Sorghum bicolor
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Status

v1.0 (March 26, 2008): This Sorghum bicolor assembly was built using the Arachne assembler with a data freeze from January 25, 2007. After the build, 28 breaks and 108 manual joins were made. 10 of these joins were across centromeres, and the size of the centromere was estimated for each chromosome based upon the amount of centromeric sequence already assembled for that chromosome. The main genome is in 10 chromosomes with many small unmapped pieces, some of which contain homologous rice genes. The Sorghum bicolor mitochondria and chloroplast were previously sequenced and are available in Genbank at NC_008360 and NC_008602. The nuclear genome sequence from the assembly was annotated using the JGI Genome Annotation Pipeline, collaborator-contributed gene models, and custom analyses.

Summary statistics for the S. bicolor v1.0 release:

Nuclear Genome Assembly v 1.0
Nuclear genome size (Mbp) 739
Sequencing read coverage depth 8x
Reported # of contigs 3,376
# of nuclear scaffolds 3,304
# of nuclear scaffolds >2 Kbp 3,376
Nuclear scaffold N/L50 6/62 Mbp
Three largest Scaffolds (Mbp) 78
74
74
Gene Model Track Sbi1_4 FilteredModels6
length (bp) of: average average
gene 2,856 2,794
transcript 1,426 1,236
exon 267 279
intron 419 456
description:
protein length (aa) 409 359
exons per gene 4.8 4.4
# of gene models in track 34,496 35,899
ESTs Data set # sequences total # mapped to genome # not mapped to genome % mapped to genome
EST clusters EstClusters_SBGI_052604_TC 20,029 18,255 1,774 91%
ESTs Ests_SorghumDbEstSequences 227,154 215,554 11,600 95%

Collaborators

References

The Sorghum bicolor genome and the diversification of grasses.

Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob-ur-Rahman, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS.

Nature. 2009 Jan 29;457(7229):551-6.

Links

Funding

This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396.