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BGI-Led Team Sequences Cucumber Genome

NEW YORK (GenomeWeb News) – An international research team led by investigators at the Beijing Genomics Institute-Shenzhen reported online in Nature Genetics yesterday that they have sequenced the draft genome of the domestic cucumber plant, Cucumis sativus.

The team used a combination of Sanger and Illumina methods to sequence the cucumber genome to more than 70 times coverage. The researchers' subsequent assembly and analysis uncovered numerous cucumber-specific genes as well as thousands of other genes that are offering clues about cucumber biology and relationships with other vascular plants, which circulate water, nutrients, and sugars using specialized vessel-like tissues.

"The cucumber genome provides a valuable resource for studying the evolution and function of the plant vascular system," senior author Jun Wang, deputy director of BGI-Shenzhen, and his co-authors wrote.

The cucumber belongs to a plant family that also includes gourds, pumpkins, and melons. Past plant research has relied heavily on the cucumber as a model for understanding both sex determination and vascular biology in this plant family

The researchers sequenced the 243.5 million base genome of a Chinese long inbred C. sativus var sativus L. line called 9930 to about 72.2 times coverage using a combination of Sanger and Illumina Genome Analyzer sequencing. About 3.9 times coverage came from Sanger sequencing, while the remaining 68.3 times coverage was generated with the Illumina platform.

By integrating information from 77 recombinant inbred lines created by crossing North American and Indian cucumber varieties, the team also came up with a cucumber genetic map containing 1,885 genetic markers. Nearly 73 percent of the assembled cucumber sequences were subsequently anchored onto the genetic map.

In contrast to other plants such as wheat or poplar, the team found that the cucumber genome does not appear to have undergone recent whole genome duplication events.

On the other hand, the researchers reported, the cucumber genome is bursting with transposons and repetitive sequences — many of which have not been detected in previously sequenced genomes.

Based on their analyses so far, the team estimates that the cucumber genome contains 26,682 genes belonging to at least 15,669 gene families. The genes are housed on seven chromosomes, five of which appear to be fusions of ten ancestral chromosomes that occurred after C. sativus diverged from the melon C. melo.

Among the many gene families present in cucumber, the team found more than 4,360 that seem to be unique to cucumber and 596 gene clusters that are shared between vascular and non-vascular plants.

Synteny and microsynteny patterns identified by comparing the genome sequence with sequences from other plants also offered hints about cucumber's evolutionary past — and its relationships with other plants.

For example, when the team compared the cucumber genome with sequenced bacterial artificial chromosomes for four melons, they found evidence suggesting cucumber and melon plants diverged from one another between about four and seven million years ago.

Finally, the researchers have already started unraveling the genetics behind cucumber traits such as sex determination, development, nutrient and water transport systems, and pathogen resistance — insights that may inform studies of melons and other related plants.

"The sequence of the cucumber genome provides an invaluable new resource for biological research and breeding of cucurbits," Wang and his team concluded. "The high collinearity between cucumber and melon genomes enables cucumber to serve as a model system in the Cucurbitaceae family for comparative genomics studies in plants."

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