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Chinese scientists decode watermelon genome, possible future benefits for crop improvement

The results were published online in Nature Genetics

An international team led by Beijing Academy of Agriculture and Forestry Sciences, BGI, and other institutes has completed the genomic sequence of watermelon (Citrullus lanatus) and the resequencing of 20 watermelon accessions.

The genomic data presented in this study will shape future efforts on watermelon genetics and evolutionary research, and also provide an invaluable resource for other plants research and crop genetic improvement. The results were published online in Nature Genetics.

Watermelon is an important cucurbit crop and one of the most important fruits that contributes to food and economic security in addition to human nutrition. It is favored for the sweet, low calorie, high fiber, nutrient rich characters–– and now, there's more. Evidence from lots of studies suggests that watermelon is also a useful crop species for genetic research because of its small genome size, and the diverse genetic mutants and variants. The availability of a reference genome for a crop is extremely important in the deeper understanding of its molecular breeding and evolutionary history. In the watermelon genome study published in Nature Genetics, researchers presented a high-quality genome sequence of an East-Asia watermelon cultivar 97103 and resequencing of 20 watermelon accessions spanning the genetic diversity of C. lanatus.

Genome-wide duplication is a common event for angiosperms, and represents an important molecular mechanism that has shaped modern plant karyotypes. To access the origin of modern cucurbit genome structures, researchers analyzed the syntenic relationships between watermelon, cucumber, melon and grape. They proposed an evolutionary model that has shaped the eleven watermelon chromosomes from the seven-chromosome eudicot ancestors, through the transition from the 21-chromosome eudicot intermediate ancestors involving 81 fissions and 91 fusions.

Many of the watermelon cultivars have narrow genetic diversity and are susceptible to a large number of diseases and pests. In the study, researchers resequenced 20 watermelon accessions representing three different C. lanatus subspecies. As expected, wild watermelon contains greater genetic diversity than the cultivars. The results provide genetic opportunity for watermelon improvement.

The watermelon crop suffers significant losses from numerous diseases. It is urgent for researchers to investigate the molecular basis for better improving the pathogen resistance of this important crop. The results in this study showed that many resistance genes were located on chromosomes in clusters, indicating tandem duplications may serve as the evolutionary basis of resistance genes in watermelon genome. Moreover, evidence from the study supported the previous hypothesis that a large portion of disease resistance genes have been lost during watermelon domestication.
The integrative genomic and transcriptomic analysis yielded important insights into aspects of phloem-based vascular that held both in watermelon and cucumber. It is noteworthy that the watermelon phloem contained 118 transcription factors (TFs), whereas in cucumber only 46 TFs were identified and 32 TFs exit in both. Moreover, the team identified several genes associated with the valuable fruit quality traits, including sugar accumulation and citrulline metabolism.

Jianguo Zhang, Project Manager from BGI, said, "The high-quality genomic sequence opens a new way for the further studies of watermelon. The data resources could serve as a robust tool for better exploring the mechanisms underlying significant economic traits and regulatory networks and further for breeding improvement. It will also promote the evolutionary research of cucurbit crops and other basic biological studies such as sugar metabolisms."

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

Media Contact:
Jianguo Zhang
Project Manager
Bicheng Yang
Public Communication Officer

Jia Liu | EurekAlert!
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