Application of Next-Generation Sequencing Technology in Southeast Asia: A Practical Framework for Advancing Wildlife Conservation

Open Access

Issue		BIO Web Conf. Volume 94, 2024 The 8^th International Conference on Biological Sciences “Leveraging Biodiversity to Support Green Economy and Climate Resilience” (ICBS 2023)


Article Number		01004
Number of page(s)		13
Section		Bioinformatics and Computational Biology
DOI		https://doi.org/10.1051/bioconf/20249401004
Published online		25 March 2024

M. Hajibabaei, S. Shokralla, X. Zhou, G.A.C. Singer, D.J. Baird, Environmental barcoding: A next-generation sequencing approach for biomonitoring applications using river benthos. PLoS ONE 6, e17497 (2011) [Google Scholar]
M.E. Carew, V.J. Pettigrove, L. Metzeling, A.A. Hoffmann, Environmental using next generation sequencing: rapid identification of macroinvertebrate bioindicator species. Front Zool 10, 45 (2013) [CrossRef] [PubMed] [Google Scholar]
D.J. Baird, M. Hajibabaei, Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing. Mol. Ecol. 21, 2039–2044 (2012) [CrossRef] [PubMed] [Google Scholar]
K.M. Ruppert, R.J. Kline, M.S. Rahman, Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA. Glob. Ecol. Conserv. 17, e00547 (2019) [Google Scholar]
M.A. Russello, E.L. Jensen, Ex situ wildlife conservation in the age of population genomics in: Hohenlohe, P.A., Rajora, O.P. (eds) Population Genomics: Wildlife. Population Genomics (Springer, Cham, 2018) [Google Scholar]
S. Camillo, Can gut microbiota analysis be beneficial for ex-situ and in-situ conservation of threatened animal species?, [Dissertation thesis], Alma Mater Studiorum Università di Bologna. (2021) [Google Scholar]
N.S. Sodhi, L. P. Koh, R. Clements, T. C. Wanger, J. K. Hill, K. C. Hamer, T. M. Lee, Conserving Southeast Asian forest biodiversity in human-modified landscapes. Biol. Conserv. 143, 2375-2384 (2010) [CrossRef] [Google Scholar]
A.C. Hughes, Understanding the drivers of Southeast Asian biodiversity loss. Ecosphere. 8, 1 (2017) [CrossRef] [Google Scholar]
N. Othman, K. Munian, H. Haris, F.F. Ramli, N.S. Sariyati, M.F. Najmuddin, M.A.B. Abdul-Latiff, A review on next-generation wildlife monitoring using environmental DNA (eDNA) detection and next-generation sequencing in Malaysia. Sains Malays. 52, 1 (2023) [Google Scholar]
N. Othman, H. Haris, Z. Fatin, M.F. Najmuddin, N.H. Sariyati, B.M. Md-Zain, M.A.B. Abdul-Latiff, A review on environmental DNA (eDNA) metabarcoding markers for wildlife monitoring research. IOP Conf. Series: Earth and Environmental Science. 736, 012054 (2021) [CrossRef] [Google Scholar]
X, Han, M.J. Gill, H. Hamilton, S.G. Vergara, B.E. Young, Progress on national biodiversity indicator reporting and prospects for filling indicator gaps in Southeast Asia. Environ. Sustain. 5, 100017 (2020) [Google Scholar]
P.F. Thomsen, J. Kielgast, L.L. Iversen, C. Wiuf, M. Rasmussen, M.T.P. Golbert, L. Orlando, E. Willerslev, Monitoring endangered freshwater biodiversity using environmental DNA. Mol. Ecol. 21, 2565-2573 (2011) [Google Scholar]
K.M. Gibson, B.N. Nguyen, L.M. Neumann, M. Miller, P. Buss, S. Daniels, M.J. Ahn, K.A. Crandall, B. Pukazhenthi, Gut microbiome differences between wild and captive black rhinoceros – implications for rhino health. Sci Rep 9, 7570 (2019) [CrossRef] [PubMed] [Google Scholar]
M.A.M. Moustafa, H.M. Chel, J.M. Thu, S. Bawn, L.L. Htum, M.M. Win, Z.M. Oo, Anthropogenic interferences lead to gut microbiome dysbiosis in Asian elephants and may alter adaptation processes to surrounding environments. Sci Rep 11, 741 (2021) [CrossRef] [PubMed] [Google Scholar]
K.R. Schwartz, E.C.M. Parsons, L. Rockwood, T.C. Wood, Integrating in-situ and ex- situ data management processes for biodiversity conservation. Front. Ecol. Evol. 5, 120 (2017) [CrossRef] [Google Scholar]
G.M. Tawfik, K.A.S. Dila, M.Y.F. Mohamed, D.N.H. Tam, N.D. Kien, A.M. Ahmed, N.T. Huy, A step by step guide for conducting a systematic review and metaanalysis with simulation data. Trop Med Health 47, 46 (2019) [CrossRef] [PubMed] [Google Scholar]
A. Fournier, I. Young, A. Rajic, J. Greig, J. LeJeune, Social and economic aspects of the transmission of pathogenic bacteria between wildlife and food animals: A thematic analysis of published research knowledge. Zoonoses and Public Health 62, 6 (2015) [Google Scholar]
N.J. Bennett, T. Satterfield, T. Environmental governance: A practical framework to guide design, evaluation, and analysis. Conserv. Lett. 11, 6 (2018) [CrossRef] [Google Scholar]
M.I. Hadi, M.Y. Alamudi, D. Suprayogi, M. Widiyanti, Detection of emerging infectious disease in Cynopterus brachyotis and Rhinolopus boorneensis as reservoirs of zoonotic diseases in Indonesia Indian J. Forensic Med. Toxicol 14, 3 (2020) [Google Scholar]
M. Visser, R. Bester, J.T. Burger, H.J. Maree, Next-generation sequencing for virus detection: covering all the bases. Virol J 13, 85 (2016) [CrossRef] [PubMed] [Google Scholar]
R. Arumugam, P. Ravichandran, S.K. Yeap, R.S.K. Sharma, S.B. Zulkifly, D. Yawah, G. Annavi, Application of High-Throughput Sequencing (HTS) to enhance the well-being of an endangered species (Malayan Tapir): characterization of gut microbiome using MG-RAST. Methods Mol Biol. 2649, 175-194 (2023) [CrossRef] [PubMed] [Google Scholar]
N.S. Mohd-Yusof, M.A.B. Abdul-Latiff, A.R. Mohd-Ridwan, A.S. Badrulisham, N. Othman, S. Yaakop, S. Md-Nor, B.M. Md-Zain, First report on metagenomic analysis of gut microbiome in Island Flying Fox (Pteropus hypomelanus) revealing latitudinal correlation as opposed to host phylogeny in island populations of Malaysia. Biodivers. Data J. 10, e69631 (2022) [CrossRef] [Google Scholar]
D. Delaune, V. Hul, E.A. Karlsson, A. Hassanin, T.P. Ou, A. Baidaliuk, F. Gambbaro, M. Prot, V.T. Tu, S. Chea, L. Keatts, J. Mazet, C.K. Johnson, P. Buchy, P. Dussart, T. Goldstein, E. Simon-Loriere, V. Doung, A novel SARS-CoV-2 related coronavirus in bats from Cambodia. Nat Commun. 12, 6563 (2021) [CrossRef] [Google Scholar]
T.T. Lam, N. Jia, Y.W. Zhang, M.H. Shum, J.F. Jiang, H.C. Zhu, Y.G. Tong, Y.X. Shi, X.B. Ni, Y.S. Liao et al. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature. 583, 7815 (2020) [Google Scholar]
G. Liu, S. Zhang, Z. Zhao, C. Li, M. Gong, Advances and limitations of next generation sequencing in animal diet analysis. Genes 12, 1854 (2021) [CrossRef] [PubMed] [Google Scholar]
M. Buglione, S. Petrelli, C. Troiano, T. Notomista, E. Rivieccio, D. Fulgione, The diet of otters (Lutra lutra) on the Agri river system, one of the most important presence sites in Italy: a molecular approach. PeerJ 8, e9606 (2020) [CrossRef] [PubMed] [Google Scholar]
N.H. Jang-Liaw, A barcoding-based scat-analysis assessment of Eurasian otter, Lutra lutra diet on Kinmen Island. Ecol. Evol. 11, 8795–8813 (2021) [CrossRef] [Google Scholar]
A. Srivathsan, A. Ang, A.P. Vogler, R. Meier, Fecal metagenomics for the simultaneous assessment of diet, parasites, and population genetics of an understudied primate. Front. Zool. 13, 17 (2016) [CrossRef] [Google Scholar]
D. R. Mitchell, S. Wroe, M.J. Ravosa, R.A. Menegaz, More challenging diets sustain feeding performance: applications toward the captive rearing of wildlife. Integr. Org. Biol. 3, 1 (2021) [Google Scholar]
N.A.F. Abdullah-Fauzi, K.V. Karuppannan, N.H.S. Mohd-Radzi, M. Gani, A.R. Mohd Ridwan, N. Othman, H. Haris, N.H. Sariyati, N.R. Aifat, M.A.B. Abdul-Latiff, M.F.A. Abdul-Razak, B.M. Md-Zain, Determining the dietary preferences of wild Asian elephants (Elephas maximus) in Taman Negara National Park, Malaysia based on sex and age using trnL DNA metabarcoding analysis. Zool Stud. 60 (2022) [Google Scholar]
N.H.S. Mohd-Radzi, K.V. Karuppannan, N.A.F. Abdullah-Fauzi, A.R. Mohd-Ridwan, N. Othman, M.A.B. Abdul-Latiff, M. Gani, M.F.A. Abdul-Razak, B.M. Md-Zain, Determining the diet of wild Asian elephants (Elephas maximus) at human– elephant conflict areas in Peninsular Malaysia using DNA metabarcoding. Biodivers. Data J 10, e89752 (2022) [CrossRef] [Google Scholar]
A.T. Reese, T.R. Kartzinel, B.L. Petrone, P.J. Turnbaugh, R.M. Pringle, A. David, Using DNA metabarcoding to evaluate the plant component of human diets: a proof of concept. mSystems. 4, e00458-19 (2019) [Google Scholar]
M. Khairulmunir, M. Gani, K.V. Karuppannan, A.R. Mohd-Ridwan, B.M. Md-Zain, High-throughput DNA metabarcoding for determining the gut microbiome of captive critically endangered Malayan tiger (Panthera tigris jacksoni) during fasting. Biodivers Data J. 11, e104757 (2023) [CrossRef] [Google Scholar]
N.A. Osman, M.A.B. Abdul-Latiff, A.R. Mohd-Ridwan, S. Yaakop, S.M. Nor, B.M. Md Zain, Diet composition of the wild stump-tailed macaque (Macaca arctoides) in Perlis State Park, Peninsular Malaysia, using a chloroplast tRNL DNA metabarcoding approach: a preliminary study. Animals 10, 2215 (2020) [CrossRef] [PubMed] [Google Scholar]
P. Karyanto, A.R. Bagasta, I.N. Nayasilana, S.M. Nor, S.S.U. Atmoko, A. Susilowati, S. Sunarto, Next generation sequencing reveals plants consumed by the vulnerable ebony langur (Trachypithecus auratus) in a fragmented mountain forest. Biodiversitas, 23, 9 (2022) [CrossRef] [Google Scholar]
K. Theissinger, C. Fernandes, G. Formenti, I. Bista, P.R. Berg, C. Bleidorn, A. Bombarely. A. Cronttini, G. Zammit, How genomics can help biodiversity conservation. Trends in Genetics. 39, 7 (2023) [Google Scholar]
C. Suwannapoom, Y.J. Wu, X. Chen, A.C. Adeola, J. Chen, W.Z. Wang, W. Z. Complete mitochondrial genome of the Thai Red Junglefowl (Gallus gallus) and phylogenetic analysis. Zool. Resear. 39, 2 (2018) [Google Scholar]
N. Rosli, F.T. Sitam, J.J. Rovie-Ryan, H.M. Gan, Y.P. Lee, H. Ithnin, M. Gani, M.F.A. Abdul-Razak, B.M. Md-Zain, M.T. Abdullah, The complete mitochondrial genome of Malayan Gaur (Bos gaurus hubbacki) from Peninsular. Mitochondrial DNA Part B 4, 2 (2019) [Google Scholar]
A. Wibowo, K. Kurniawan, D. Atminarso, T.H. Prihadi, L.J. Baumgartner, M.L. Rourke, S. Nagai, N. Hubert, A. Vasemagi, Assessing freshwater fish biodiversity of Kumbe River, Papua (Indonesia) through environmental DNA metabarcoding. Pac. Conserv. Biol. 29, 4 (2022) [Google Scholar]
N.F.K. Mokhtar, S.Z. Imran, M.G. Han, M.C. Leong, M.N.M. Desa, R.M.H.R. Nhari, N.N.M. Zaki, Y.A. Yusof, S. Mustafa, A.M. Hashim, Next Generation Sequencing-based DNA metabarcoding for animal species profiling in fish feed, Food Addit Contam Part A 39, 7 (2022) [Google Scholar]
D. I. Roesma, H.T. Djong, M.N. Janra, D.R. Aidil, Freshwater vertebrates monitoring in Maninjau Lake, West Sumatra, Indonesia using environmental DNA. Biodiversitas 22, 5 (2021) [CrossRef] [Google Scholar]
M.N. Kunde, A. Barlow, A.M. Klittich, A. Yakupova, R.P. Patel, J. Fickel, D.W. Förster, First mitogenome phylogeny of the sun bear Helarctos malayanus reveals a deep split between Indochinese and Sundaic lineages. Ecol. Evol. 13, 4 (2023) [CrossRef] [Google Scholar]
C.M. Ferreira, H. Sabino-Marques, S. Barbosa, P. Costa, C. Encarnação, R. Alpizar-Jara, R. Pita, P. Beja, A. Mira, J.B. Searle, J. Paupério, P.C. Alves, Genetic non-invasive sampling (gNIS) as a cost-effective tool for monitoring elusive small mammals. Eur J Wildl Res 64, 46 (2018) [CrossRef] [Google Scholar]
M.A.B. Abdul-Latiff, N.R. Aifat, S. Yaakop, B.M. Md-Zain, A noninvasive molecular approach: exploiting species-locus specific PCRprimers in defeating numts and DNA cross contamination of Cercopithecidae. J Anim Plant Sci 27, 3 (2017) [Google Scholar]
H. Haris, N.H. Sariyati, N. Othman, Z. Fatin, M.F. Najmuddin, B.M. Md-Zain, M.A.B. Abdul-Latiff, Phylogenetic position of Trachypithecus obscurus obscurus based on D-loop region of mitochondrial DNA in Gunung Ledang, Johor, Malaysia. Malay. Nat. J. 73, 4 (2021) [Google Scholar]
P.F. Thomsen, E. Willerslev, Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity. Biol. Conserv. 183, 4-18 (2015) [CrossRef] [Google Scholar]
M. Leray, C.P. Meyer, S.C. Mills, Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet. PeerJ 3, e1047 (2015) [CrossRef] [PubMed] [Google Scholar]
M. Helmy, M. Awad, K.A. Mosa, Limited resources of genome sequencing in developing countries: Challenges and solutions. Appl. Transl. Genom 9, 15-19 (2016) [Google Scholar]
X. Anita, J.M.L. Manickam, M.A. Bhagyaveni, Two-way acknowledgment-based trust framework for wireless sensor networks. Int. J. Distrib. Sens. Net. 9, 5 (2014) [Google Scholar]

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