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A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat
- Source :
- BMC Genomics, BMC Genomics, Vol 10, Iss 1, p 496 (2009), Gu, Yong Q; Ma, Yaqin; Huo, Naxin; Vogel, John P; You, Frank M; Lazo, Gerard R; et al.(2009). A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat. BMC Genomics, 10(1), 496. doi: http://dx.doi.org/10.1186/1471-2164-10-496. Retrieved from: http://www.escholarship.org/uc/item/0dd8d1c2
- Publication Year :
- 2009
- Publisher :
- BioMed Central, 2009.
-
Abstract
- BackgroundBrachypodium distachyon(Brachypodium) has been recognized as a new model species for comparative and functional genomics of cereal and bioenergy crops because it possesses many biological attributes desirable in a model, such as a small genome size, short stature, self-pollinating habit, and short generation cycle. To maximize the utility ofBrachypodium as a model for basic and applied research it is necessary to develop genomic resources for it. A BAC-based physical map is one of them. A physical map will facilitate analysis of genome structure, comparative genomics, and assembly of the entire genome sequence.ResultsA total of 67,151BrachypodiumBAC clones were fingerprinted with the SNaPshot HICF fingerprinting method and a genome-wide physical map of theBrachypodiumgenome was constructed. The map consisted of 671 contigs and 2,161 clones remained as singletons. The contigs and singletons spanned 414 Mb. A total of 13,970 gene-related sequences were detected in the BAC end sequences (BES). These gene tags aligned 345 contigs with 336 Mb of rice genome sequence, showing thatBrachypodiumand rice genomes are generally highly colinear. Divergent regions were mainly in the rice centromeric regions. A dot-plot ofBrachypodiumcontigs against the rice genome sequences revealed remnants of the whole-genome duplication caused by paleotetraploidy, which were previously found in rice and sorghum.Brachypodiumcontigs were anchored to the wheat deletion bin maps with the BES gene-tags, opening the door toBrachypodium-Triticeae comparative genomics.ConclusionThe construction of theBrachypodiumphysical map, and its comparison with the rice genome sequence demonstrated the utility of the SNaPshot-HICF method in the construction of BAC-based physical maps. The map represents an important genomic resource for the completion ofBrachypodiumgenome sequence and grass comparative genomics. A draft of the physical map and its comparisons with rice and wheat are available athttp://phymap.ucdavis.edu/brachypodium/.
- Subjects :
- Chromosomes, Artificial, Bacterial
lcsh:QH426-470
lcsh:Biotechnology
Genomics
Computational biology
Poaceae
Genome
Evolution, Molecular
Contig Mapping
lcsh:TP248.13-248.65
Genetics
Genome size
Triticum
Whole genome sequencing
Comparative genomics
Expressed Sequence Tags
biology
food and beverages
Oryza
biology.organism_classification
Physical Chromosome Mapping
DNA Fingerprinting
lcsh:Genetics
Brachypodium
Brachypodium distachyon
Edible Grain
Functional genomics
Genome, Plant
Biotechnology
Research Article
Subjects
Details
- Language :
- English
- ISSN :
- 14712164
- Volume :
- 10
- Database :
- OpenAIRE
- Journal :
- BMC Genomics
- Accession number :
- edsair.doi.dedup.....78df853b787eddaed0cff25287bb3ff1