Cucumis sativis, or cucumber, is a member of the Curcurbiteae which includes important crops such as melon, watermelon, squash and pumpkin. The Gy14 gynoecious inbred line was sequenced de novo using an appropriate mixture of random shotgun and paired-end shotgun reads sequenced with 454-XLR technology. The completeness of the 203 Mbp assembly is supported by the mapping of over 99% of the ~2 million 454-XLR ESTs. Comparison with the genetic map of cucumber supports the long-range accuracy of the assembly, as does the gross comparative analysis vs. other related plant genomes. These results demonstrate the use of next generation long-read pyrosequencing methods for the sequencing of complex genomes.
The cucumber genome project collaborators include Jason Affourtit, Chinnappa Kodira, James R. Knight, Brian A. Desany, Mohammed Mohiuddin, Gerald Irzyk, Cynthia Turcotte, and Pascal Bouffard (454); Tim T Harkins (Roche); Jason Miller, Sergey Koren, Brian Walenz, and Granger Sutton (JCVI); Therese Mitros and Dan Rokhsar (Berkeley and DOE JGI), and Yiqun Weng and Jack Staub (USDA). A manuscript describing the sequencing and analysis of the genome is in preparation.
- Approximately 203Mb in 4219 scaffolds
- Scaffold N50 (L50) = 51 (993 Kbp)
- Contig N50 (L50) = 1476 (37.6 Kbp)
- 21491 loci containing protein-coding transcripts
- 32528 protein-coding transcripts
Note: As of April 13, 2012, the Roche/JGI v1 annotation has been corrected for a small number of errors in primary transcript classification (longest at locus) and some duplicate alternative transcript models have also been removed. Files available for FTP download have been updated as well. The new total counts for gene loci and total transcripts are reflected above. Affected transcripts and loci are listed in three files (duplicate.tr.inactivated.txt, brandnew.loci.dueToNestedGene.txt, locus2CorrectLocus.txt) available from the FTP site here. Please note that we have not yet updated the gene families, so some cucumber gene family membership counts will be invalid. This will be addressed in an upcoming Phytozome release.