Daily Archives: November 20, 2012

November 19, 2012

BGI Shenzhen

An international research team led by Nanjing Agricultural University and BGI, has completed the first genomic sequence of pear by an approach using the combination of BAC-by-BAC strategy and next-gen sequencing. The pear genome not only provides an invaluable new resource for breeding improvement of this important crop, but also sheds new light on the genome evolution and other genome-wide comparative studies. The results were published online in Genome Research.

As one of the oldest fruit crops, pear has more than 3,000 years of cultivation history and is likely to have originated during the Tertiary period (65 million years ago) in southwestern China. This important fruit crop is genetically diverse with more than 5,000 cultivars and accessions present all over the world that could be divided into two major groups, the European or Occidental pears and the Asiatic or Oriental pears.

Unlike many crops, pear is known to be highly heterozygous, which is a big challenge for de novo assembly based on current strategies. In this study, researchers sequenced and assembled the pear genome, P. bretschneideri Rehd. cv. Dangshansuli using a combination of BAC-by-BAC and next generation sequencing technology. This approach is developed by BGI, which can be used to study the genomes with high level of heterozygosity and/or repetitive sequences. After data process, the assembled pear genome size is about 512.0 Mb, with a total of 42,812 protein-coding genes.

In this study, researchers identified repetitive sequences of 271.9 Mb, accounting for 53.1% of the pear genome. By comparison with the apple genome, they found the size differences between pear and apple genome were mostly contributed by content diversity in transposable elements (TEs), while genic regions are similar in both species.

Through comparative genomics and evolution analysis, researchers found pear, apple and strawberry shared an ancient whole-genome duplication (WGD) event that took place about 140 million years ago. About 30~45 million years ago, pear and apple shared a recent WGD event. After the two WGD events, pear and apple diverged from each other about 5.4~21.5 million years ago. Moreover, researchers inferred that the nine ancestral chromosomes formerly reported in apple, are not only the origin of the Pyreae tribe, but also serve as the ancestors of the whole Rosaceae family.

The availability of pear genome sequence provides an invaluable new resource for biological studies. In the study, researchers worked on the mechanisms underlying important biological processes of pear including stone cell formation, sugar accumulatin, aroma formation. Six candidate SFB genes were predicted to be related with self incompatibility, and 66 lignin synthesis-related gene families were identified, including HCT genes associated with lignin synthesis, C3H and CCOMT that related with the accumulation of both G-lignin and S-lignin, as well as three gene families of S6PDH, SDH, and SOT that involved in sorbitol metabolism. Furthermore, researchers also found that the metabolism of -linolenic acid was likely to play an important role in aroma formation in pear fruit.

Zhiwen Wang, Project Manager of BGI, said, BAC to BAC strategy is an excellent method to assemble the genomes with high heterozygosity. The completed sequencing of pear genome offers invaluable data resource for better tracing the evolutionary history of Rosaceae crops. I expect that our efforts could promote the breeding improvement and yield more delicious pears.

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New Knowledge For Breeding Improvement And Evolutionary Trace Analysis Provided By Pear Genome

Public release date: 19-Nov-2012 [ | E-mail | Share ]

Contact: Jia Liu liujia@genomics.cn BGI Shenzhen

November 19, 2012, Shenzhen, China An international research team led by Nanjing Agricultural University and BGI, has completed the first genomic sequence of pear by an approach using the combination of BAC-by-BAC strategy and next-gen sequencing. The pear genome not only provides an invaluable new resource for breeding improvement of this important crop, but also sheds new light on the genome evolution and other genome-wide comparative studies. The results were published online in Genome Research.

As one of the oldest fruit crops, pear has more than 3,000 years of cultivation history and is likely to have originated during the Tertiary period (65 million years ago) in southwestern China. This important fruit crop is genetically diverse with more than 5,000 cultivars and accessions present all over the world that could be divided into two major groups, the European or "Occidental" pears and the Asiatic or "Oriental" pears.

Unlike many crops, pear is known to be highly heterozygous, which is a big challenge for de novo assembly based on current strategies. In this study, researchers sequenced and assembled the pear genome, P. bretschneideri Rehd. cv. Dangshansuli using a combination of BAC-by-BAC and next generation sequencing technology. This approach is developed by BGI, which can be used to study the genomes with high level of heterozygosity and/or repetitive sequences. After data process, the assembled pear genome size is about 512.0 Mb, with a total of 42,812 protein-coding genes.

In this study, researchers identified repetitive sequences of 271.9 Mb, accounting for 53.1% of the pear genome. By comparison with the apple genome, they found the size differences between pear and apple genome were mostly contributed by content diversity in transposable elements (TEs), while genic regions are similar in both species.

Through comparative genomics and evolution analysis, researchers found pear, apple and strawberry shared an ancient whole-genome duplication (WGD) event that took place about 140 million years ago. About 30~45 million years ago, pear and apple shared a recent WGD event. After the two WGD events, pear and apple diverged from each other about 5.4~21.5 million years ago. Moreover, researchers inferred that the nine ancestral chromosomes formerly reported in apple, are not only the origin of the Pyreae tribe, but also serve as the ancestors of the whole Rosaceae family.

The availability of pear genome sequence provides an invaluable new resource for biological studies. In the study, researchers worked on the mechanisms underlying important biological processes of pear including stone cell formation, sugar accumulatin, aroma formation. Six candidate SFB genes were predicted to be related with self incompatibility, and 66 lignin synthesis-related gene families were identified, including HCT genes associated with lignin synthesis, C3'H and CCOMT that related with the accumulation of both G-lignin and S-lignin, as well as three gene families of S6PDH, SDH, and SOT that involved in sorbitol metabolism. Furthermore, researchers also found that the metabolism of -linolenic acid was likely to play an important role in aroma formation in pear fruit.

Zhiwen Wang, Project Manager of BGI, said, "BAC to BAC strategy is an excellent method to assemble the genomes with high heterozygosity. The completed sequencing of pear genome offers invaluable data resource for better tracing the evolutionary history of Rosaceae crops. I expect that our efforts could promote the breeding improvement and yield more delicious pears."

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Pear genome provides new insight into breeding improvement and evolutionary trace analysis

GAITHERSBURG, Md.--(BUSINESS WIRE)--

OpGen, Inc., a commercial stage DNA analysis company, today announced the Argus Whole Genome Mapping System continues to gain broad adoption among genome sequencing centers worldwide. Five leading international genomic sequencing centers have joined the growing list of centers utilizing OpGens technology to enhance their next-generation sequencing capabilities. The centers include The Genome Institute at Washington University, St. Louis, MO; The Genome Analysis Centre (TGAC), Norwich, UK; Genoscope, Evry, France; National High-throughput DNA Sequencing Centre at the Centre for GeoGenetics, Copenhagen, Denmark; and Genome Institute of Singapore. These organizations join our growing customer base that includes Wellcome Trust Sanger Institute and BGI, public health and biodefense agencies, and research and service labs that are utilizing the companys Whole Genome Mapping technologies and services.

We adopted OpGens Argus System after evaluating the value of adding Whole Genome Mapping to improve whole genome sequences, said George Weinstock, Ph.D., associate director of The Genome Institute at Washington University. We combined Whole Genome Maps with sequence assemblies to correct errors and misassemblies in bacterial samples from the Human Microbiome Project, and now we are using the technology in larger genome projects.

OpGens Argus Whole Genome Mapping System is the only commercially available technology that can provide a high resolution, complete visual map of a whole genome and individual chromosomes. OpGens unique single molecule analysis technology provides a whole genome view that compliments genome assembly and enables scientists to identify highly repetitive regions, tandem repeats and translocations that are very difficult to identify and clarify with sequencing alone. Sequencing projects can now be finished and validated with less investment in time, cost and computational effort.

Our research focuses on a wide variety of projects from microbes to crop plants and mammals, said Matthew Clark, Ph.D., sequencing technology development team leader at The Genome Analysis Centre. Many of our projects are de novo assembly projects, where, without a closelyrelatedgenome sequence, it can be difficult to critically assess the results. We often combine different sequencing technologies, and we are finding that regardless of the sequencing platform, error correction, or assembler used, OpGens Whole Genome Mapping identifies misassemblies and provides the highest quality de novo assembly for further research.

We are successfully expanding our customer base among major global sequencing centers, said Douglas White, president and chief executive officer of OpGen. By providing the highest quality, validated sequence assemblies, our goal is to enable translational research that will meet the highest standards for clinical applications.

About OpGen, Inc.

OpGen, Inc. is a leading innovator in providing rapid, accurate genomic and DNA analysis systems and services. The companys Argus Whole Genome Mapping System, GenomeBuilder and MapIt Services provide high resolution, whole genome maps for sequence assembly and finishing, strain typing and comparative genomics in the life sciences market. OpGens powerful technology dramatically improves the quality of data and time-to results by providing sequence information from single DNA molecules more rapidly and less expensively than previously possible. The company is dedicated to positively influencing individual healthcare outcomes, advancing scientific research and enhancing public health by delivering precise, actionable information and results to customers in the life science and healthcare communities. OpGens customers include leading genomic research centers, biodefense organizations, academic institutions, clinical research organizations and biotechnology companies. For more information, visit http://www.opgen.com.

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OpGen Announces Expanded Adoption of Argus® Whole Genome Mapping System