Kornsorn Srikulnath1,2,3,4,5, Worapong Singchat6,7, Nararat Laopichienpong6,7, Syed Farhan Ahmad6,7, Maryam Jehangir6,8, Navapong Subpayakom6,7, Aorarat Suntronpong6,7, Kornsuang Jangtarwan6,7, Tavun Pongsanarm6,7, Thitipong Panthum6,7, Nattakan Ariyaraphong6,7, Jitlada Camcuan6,7, Prateep Duengkae7,9, Sahabhop Dokkaew10, Narongrit Muangmai11. 1. Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand. kornsorn.s@ku.ac.th. 2. Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand. kornsorn.s@ku.ac.th. 3. Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok, 10900, Thailand. kornsorn.s@ku.ac.th. 4. Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok, 10900, Thailand. kornsorn.s@ku.ac.th. 5. Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima, 739-8526, Japan. kornsorn.s@ku.ac.th. 6. Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand. 7. Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand. 8. Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil. 9. Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok, 10900, Thailand. 10. Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand. 11. Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
Abstract
BACKGROUND: The Siamese fighting fish (Betta splendens, also known as the betta) is well known in aquarium markets, and also presents an exciting new research model for studying parental care, aggressive behavior, and cryptically diverse pigmentation. However, concentrated efforts are required, both in the context of conservation biology and in its genetics, to address the problems of ongoing outbreeding depression, loss of biodiversity, and lack of scientific biological information. OBJECTIVE: The evolutionary dynamics of the betta must be better understood at the genomic scale in order to resolve the phylogenetic status of unrecognized species, develop molecular markers to study variation in traits, and identify interesting sets of genes encoding various bioresource functions. METHODS: The recent revolution in multi-omics approaches such as genomics, transcriptomics, epigenomics, and proteomics has uncovered genetic diversity and gained insights into many aspects of betta bioresources. RESULTS: Here, we present current research and future plans in an ongoing megaproject to characterize the betta genome as de novo assemblies, genes and repeat annotations, generating data to study diverse biological phenomena. We highlight key questions that require answers and propose new directions and recommendations to develop bioresource management to protect and enhance the betta genus. CONCLUSION: Successful accomplishment of these plans will allow the creation of a reference annotated genome and provide valuable information at the molecular level that can be utilized to sustain biodiversity and eco-management of the betta to improve breeding programs for future biomedical research.
BACKGROUND: The Siamese fighting fish (Betta splendens, also known as the betta) is well known in aquarium markets, and also presents an exciting new research model for studying parental care, aggressive behavior, and cryptically diverse pigmentation. However, concentrated efforts are required, both in the context of conservation biology and in its genetics, to address the problems of ongoing outbreeding depression, loss of biodiversity, and lack of scientific biological information. OBJECTIVE: The evolutionary dynamics of the betta must be better understood at the genomic scale in order to resolve the phylogenetic status of unrecognized species, develop molecular markers to study variation in traits, and identify interesting sets of genes encoding various bioresource functions. METHODS: The recent revolution in multi-omics approaches such as genomics, transcriptomics, epigenomics, and proteomics has uncovered genetic diversity and gained insights into many aspects of betta bioresources. RESULTS: Here, we present current research and future plans in an ongoing megaproject to characterize the betta genome as de novo assemblies, genes and repeat annotations, generating data to study diverse biological phenomena. We highlight key questions that require answers and propose new directions and recommendations to develop bioresource management to protect and enhance the betta genus. CONCLUSION: Successful accomplishment of these plans will allow the creation of a reference annotated genome and provide valuable information at the molecular level that can be utilized to sustain biodiversity and eco-management of the betta to improve breeding programs for future biomedical research.
Authors: Kerstin Howe; Matthew D Clark; Carlos F Torroja; James Torrance; Camille Berthelot; Matthieu Muffato; John E Collins; Sean Humphray; Karen McLaren; Lucy Matthews; Stuart McLaren; Ian Sealy; Mario Caccamo; Carol Churcher; Carol Scott; Jeffrey C Barrett; Romke Koch; Gerd-Jörg Rauch; Simon White; William Chow; Britt Kilian; Leonor T Quintais; José A Guerra-Assunção; Yi Zhou; Yong Gu; Jennifer Yen; Jan-Hinnerk Vogel; Tina Eyre; Seth Redmond; Ruby Banerjee; Jianxiang Chi; Beiyuan Fu; Elizabeth Langley; Sean F Maguire; Gavin K Laird; David Lloyd; Emma Kenyon; Sarah Donaldson; Harminder Sehra; Jeff Almeida-King; Jane Loveland; Stephen Trevanion; Matt Jones; Mike Quail; Dave Willey; Adrienne Hunt; John Burton; Sarah Sims; Kirsten McLay; Bob Plumb; Joy Davis; Chris Clee; Karen Oliver; Richard Clark; Clare Riddle; David Elliot; David Eliott; Glen Threadgold; Glenn Harden; Darren Ware; Sharmin Begum; Beverley Mortimore; Beverly Mortimer; Giselle Kerry; Paul Heath; Benjamin Phillimore; Alan Tracey; Nicole Corby; Matthew Dunn; Christopher Johnson; Jonathan Wood; Susan Clark; Sarah Pelan; Guy Griffiths; Michelle Smith; Rebecca Glithero; Philip Howden; Nicholas Barker; Christine Lloyd; Christopher Stevens; Joanna Harley; Karen Holt; Georgios Panagiotidis; Jamieson Lovell; Helen Beasley; Carl Henderson; Daria Gordon; Katherine Auger; Deborah Wright; Joanna Collins; Claire Raisen; Lauren Dyer; Kenric Leung; Lauren Robertson; Kirsty Ambridge; Daniel Leongamornlert; Sarah McGuire; Ruth Gilderthorp; Coline Griffiths; Deepa Manthravadi; Sarah Nichol; Gary Barker; Siobhan Whitehead; Michael Kay; Jacqueline Brown; Clare Murnane; Emma Gray; Matthew Humphries; Neil Sycamore; Darren Barker; David Saunders; Justene Wallis; Anne Babbage; Sian Hammond; Maryam Mashreghi-Mohammadi; Lucy Barr; Sancha Martin; Paul Wray; Andrew Ellington; Nicholas Matthews; Matthew Ellwood; Rebecca Woodmansey; Graham Clark; James D Cooper; James Cooper; Anthony Tromans; Darren Grafham; Carl Skuce; Richard Pandian; Robert Andrews; Elliot Harrison; Andrew Kimberley; Jane Garnett; Nigel Fosker; Rebekah Hall; Patrick Garner; Daniel Kelly; Christine Bird; Sophie Palmer; Ines Gehring; Andrea Berger; Christopher M Dooley; Zübeyde Ersan-Ürün; Cigdem Eser; Horst Geiger; Maria Geisler; Lena Karotki; Anette Kirn; Judith Konantz; Martina Konantz; Martina Oberländer; Silke Rudolph-Geiger; Mathias Teucke; Christa Lanz; Günter Raddatz; Kazutoyo Osoegawa; Baoli Zhu; Amanda Rapp; Sara Widaa; Cordelia Langford; Fengtang Yang; Stephan C Schuster; Nigel P Carter; Jennifer Harrow; Zemin Ning; Javier Herrero; Steve M J Searle; Anton Enright; Robert Geisler; Ronald H A Plasterk; Charles Lee; Monte Westerfield; Pieter J de Jong; Leonard I Zon; John H Postlethwait; Christiane Nüsslein-Volhard; Tim J P Hubbard; Hugues Roest Crollius; Jane Rogers; Derek L Stemple Journal: Nature Date: 2013-04-17 Impact factor: 49.962