March 13, 2013, Shenzhen, China - In a collaborative study published online today in Nature Communications, researchers from Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, BGI-Shenzhen, and University of Arizona have completed the genome sequencing of wild rice Oryza brachyantha. This work provides new insights for researchers to understand the function and evolution of Oryza genomes.
The genus Oryza is an idea model system for studying plant comparative genomics, evolutionary biology and functional biology. There are two cultivated rice and more than twenty wild rice species. Among them, the wild relatives can provide invaluable genomic resources for rice improvement. As the most diverged wild relative of O. sativa (rice), O. Brachyantha has resistance against many rice pathogens and various stress environments. It was also proved to have the most compact genome in the genus Oryza, suggesting the genome may not experience many changes after the divergence of Oryza species.
In this study, researchers generated a high-quality reference genome sequence of O. brachyantha (~261Mb), and 96% genome sequences are anchored on 12 chromosomes based upon BAC-based physical map. After the comprehensive analysis, they found that the compact genome of O. brachyantha was caused by the silencing of LTR (Long terminal Repeats) retrotransposons and massive internal deletions of ancient elements.
Compared with the rice genome, the team found that many gene families were expanded in rice, where tandem duplications and gene movements mediated by double-strand break repair are responsible for the amplification of these genes. Researchers also observed that segmental and tandem duplications, further expanded by transposable element insertions, contributed to transition from euchromatin to heterochromatin in the rice genome, reflecting the dynamic nature of the Oryza genomes.
Quanfei Huang, Project Manager from BGI, said "This work revealed many important genomic mechanisms underlying Oryza genome, such as the genome size variation, gene movement and transition of euchromatin to heterochromatin. In the near future, I believe there will be more genomes of Oryza species to be cracked, enabling the genus Oryza be an unparalleled system for functional and evolutionary studies in plants."
About BGI
BGI was founded in 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, which includes both private non-profit genomic research institutes and sequencing application commercial units, and its affiliates, BGI Americas, headquartered in Cambridge, MA, and BGI Europe, headquartered in Copenhagen, Denmark, 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 250 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, have sequenced the human Gut metagenome, and a significant proportion of the genomes for 1,000 genomes. For more information about BGI please visit http://www.genomics.cn.
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Bicheng Yang, Ph.D.
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Journal
Nature Communications