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Published online: 16 December 2009 | doi:10.1038/nchina.2009.237

Genomics: Panda genome decoded

Felix Cheung

Introduction

© (2009) istockphoto.com/Michael Flippo

The giant panda is a much-loved national icon of China. It belongs to the order Carnivora, despite having an almost exclusively herbivorous diet. The latest population survey using faecal samples puts the number of pandas living in the wild at less than 3,000. Jian Wang and Jun Wang at the Beijing Genomic Institute in Shenzhen and co-workers¹ have now generated and assembled a draft sequence of the giant panda genome. The information will give international scientists deep insights into the genetic basis of panda biology and contribute new ideas for the conservation of this endangered species.

The researchers used next-generation Illumina sequencing technology to generate 176 gigabases of usable sequences with an average read length of 52 base pairs for a three-year-old female panda from the Chengdu breeding base. They then used SOAPdenovo — a genome assembler developed specifically for use with short-read sequences — to assemble a 2.25-gigabase draft sequence that covers approximately 94% of the panda genome.

The researchers determined that 90% of the remaining gaps contained carnivore-specific repeats. They also found that in comparison to the human and dog genome, the panda genome has a lower divergence rate of evolution. The findings provide answers to many important questions, including the root cause for the panda's strict bamboo diet despite being a carnivoran.

The authors of this work are from:
Beijing Genomics Institute, Shenzhen, China; Department of Biology, University of Copenhagen, Copenhagen, Denmark; Graduate University of Chinese Academy of Sciences, Beijing, China; Institutes of Biomedical Sciences, Fudan University, Shanghai, China; Bio-X Center, Key Laboratory for Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, Shanghai, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Genome Research Institute, Shenzhen University Medical School, Shenzhen, China; Chengdu Research Base of Giant Panda Breeding, Chengdu, China; Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Banting and Best Department of Medical Research, Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada; Departments of Integrative Biology and Statistics, University of California, Berkeley, California, USA; Key Laboratory of Child Development and Learning Science, Southeast University, Nanjing, China; San Diego Zoo's Institute for Conservation Research, Escondido, California, USA; School of Biological Sciences, University of Hong Kong, Hong Kong, China; State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China; State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, Guanghou, China; Institute of Population Genetics, University of Veterinary Medicine, Vienna, Austria; Biodiversity and Ecological Processes Group, Cardiff School of Biosciences, Cardiff University, Cardiff, UK; Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovakia; School of Life Science, Sichuan University, Chengdu, China; Department of Computer Science, University of Hong Kong, Hong Kong, China; South China University of Technology, Guangzhou, China; China Conservation and Research Centre for Giant Panda, Wolong National Nature Reserve, Wolong, China; Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta, Canada; University of Washington Genome Center, Seattle, Washington, USA.

Reference

1. Li, R. et al. The sequence and de novo assembly of the giant panda genome. Nature doi:10.1038/nature08696 (2009). | Article | OpenURL