima) edulis subgroups in the maximum parsimony and Bayesian trees is indistinct and further taxonomic revisions are necessary. In terms of sister relationship, both phylogenetic trees suggest that subgenus Holothuria is a sister taxon of subgenus Roweothuria while the other sister relationships were unclear due to the undetermined species, paraphyly and polyphyly of a number of subgenera. Further studies with more specimens of genus Holothuria from broader geographical locations and various mtDNA genes along with morphological approaches may facilitate to provide better insights into the molecular phylogeny of subgenera of Holothuria

Phylogenetic relationships within the Genus Holothuria inferred from 16S Mitochondiral rRNA Gene Sequences

This study aimed to resolve the taxonomic status of a morphologically undetermined sea cucumber species of order Apodida from Malaysia (GenBank accession no.: FJ223867) using partial 16S mitochondrial rRNA gene sequences and subsequently to determine the validity of morphological taxonomy of Holothuria species into its current subgenera. The undetermined species clustered with all taxa of Holothuria in previous study. Phylogenetic analyses using maximum parsimony and Bayesian methods suggest that the undetermined species was genetically closer to Holothuria (Lessonothuria) pardalis and Holothuria (Acanthotrapeza) coluber; and its position in both phylogenetic trees further suggests its status as a Holothuria taxon. Subgenera of Holothuria, Merthensiothuria and Metriatyla are monophyletic with strong bootstrap supports and posterior probabilities of clades, thus strengthening their morphological taxonomies. Nonetheless, the non-monophyly of subgenera of Halodeima, Microthele and Platyperona suggests a requirement for their taxonomic revisions using integrative taxonomy. The status of Holothuria (Halodeima) edulis subgroups in the maximum parsimony and Bayesian trees is indistinct and further taxonomic revisions are necessary. In terms of sister relationship, both phylogenetic trees suggest that subgenus Holothuria is a sister taxon of subgenus Roweothuria while the other sister relationships were unclear due to the undetermined species, paraphyly and polyphyly of a number of subgenera. Further studies with more specimens of genus Holothuria from broader geographical locations and various mtDNA genes along with morphological approaches may facilitate to provide better insights into the molecular phylogeny of subgenera of Holothuria

A Study on The Potential Pathways For Existing Drugs Against COVID-19

Coronavirus infectious disease 2019 (COVID-19) is a global pandemic declared by the World Health Organization (WHO) in March 2020. This emerging infectious disease is rapidly transmitted and does not only pose a global threat to public health but also badly affects the economy. At present, there is no effective drug to treat COVID-19, leading to a significant challenge upon current global attempts at restraining the outbreak. There are several currently available drugs, also considered as the repurposed drugs are in use for treatment against COVID-19. However, these drugs are not as efficient as it is hoped. Therefore, this study is conducted to further explore into other established antivirus that could function better for COVID-19 treatment. In addition, the pathways that associated with the drugs are identified and potential targeted proteins for the repurposed drugs are also pointed out. The articles for review were selected from several search engine databases, which are ScienceDirect, SpringerLink, PubMed, and Scopus including the keywords COVID-19, SARS, MERS, potential pathways for antiviral drugs as well as repurposed drugs, with more than 50 primary research articles identified. Findings and analysis have discovered potential repurposed drugs that could be used for COVID-19, namely bisoxatin, nitazoxanide and teicoplanin which could be involved in corona-related pathways. Meanwhile, the associated pathways are JAK-STAT, Neprilysin (NEP) and cGAS-STING that counteract excessive immune response and act as a medium for the drugs to access antiviral activities. The repurposed drugs target protein identification is also a critical significance and it was found that S-protein, TMPRSS2, RdRp and RDB which are the signalling protein can be interrupted by the repurposed drugs, presenting a promising antivirus against SARS-CoV-2.  It is concluded that this study will provide information to assist logical design of the repurposed drug for its effectiveness as antivirus against COVID-19

16S rRNA Barcoding technique for species identification of processed sea cucumbers from selected Malaysian markets

In food industry, wide-ranging processing of sea cucumbers (Phylum Echinodermata: Class Holothuroidea) including gutting, boiling, roasting, and subsequent preservation procedures are frequently needed prior to marketing. These processes cause body deformation of the sea cucumbers, thus leading to difficulties in species identification and confirmation of the processed sea cucumbers or beche-de-mer. Furthermore, beche-de-mer products in Malaysian markets are often unlabelled or mislabelled. Economic fraud, health hazards, and illegal trade of protected species are the potential major consequences of the issues. Therefore, a reliable, reproducible, and rapid technique for species identification is required. For that reason, this study was conducted to determine species identity of 25 beche-de-mer specimens that were not tagged with species details from four selected Malaysian markets. Five reference samples were also included in the analyses consisting of fresh samples that were morphologically identified as Stichopus horrens and Holothuria (Mertensiothuria) leucospilota from Pangkor Island, Perak, Malaysia. Phylogenetic analyses of 30 partial sequences of non-protein-coding 16S mitochondrial ribosomal RNA (rRNA) gene using five main methods i.e. Neighbour-Joining (NJ), Maximum Likelihood (ML), Minimum Evolution (ME), Unweighted Pair Group Method with Arithmetic Mean (UPGMA), and Maximum Parsimony (MP) showed the presence of two main clusters of the beche-demer specimens: Stichopodidae (gamat family) and Holothuriidae (timun laut family). The beche-de-mer specimens of S. horrens, Stichopus herrmanni, and Thelenota anax were the three gamat species that clustered under the family Stichopodidae. Meanwhile, the beche-de-mer specimens of H. leucospilota, Holothuria (Halodeima) edulis, Holothuria (Metriatyla) scabra, and H. scabra var. versicolor were the four timun laut species that clustered under the family Holothuriidae. In fact, the outcomes of this study suggested the potential of 16S mitochondrial rRNA gene sequencing technique to be used by the enforcement agencies in monitoring and overcoming the issues of species substitution and product mislabeling of beche-de-mer products in Malaysian markets

16S rRNA barcoding technique for species identification of processed sea cucumbers from selected Malaysian markets

In food industry, wide-ranging processing of sea cucumbers (Phylum Echinodermata: Class Holothuroidea) including gutting, boiling, roasting, and subsequent preservation procedures are frequently needed prior to marketing. These processes cause body deformation of the sea cucumbers, thus leading to difficulties in species identification and confirmation of the processed sea cucumbers or beche-de-mer. Furthermore, beche-de-mer products in Malaysian markets are often unlabelled or mislabelled. Economic fraud, health hazards, and illegal trade of protected species are the potential major consequences of the issues. Therefore, a reliable, reproducible, and rapid technique for species identification is required. For that reason, this study was conducted to determine species identity of 25 beche-de-mer specimens that were not tagged with species details from four selected Malaysian markets. Five reference samples were also included in the analyses consisting of fresh samples that were morphologically identified as Stichopus horrens and Holothuria (Mertensiothuria) leucospilota from Pangkor Island, Perak, Malaysia. Phylogenetic analyses of 30 partial sequences of non-protein-coding 16S mitochondrial ribosomal RNA (rRNA) gene using five main methods i.e. Neighbour-Joining (NJ), Maximum Likelihood (ML), Minimum Evolution (ME), Unweighted Pair Group Method with Arithmetic Mean (UPGMA), and Maximum Parsimony (MP) showed the presence of two main clusters of the beche-demer specimens: Stichopodidae (gamat family) and Holothuriidae (timun laut family). The beche-de-mer specimens of S. horrens, Stichopus herrmanni, and Thelenota anax were the three gamat species that clustered under the family Stichopodidae. Meanwhile, the beche-de-mer specimens of H. leucospilota, Holothuria (Halodeima) edulis, Holothuria (Metriatyla) scabra, and H. scabra var. versicolor were the four timun laut species that clustered under the family Holothuriidae. In fact, the outcomes of this study suggested the potential of 16S mitochondrial rRNA gene sequencing technique to be used by the enforcement agencies in monitoring and overcoming the issues of species substitution and product mislabeling of beche-de-mer products in Malaysian markets

Checklist of Marine Fungi and Yeasts Associated with Holothuria (Mertensiothuria) leucospilota from Pangkor Island

Marine microorganisms such as fungi and yeasts can adapt to extreme marine environment conditions and play different roles especially in the nutrient cycling and as bioindicator of ocean change. This study was carried out to isolate and identify fungi and yeasts associated with Holothuria (Mertensiothuria) leucospilota from Pangkor Island, Perak, Malaysia. Two specimens of H. leucospilota were collected from Giam Island and Teluk Nipah Beach of Pangkor Island. Nine samples of fungi and ten samples of yeasts were isolated from the internal and external parts of the H. leucospilota specimens such as cuticle, tentacle, coelomic fluid, cloaca, cuvierian tubules, and surrounding sediment and seawater. Polymerase Chain Reaction (PCR) and DNA sequencing of the Internal Transcribed Spacer (ITS) region were applied for species identification of the microorganisms. Sequence analyses of the ITS region resulted in the identification of five genera of fungi i.e. Cladosporium, Curvularia, Polyporaceae, Acremonium, and Penicillium; and four genera of yeasts i.e. Sterigmatomyces, Pichia, Debaryomyces, and Candida with some of them could be identified up to the species level. The fungi and yeasts isolated from the H. leucospilota specimens from Pangkor Island could have potential biotechnological applications which can be further characterised

An update on diversity of sea cucumber (Echinodermata: Holothuroidea) in Malaysia

Sea cucumbers (Echinodermata: Holothuroidea) are regarded as an important part of Malaysia’s marine heritage due to their diversity and commercial value. Several ecological studies have been conducted aimed at documenting the distribution of sea cucumbers in Malaysia. It is estimated that more than 80 species of sea cucumber are present in Malaysia. Nevertheless, a large number of undetermined species have been recorded, thus requiring further research to update the species identification. Molecular approaches are capable of providing insights into the phylogeny of sea cucumbers and can support the outcomes of traditional morphological approaches, and a number of molecular ecological studies have been recorded in Malaysia since 1999