Category Archives: Genome

DAVIS The genome sequence of watermelon has been published by an international consortium of scientists including researchers at UC Davis. The information could dramatically accelerate both breeding of more nutritious, tasty and disease-resistant fruit, and progress on understanding the role of the plant vascular system as an information superhighway. The watermelon genome sequence was published Sunday (Nov. 25) in the online version of the journal Nature Genetics.

The genome of the domesticated watermelon contains 23,440 genes, roughly the same number of genes as in humans. The team compared the genomes of 20 different watermelons and developed a first-generation genetic variation map for watermelon. This information allowed them to identify genomic regions that have been under human selection, including those associated with fruit color, taste and size.

Professor William Lucas, chair of the Department of Plant Biology and one of the leaders of the genome project, and colleagues at UC Davis are using the previously published cucumber genome and the newly decoded watermelon genome to explore fundamental questions about the plant vascular system, which carries water and nutrients through the plant. They hope to discover the role played by proteins and RNA species that traffic through the vascular system, many of which are likely to be involved in regulating important agricultural traits.

"Watermelons are a model system for studying the evolution of long-distance signaling processes that occur through the plant vascular system. Knowledge relating to these regulatory mechanisms can be harnessed by breeders to develop watermelons having enhanced properties, including increased water use efficiency, enhanced nutritional value and engineered resistance to pathogens," Lucas said.

The researchers also discovered that a large portion of disease resistance genes were lost in the domestication of watermelon. Breeders ultimately may be able to use the genome information to recover some of these natural disease defenses.

Believed to have originated in Africa, watermelons were cultivated by Egyptians more than 4,000 years ago, and the fruit was a source of water in dry, desert conditions. They are now consumed throughout the world, with more than 200 varieties in global commercial production. China leads in global production of the fruit, and the United States ranks fourth with more than 40 states involved in the industry.

Despite being more than 90 percent water, watermelons contain important nutrients like vitamins A and C and lycopene, a compound that gives some fruits and vegetables their red and orange color. The fruit also contains citrulline, a novel amino acid that has been reported to have beneficial effects in terms of maintaining a healthy heart.

Institutions collaborating on the project in addition to UC Davis were: Beijing Academy of Agriculture and Forestry Sciences, China; Boyce Thompson Institute for Plant Research, Cornell University; BGI-Shenzhen, China; Fudan University, Shanghai, China; Beijing University of Agriculture, China; Institut National de la Recherche Agrinomique, France; Chinese Academy of Agricultural Sciences, Beijing, China; Beijing Normal University, China; Huazhong Agriculture University, Wuhan, China; University of Bonn, Germany; Xinjiang Academy of Agricultural Sciences, China; Beijing Novogene Bioinformation Technology Co. Ltd., China; U.S. Department of Agriculture, Charleston, S.C.; USDA Robert W. Holley Center for Agriculture and Health, Ithaca, N.Y.; University of Copenhagen, Denmark.

The project was funded by grants from the Chinese, U.S. and French governments.

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Watermelon genome reveals botanic clues

Newswise ITHACA, N.Y. Are juicier, sweeter, more disease-resistant watermelons on the way? An international consortium of more than 60 scientists from the United States, China, and Europe has published the genome sequence of watermelon (Citrullus lanatus) information that could dramatically accelerate watermelon breeding toward production of a more nutritious, tastier and more resistant fruit. The watermelon genome sequence was published in the Nov. 25 online version of the journal Nature Genetics.

The researchers discovered that a large portion of disease resistance genes were lost in the domestication of watermelon. With the high-quality watermelon sequence now complete, it is hoped that breeders can now use the information to recover some of these natural disease defenses.

The authors reported that the genome of the domesticated watermelon contained 23,440 genes, roughly the same number of genes as in humans. The group compared the genomes of 20 different watermelons and developed a first-generation genetic variation map for watermelon. This information allowed them to identify genomic regions that have been under human selection, including those associated with fruit color, taste and size.

Watermelons are an important cash crop and among the top five most consumed fresh fruits; however, cultivated watermelons have a very narrow genetic base, which presents a major bottleneck to its breeding. Decoding the complete genome of the watermelon and resequencing watermelons from different subspecies provided a wealth of information and toolkits to facilitate research and breeding, said Zhangjun Fei, a scientist at the Boyce Thompson Institute for Plant Research at Cornell University, and one of the leaders of this project.

Fei worked with BTI scientists on different aspects of the research, including James Giovannoni, to generate the gene expression data through RNA-sequencing and Lukas Mueller to provide additional analysis to confirm the quality of the genome assembly. Fei also collaborated with Amnon Levi, a research geneticist at the USDA-ARS, U.S. Vegetable Laboratory, Charleston, S.C., on genetic mapping and identifying candidate genes that might be useful to enhance disease resistance in watermelon. The genome sequences of the watermelon are publicly available at the Cucurbit Genomics Database (www.icugi.org), which is created and maintained by Feis group.

Believed to have originated in Africa, watermelons were cultivated by Egyptians more than 4,000 years ago, where the fruit was a source of water in dry, desert conditions. They are now consumed throughout the world with over 400 varieties in global commercial production. China leads in global production of the fruit, and the United States ranks fourth with more than 40 states involved in the industry. Despite being over 90 percent water, watermelons do contain important nutrients such as vitamins A and C, and lycopene, a compound that gives some fruits and vegetables their red color and appears to reduce the risk of certain types of cancer. Watermelon is also a natural source of citrulline, a non-essential amino acid with various health and athletic performance benefits.

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Genome Decoded: Scientists Find Clues to Disease Resistant Watermelons

ScienceDaily (Nov. 26, 2012) Are juicier, sweeter, more disease-resistant watermelons on the way? An international consortium of more than 60 scientists from the United States, China, and Europe has published the genome sequence of watermelon (Citrullus lanatus) -- information that could dramatically accelerate watermelon breeding toward production of a more nutritious, tastier and more resistant fruit. The watermelon genome sequence was published in the Nov. 25 online version of the journal Nature Genetics.

The researchers discovered that a large portion of disease resistance genes were lost in the domestication of watermelon. With the high-quality watermelon sequence now complete, it is hoped that breeders can now use the information to recover some of these natural disease defenses.

The authors reported that the genome of the domesticated watermelon contained 23,440 genes, roughly the same number of genes as in humans. The group compared the genomes of 20 different watermelons and developed a first-generation genetic variation map for watermelon. This information allowed them to identify genomic regions that have been under human selection, including those associated with fruit color, taste and size.

"Watermelons are an important cash crop and among the top five most consumed fresh fruits; however, cultivated watermelons have a very narrow genetic base, which presents a major bottleneck to its breeding. Decoding the complete genome of the watermelon and resequencing watermelons from different subspecies provided a wealth of information and toolkits to facilitate research and breeding," said Zhangjun Fei, a scientist at the Boyce Thompson Institute for Plant Research at Cornell University, and one of the leaders of this project.

Fei worked with BTI scientists on different aspects of the research, including James Giovannoni, to generate the gene expression data through RNA-sequencing and Lukas Mueller to provide additional analysis to confirm the quality of the genome assembly. Fei also collaborated with Amnon Levi, a research geneticist at the USDA-ARS, U.S. Vegetable Laboratory, Charleston, S.C., on genetic mapping and identifying candidate genes that might be useful to enhance disease resistance in watermelon. The genome sequences of the watermelon are publicly available at the Cucurbit Genomics Database, which is created and maintained by Fei's group.

Believed to have originated in Africa, watermelons were cultivated by Egyptians more than 4,000 years ago, where the fruit was a source of water in dry, desert conditions. They are now consumed throughout the world -- with over 400 varieties in global commercial production. China leads in global production of the fruit, and the United States ranks fourth with more than 40 states involved in the industry. Despite being over 90 percent water, watermelons do contain important nutrients such as vitamins A and C, and lycopene, a compound that gives some fruits and vegetables their red color and appears to reduce the risk of certain types of cancer. Watermelon is also a natural source of citrulline, a non-essential amino acid with various health and athletic performance benefits.

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The above story is reprinted from materials provided by Cornell University.

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Watermelon genome decoded: Scientists find clues to disease resistant watermelons

Public release date: 26-Nov-2012 [ | E-mail | Share ]

Contact: John Carberry johncarberry@cornell.edu 607-255-5353 Cornell University

ITHACA, N.Y. Are juicier, sweeter, more disease-resistant watermelons on the way? An international consortium of more than 60 scientists from the United States, China, and Europe has published the genome sequence of watermelon (Citrullus lanatus) information that could dramatically accelerate watermelon breeding toward production of a more nutritious, tastier and more resistant fruit. The watermelon genome sequence was published in the Nov. 25 online version of the journal Nature Genetics.

The researchers discovered that a large portion of disease resistance genes were lost in the domestication of watermelon. With the high-quality watermelon sequence now complete, it is hoped that breeders can now use the information to recover some of these natural disease defenses.

The authors reported that the genome of the domesticated watermelon contained 23,440 genes, roughly the same number of genes as in humans. The group compared the genomes of 20 different watermelons and developed a first-generation genetic variation map for watermelon. This information allowed them to identify genomic regions that have been under human selection, including those associated with fruit color, taste and size.

"Watermelons are an important cash crop and among the top five most consumed fresh fruits; however, cultivated watermelons have a very narrow genetic base, which presents a major bottleneck to its breeding. Decoding the complete genome of the watermelon and resequencing watermelons from different subspecies provided a wealth of information and toolkits to facilitate research and breeding," said Zhangjun Fei, a scientist at the Boyce Thompson Institute for Plant Research at Cornell University, and one of the leaders of this project.

Fei worked with BTI scientists on different aspects of the research, including James Giovannoni, to generate the gene expression data through RNA-sequencing and Lukas Mueller to provide additional analysis to confirm the quality of the genome assembly. Fei also collaborated with Amnon Levi, a research geneticist at the USDA-ARS, U.S. Vegetable Laboratory, Charleston, S.C., on genetic mapping and identifying candidate genes that might be useful to enhance disease resistance in watermelon. The genome sequences of the watermelon are publicly available at the Cucurbit Genomics Database, which is created and maintained by Fei's group.

Believed to have originated in Africa, watermelons were cultivated by Egyptians more than 4,000 years ago, where the fruit was a source of water in dry, desert conditions. They are now consumed throughout the world with over 400 varieties in global commercial production. China leads in global production of the fruit, and the United States ranks fourth with more than 40 states involved in the industry. Despite being over 90 percent water, watermelons do contain important nutrients such as vitamins A and C, and lycopene, a compound that gives some fruits and vegetables their red color and appears to reduce the risk of certain types of cancer. Watermelon is also a natural source of citrulline, a non-essential amino acid with various health and athletic performance benefits.

###

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Genome decoded: Scientists find clues to more disease-resistant watermelons

An international team has managed to sequence the watermelon genome in the hopes that it could help create a sweeter, more nutritious and more disease-resistant fruit.

More than 60 scientists from China, the U.S. and Europe worked together and have published the genome sequence in the journal Nature Genetics.

Due to the domestication and large-scale farming of watermelons, much of the fruits disease-resistant genes were lost.

Researchers examined the genomes of 20 different watermelons and developed what they call a first-generation genetic map for watermelon. This means breeders can now try to produce new crops using genetic information that specifies size, colour and taste among many other factors.

"Decoding the complete genome of the watermelon provided a wealth of information and toolkits to facilitate research and breeding," said Zhangjun Fei of Cornell University and one of the leaders of the project.

The report said domesticated watermelons contained 23,440 genes, about the same as humans.

Watermelon, one of the top five fresh fruits consumed in the world, are believed to have originated in Africa and then cultivated by the Egyptians more than 4,000 years ago.

With China being the No. 1 producer, there are now about 400 varieties in commercial production around the world.

Watermelons contain nutrients such as vitamins A and C and lycopene, a compound which is believed to reduce certain types of cancer.

The genome sequences of the watermelon are publicly available at the Cucurbit Genomics Database.

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Sweeter, juicier watermelons possible with genome info

NEW YORK--(BUSINESS WIRE)--

The New York Genome Center (NYGC) today announced the appointment of Robert B. Darnell, M.D., Ph.D., one of the worlds leading experts in the emerging area of RNA genomics, as its President & Scientific Director. In this role, Dr. Darnell will leverage his 22 years of experience in molecular neuro-oncology and leadership in RNA genomics, spanning multiple diseases and therapeutic areas, to lead the New York Genome Center. Dr. Darnell will direct all aspects of the NYGC, including its scientific and research activities, and the recruitment and development of a world-class scientific team in genomic research and medicine. Dr. Darnell, who previously advised the NYGC as a member of its Founding Board and Executive Committee, also joins the NYGC Board of Directors. Nancy J. Kelley, J.D., M.P.P., Founding Executive Director and Member of the NYGC Board of Directors, takes on the additional title of Chief Operating Officer.

Dr. Darnell is an internationally recognized research scientist and physician who is responsible for pioneering translational studies in paraneoplastic neurologic syndromes, which linked tumor immunity to autoimmune brain disease, leading to new antitumor strategies being tested in cancer patients. Studying these patients led his team to discover neuron-specific systems that regulate RNA expression, and to the invention of HITS-CLIP, now the gold standard with which to study RNA regulation in vivo. His innovative studies of mRNA splicing, translation, and miRNA regulation in clinical and experimental settings are offering new ways to explore the dark matter of the human genome, and to overlay genome-wide sequence information with human diseases, including brain disease and cancer.

The appointment of Dr. Darnell as our President & Scientific Director marks a momentous occasion for the New York Genome Center as we build our science and research capability, said Russ Carson and Ivan Seidenberg, Co-Chairs of the NYGC Board of Directors. Bob is deeply committed to our goal of having the New York Genome Center become an independent research institution and a world-class collaborative center for translational genomic research, linking sequencing, bioinformatics, and computational biology to the care of patients. Carson and Seidenberg also stated, As the Founding Executive Director, Nancy Kelley has been a driving force in the development of NYGC and will play an expanded role in delivering this important science to clients worldwide. The entire Board is excited to work with Bob and Nancy to deliver the benefit of the many breakthrough advancements in genomics.

Dr. Darnell stated, I am extremely honored and excited to join the New York Genome Center at this key point in its development, and to have the opportunity to shape, inform, and lead this institution to achieve the Centers ambitious plans. I look forward to launching a new multi-institutional scientific effort in New York to accelerate genomics-based fundamental research and to realize its potential to revolutionize clinical medicine.

Dr. Darnell will remain the Heilbrunn Professor of Cancer Biology at The Rockefeller University, one of NYGC's Institutional Founding Members (IFMs), and an Investigator of the Howard Hughes Medical Institute. He has numerous academic connections with the IFMs; in addition to his position at RU, Dr. Darnell is an Adjunct Attending Physician at Memorial Sloan-Kettering Cancer Center, an alumnus of Columbia College, and received his medical and neurology training at the Mt. Sinai School of Medicine and the Weill Cornell Medical College.

Tom Maniatis, Chairman of the Department of Biochemistry and Molecular Biophysics at Columbia University, a Member of the NYGC Board of Directors, and a key architect of NYGCs scientific vision, stated, I warmly welcome Bob to his position as President & Scientific Director, one for which he is exceptionally well-suited. It is widely recognized that the rate-limiting step in fulfilling the promise of genomics is extracting meaningful biological insights and clinically actionable information from massive genomic data sets. I believe that Bob is uniquely qualified as a leader, scientist, and clinician to place the NYGC at the forefront of solving this problem by building a strong internal bioinformatics program at NYGC and coordinating the efforts of a powerful bioinformatics consortium among the IFMs.

Over the next five years, NYGC expects to create more than 500 science-related jobs, most of which will be in basic and clinical research, integrating bioinformatics, computational biology and high throughput sequencing.

About Dr. Darnell

Robert B. Darnell, M.D., Ph.D., is an Investigator with the Howard Hughes Medical Institute and is the Robert and Harriet Heilbrunn Professor of Cancer Biology at The Rockefeller University in New York City, where he serves as the Director for Science Programs at the Center for Clinical and Translational Research. He is Senior Physician at the Rockefeller University Hospital and is an Adjunct Attending Neuro-Oncologist at the Memorial Sloan-Kettering Cancer Center (MSKCC). Dr. Darnell is a leading expert in the study of paraneoplastic neurologic syndromes, rare disorders triggered by an immune system response to common cancers, that he has studied with his clinical colleague Dr. Jerome Posner at MSKCC. His patient-oriented studies led him to discover that neurons have unique mechanisms governing the regulation of RNA, the transcribed copies of our genes. He went on to pioneer the development of a new method, termed HITS-CLIP, to study RNA regulation in intact brain. HITS-CLIP is now the gold standard for the study of RNA regulation, and is being widely applied in neurobiology, cancer biology, immunology and virology, as well as being used to explore the dark matter of the human genome. Dr. Darnells work has resulted in numerous awards, including the Derek Denny-Brown Young Neurological Scholar Award, the Burroughs Wellcome Fund Clinical Scientist Award in Translational Research, the Emerald Foundation Distinguished Investigator Award, and an NIH Directors Transformative Research Award, and he holds several patents and Investigational New Drug applications. Dr. Darnell serves on the Editorial Boards of the journals Molecular and Cellular Biology and eLIFE. In 2010, he was elected member of the Institute of Medicine of the National Academy of Sciences, member of the Association of American Physicians and Fellow of the American Association for the Advancement of Science. Dr. Darnell currently serves on the Board of Scientific Councilors of the Jackson Laboratory, the NINDS Advisory Council, and was a member of the Founding Board and is an Executive Committee Member of the New York Genome Center.

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New York Genome Center Appoints Dr. Robert B. Darnell, World Leader in Biomedical Research, as President & Scientific ...

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