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

Abstract

<p>Abstract</p> <p>Background</p> <p><it>Brachypodium distachyon </it>(<it>Brachypodium</it>) 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 <it>Brachypodiu</it>m 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.</p> <p>Results</p> <p>A total of 67,151 <it>Brachypodium </it>BAC clones were fingerprinted with the SNaPshot HICF fingerprinting method and a genome-wide physical map of the <it>Brachypodium </it>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 <it>Brachypodium </it>and rice genomes are generally highly colinear. Divergent regions were mainly in the rice centromeric regions. A dot-plot of <it>Brachypodium </it>contigs against the rice genome sequences revealed remnants of the whole-genome duplication caused by paleotetraploidy, which were previously found in rice and sorghum. <it>Brachypodium </it>contigs were anchored to the wheat deletion bin maps with the BES gene-tags, opening the door to <it>Brachypodium</it>-Triticeae comparative genomics.</p> <p>Conclusion</p> <p>The construction of the <it>Brachypodium </it>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 <it>Brachypodium </it>genome sequence and grass comparative genomics. A draft of the physical map and its comparisons with rice and wheat are available at <url>http://phymap.ucdavis.edu/brachypodium/</url>.</p