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The genome of mesopolyploid crop Brassica rapa sheds new light on the study of genome evolution

29.08.2011
Study published online today in Nature Genetics

The Institute of Vegetables and Flowers Chinese Academy of Agricultural Science, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, and BGI, the world's largest genomics organization, announced today that they were among the research organizations comprising the Brassica rapa Genome Sequencing Project Consortium (BrGSPC) that completed the genome sequence and analysis of the mesopolyploid crop B. rapa, a Chinese cabbage. The findings are published online today in Nature Genetics.

This study marks a significant milestone in Brassica crops genome research, providing a new important resource for studying the evolutionary history of polyploid genomes and opening a brand way for the genetic improvement of Brassica oil and vegetable crops.

Brassica crops are used for human nutrition and provide opportunities for the study of genome evolution. These crops include important vegetables (B. rapa, Brassica oleracea) as well as oilseed crops (Brassica napus, B. rapa, Brassica juncea and Brassica carinata), which contribute to approximately 10% of the world's vegetable crop produce and approximately 12% of the worldwide edible oil supplies. The species B. rapa is a major vegetable or oil crop in Asia and Europe. It also serves as an excellent model system to study polyploidy-related genome evolution because of its paleohexaploid ancestry and its close evolutionary relationships with Arabidopsis thaliana and other Brassica species with larger genomes.

Since the Brassica rapa Genome Sequencing Project (BrGSP) was initiated about three years ago, scientists from China, United Kingdom, USA, Korea, Canada, France and Australia have been working on the studies of B. rapa genome, aiming to assist botanists and breeders worldwide in improving production, quality, nutritional value and disease resistance of B. rapa varieties. In this project, Chinese Scientists have been playing a leading role by the advanced next-generation sequencing technology. In 2009, BrGSPC terminated all the sequencing plans and took the B. rapa genome sequenced by Chinese Scientists as B. rapa (Chinese cabbage) reference sequence.

With the advanced genome sequencing capability of BGI, B. rapa was sequenced and assembled by BGI's Short Oligonucleotide Analysis Package, SOAPdenovo. The assembled Brassica rapa genome size was approximately 283.8 Mb, which was estimated to cover >98% of the gene space. After the annotation and analysis, 41,174 protein-coding genes were identified in B. rapa genome. So far, B. rapa is the closest sequenced species relatives to A. thaliana, and they show high similarity in functional genes, although they have undergone differentiation about 13 ~ 17 million years ago. The B. rapa genome sequence could lays an important foundation for better exploring structural and functional evolution of A. thaliana and other Brassica species.

The Brassica mesohexaploidy also offers an opportunity to study gene retention in triplicated genomes. In particular, variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. Some auxin- related genes families also were expanded or some genes over retained, which may contribute to the evolution and development of morphological variants. In this study, the researchers also found that the genes associated with response to important environmental factors including salt, cold, osmotic stress, light, wounding, pathogen (broad spectrum) defense, and both cadmium and zinc ions, were evidently over retained. It suggested that genome triplication may have expanded gene families that underlie environmental adaptability as observed in other polyploid species.

About Institute of Vegetables and Flowers Chinese Academy of Agricultural Science

Established in 1958, the Institute of Vegetables and Flowers (IVF), Chinese Academy of Agricultural Sciences (CAAS) is a national research institution specialized for applied and applied basic research of vegetables and flowers. Its major mandates are to develop applied technologies and basic theories, promote the application of scientific achievements to meet the needs of the vegetable and flower industry in China. It is also responsible for organizing national key research program, carrying out personnel training and exchange and cooperation with institutions and organizations both at home and abroad. Its current research disciplines cover germplasm, genetics and genomics, breeding, genetic engineering, plant nutrition and physiology, plant pathology and product processing.

About Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences

The Oil Crops Research Institute (OCRI)of the Chinese Academy of Agricultural Sciences(CAAS)is a national center specialized for oil crops research and development . It was established in 1960, sponsored by the Ministry of Agriculture(MOA).The location of OCRI's headquarter in Wuhan, named as Baojian, was one of the originating sites of modern agricultural education and technology development in China as Mr Zhang Zhidong in late Qing Dynasty once first set up the Hubei Agronomy School in 1898 here. OCRI has rapeseed, soybean, peanut and sesame as its mandate crops with a mission to conduct basic and applied research which can lead to enhanced productivity and utilization of the oil crops. The current research disciplines cover germplasm, genetics, breeding, functional genomic, genetic engineering, safety assessment of genetic modified organisms (GMOS), plant nutrition and physiology, plant pathology, chemical analysis, food safety and product processing. For more information, please visit www.oilcrops.com.cn/english/index.html

About BGI

BGI was founded in Beijing, China on September 9th, 1999 with the mission of being a premier scientific partner to the global research community. The goal of BGI is to make leading-edge genomic science highly accessible through its investment in infrastructure that leverages the best available technology, economies of scale, and expert bioinformatics resources. BGI, and its affiliates, BGI Americas and BGI Europe, have established partnerships and collaborations with leading academic and government research institutions as well as global biotechnology and pharmaceutical companies, supporting a variety of disease, agricultural, environmental, and related applications.

BGI has established a proven track record of excellence, delivering results with high efficiency and accuracy for innovative, high-profile research which has generated over 170 publications in top-tier journals such as Nature and Science. These accomplishments include sequencing one percent of the human genome for the International Human Genome Project, contributing 10 percent to the International Human HapMap Project, carrying out research to combat SARS and German deadly E. coli, playing a key role in the Sino-British Chicken Genome Project, and completing the sequence of the rice genome, the silkworm genome, the first Asian diploid genome, the potato genome, and, most recently, 1000 genomes and human Gut metagenome.

For more information about BGI, please visit www.genomics.cn or www.bgisequence.com

Contact Information:

Xiaowu Wang
Deputy Director of the Institute of Vegetables and Flowers
Chinese Academy of Agricultural Science
wangxw@mail.caas.net.cn
www.ivfcaas.ac.cn
Bicheng Yang
Public Communication Officer
BGI
+86-755-82639701
yangbicheng@genomics.cn
www.genomics.cn

Liu Jia | EurekAlert!
Further information:
http://www.genomics.cn
http://www.ivfcaas.ac.cn

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