July 11, 2011
BGI Contributes Whole Genome Sequencing And Bioinformatics Expertise To Potato Genome Research
Also provides initial update on '1,000 Plant & Animal Reference Genomes Project' at 2nd annual conference
BGI (previously known as the Beijing Genomics Institute), the largest genomic organization in the world, announced today that it was among the research organizations comprising the Potato Genome Sequencing Consortium (PGSC) that completed the genome sequence and analysis of the tuber crop potato, published as an Advance Online Publication in Nature.
This study marks an important milestone in Potato (Solanum tuberosum L.) genome research, revealing new insights into the evolutionary history of the potato genome, causes of inbreeding depression, and potential mechanisms of tuber initiation and development. These insights will generate great interest among botanists and breeders worldwide and facilitate the genetic engineering of this vital crop.
"BGI and its collaborators carried out the de novo sequencing, genome assembly and annotation of the potato genome, elucidating the evolutionary history of the genome and providing the foundation for biological analysis," stated Xun Xu, Vice President of Research and Development at BGI, and co-senior author of the report.
With the advanced genome sequencing capability of BGI, the homozygous doubled-monoploid DM1-3 516 R44 (DM) potato clone was sequenced by whole genome shotgun sequencing (WGS) approach with high coverage depths. The genome was then assembled by BGI's Short Oligonucleotide Analysis Package, SOAPdenovo, and 86% of the estimated total genome (844Mb) was assembled.
Researchers from BGI also aided in the potato gene annotation, of which 39,031 protein-coding genes were predicted. It is reported that at least two genome duplication events present in potato, indicating a paleopolyploid origin. Findings related with haplotype diversity, tuber biology and disease resistance are also reported.
"We found important genetic basis related to inbreeding depression and tuber biology based on our bioinformatics analysis," said Xu Xun, who considers the potato as one of the most important plant genomes in light of growing food shortages due to global population growth and climate change.
BGI is the only genomic organization with an extensive focus on agricultural genomics research. Its accomplishments include sequencing the rice genome, silkworm genome, cucumber genome, soybean genome and maize genome, among others. In January 2010, BGI launched the "1,000 Plant & Animal Reference Genomes Project" with the goal of generating reference genomes for 1,000 economically and scientifically important plant/animal species. BGI's 2nd International Conference on the Progress of "1000 Plant & Animal Reference Genomes Project" is being held in Shenzhen from July 10-12, 2011.
Reporting from the conference, Dr. Bicheng Yang, Director of Global Marketing at BGI stated, "Together with our collaborators, so far we have initiated 505 plant and animal genome projects, completed fine or draft genome maps for over 100 species and finished the sequencing of about 200 species. Many other genomes are undergoing active sequencing." She congratulated the PGSC consortium on its breakthrough in potato genome research and said BGI is proud to be a contributor to the project.
Last week, July 6, at Bio-IT APAC Conference & Expo 2011, BGI released SOAPdenovo 2, the latest update of BGI's SOAPdenovo package. SOAPdenovo 2 is reported to assemble genomes with improved efficiency and consistency, and can support a broader range of analyses. SOAPdenovo 2 can be downloaded at http://soap.genomics.org.cn/.
"BGI is making continuous efforts for the advancement of plant and animal genomes research. We will provide the most advanced infrastructure for our partners and look for more collaboration in this field." stated Dr. Yang. The progress of "1000 Plant & Animal Reference Genomes Project" can be found at http://ldl.genomics.org.cn/page/pa-research.jsp.
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