Research Highlights

• Subject Category:
  • Genetics

Published online: 11 November 2009 | doi:10.1038/nchina.2009.219

Genomics: The greatest thing since sliced cucumber

Felix Cheung

Introduction

© (2009) istockphoto.com/Wiktor Abramczyk

Cucumber — a close relative of melon, squash and pumpkin — is not only an economically important crop, but also a model system for studying sex determination and plant vascular systems. Yongchen Du and Sanwen Huang at the Chinese Academy of Agricultural Sciences in Beijing, Jun Wang and Songgang Li at the Beijing Genomic Institute in Shenzhen and co-workers¹ have generated the genome sequence of cucumber using a novel sequencing strategy.

The strategy takes advantage of the long read and clone length of traditional Sanger sequencing technology as well as the high depth and low cost of next-generation Illumina sequencing technology. The researchers used this 'hybrid' approach to generate 26.5 billion high-quality base pairs, or 72.2-fold genome coverage for cucumber — of which the Sanger reads provided 3.9-fold coverage and the Illumina reads provided 68.3-fold coverage.

The draft genome sequence offers an insight into cucumber traits, such as sex expression, disease resistance, taste and aroma, and the biosynthesis of cucurbitacin (a bitter compound with anti-cancer properties). It also provides a genetic knowledge base for developing elite cultivars and studying the evolution and function of the plant vascular system. The researchers have so far identified 686 gene clusters in the cucumber genome that are responsible for phloem (a type of vascular tissue) function.

The authors of this work are from:
Key Laboratory of Horticultural Crops Genetic Improvement, Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics Technology, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China; Beijing Genomics Institute, Shenzhen, China; Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark; Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, USA; College of Life Sciences, Beijing Normal University, Beijing, China; National Maize Improvement Center of China, Key Laboratory of Crop Genetic Improvement and Genome, Ministry of Agriculture, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China; Boyce Thompson Institute and USDA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, New York, USA; High-Tech Research Center, Shandong Academy of Agricultural Sciences, Jinan, China; US Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Department of Horticulture, University of Wisconsin, Madison, Wisconsin, USA; Diversity Arrays Technology, Canberra, Australia; Wageningen UR Plant Breeding, Wageningen, The Netherlands; Graduate University of Chinese Academy of Sciences, Beijing, China; High School Affiliated to Renmin University of China, Beijing, China; Division of Applied Life Science (BK21 and WCU program), PMBBRC and EB-NCRC, Gyeongsang National University, Jinju, South Korea; National Engineering Research Center for Vegetables, Beijing, China; Institute of Human Genetics, University of Aarhus, Aarhus, Denmark; Department of Biology, University of Copenhagen, Copenhagen, Denmark; South China University of Technology, Guangzhou, China.

Reference

1. Huang, S. et al. The genome of the cucumber, Cucumis sativus L. Nature Genet. doi:10.1038/ng.475 (2009). | Article | OpenURL