A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat

Persistent Link:
http://hdl.handle.net/10150/610004
Title:
A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat
Author:
Gu, Yong; Ma, Yaqin; Huo, Naxin; Vogel, John; You, Frank; Lazo, Gerard; Nelson, William; Soderlund, Carol; Dvorak, Jan; Anderson, Olin; Luo, Ming-Cheng
Affiliation:
Genomics and Gene Discovery Research Unit, USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA; Department of Plant Sciences, University of California, Davis, CA 95616, USA; BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
Issue Date:
2009
Publisher:
BioMed Central
Citation:
BMC Genomics 2009, 10:496 doi:10.1186/1471-2164-10-496
Journal:
BMC Genomics
Rights:
© 2009 Gu et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND:Brachypodium 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 of Brachypodium 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.RESULTS:A total of 67,151 Brachypodium BAC clones were fingerprinted with the SNaPshot HICF fingerprinting method and a genome-wide physical map of the Brachypodium genome 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 that Brachypodium and rice genomes are generally highly colinear. Divergent regions were mainly in the rice centromeric regions. A dot-plot of Brachypodium contigs against the rice genome sequences revealed remnants of the whole-genome duplication caused by paleotetraploidy, which were previously found in rice and sorghum. Brachypodium contigs were anchored to the wheat deletion bin maps with the BES gene-tags, opening the door to Brachypodium-Triticeae comparative genomics.CONCLUSION:The construction of the Brachypodium physical 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 of Brachypodium genome sequence and grass comparative genomics. A draft of the physical map and its comparisons with rice and wheat are available at http://phymap.ucdavis.edu/brachypodium/ webcite.
EISSN:
1471-2164
DOI:
10.1186/1471-2164-10-496
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2164/10/496

Full metadata record

DC FieldValue Language
dc.contributor.authorGu, Yongen
dc.contributor.authorMa, Yaqinen
dc.contributor.authorHuo, Naxinen
dc.contributor.authorVogel, Johnen
dc.contributor.authorYou, Franken
dc.contributor.authorLazo, Gerarden
dc.contributor.authorNelson, Williamen
dc.contributor.authorSoderlund, Carolen
dc.contributor.authorDvorak, Janen
dc.contributor.authorAnderson, Olinen
dc.contributor.authorLuo, Ming-Chengen
dc.date.accessioned2016-05-20T08:56:13Z-
dc.date.available2016-05-20T08:56:13Z-
dc.date.issued2009en
dc.identifier.citationBMC Genomics 2009, 10:496 doi:10.1186/1471-2164-10-496en
dc.identifier.doi10.1186/1471-2164-10-496en
dc.identifier.urihttp://hdl.handle.net/10150/610004-
dc.description.abstractBACKGROUND:Brachypodium 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 of Brachypodium 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.RESULTS:A total of 67,151 Brachypodium BAC clones were fingerprinted with the SNaPshot HICF fingerprinting method and a genome-wide physical map of the Brachypodium genome 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 that Brachypodium and rice genomes are generally highly colinear. Divergent regions were mainly in the rice centromeric regions. A dot-plot of Brachypodium contigs against the rice genome sequences revealed remnants of the whole-genome duplication caused by paleotetraploidy, which were previously found in rice and sorghum. Brachypodium contigs were anchored to the wheat deletion bin maps with the BES gene-tags, opening the door to Brachypodium-Triticeae comparative genomics.CONCLUSION:The construction of the Brachypodium physical 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 of Brachypodium genome sequence and grass comparative genomics. A draft of the physical map and its comparisons with rice and wheat are available at http://phymap.ucdavis.edu/brachypodium/ webcite.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2164/10/496en
dc.rights© 2009 Gu et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.titleA BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheaten
dc.typeArticleen
dc.identifier.eissn1471-2164en
dc.contributor.departmentGenomics and Gene Discovery Research Unit, USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USAen
dc.contributor.departmentDepartment of Plant Sciences, University of California, Davis, CA 95616, USAen
dc.contributor.departmentBIO5 Institute, University of Arizona, Tucson, AZ 85721, USAen
dc.identifier.journalBMC Genomicsen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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