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United States Department of Agriculture

Agricultural Research Service

Title: Construction and Characterization of Two Bac Libraries from Brachypodium Distachypon, a New Model for Grass Genomics

Authors
item Gu, Yong
item Lazo, Gerard
item Vogel, John
item Coleman-Derr, Devin - UC DAVIS
item Luo, Ming-Cheng - UC DAVIS
item Thilmony, Roger
item Garvin, David
item Anderson, Olin
item Huo, Naxin - UC DAVIS

Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 1, 2006
Publication Date: October 19, 2006
Citation: Gu, Y., Lazo, G., Vogel, J., Coleman-Derr, D., Luo, M.C., Thilmony, R., Garvin, D., Anderson, O., Huo, N. 2006. Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics. Genome. 49(9):1099-1108.

Interpretive Summary: Because of its extremely large genome size, cloning of agronomically important genes in wheat and barley still represents a great challenge. Brachypodium has a very small and simple genome. This grass species is also evolutionarily closely related to wheat and barley. Therefore, it can serve as model species to enhance our understanding of the genome complex of the wheat and barley genomes and develop more effective strategies for map-based cloning of genes in wheat and barley. In this study, we constructed two large insert genomic DNA for the Brachypodium. These two libraries provide a valuable resource for promoting genomics research on this emerging model species

Technical Abstract: Brachypodium is well suited to be a model system for temperate grasses because of its compact genome and a range of biological features. In an effort to develop resources for genome research in this emerging model species, we constructed two bacterial artificial chromosome (BAC) libraries from the diploid Brachypodium accession BD21 using cloning enzymes HindIII and BamHI. A total of 73,728 clones, 36,864 per BAC library, were picked and arrayed in 192 384-well plates. The average insert size is estimated to be 100 kb and 105 kb for the BamHI and HindIII libraries, respectively. Inserts of chloroplast origin account for 4.4 % and 2.4%, respectively. The two libraries represent a 9.4- and 9.9- fold haploid genome equivalents, with a total of 19.3-fold, based on a genome size of 355Mb reported for the diploid Brachypodium, implying a 99.99% probability of recovering any specific sequence from each library. Eight starch biosynthesis genes were used to validate the theoretical genome coverage and gave an estimated coverage of 11.6- and 19.6-fold genome equivalents. To obtain a first view of the sequence composition of the Brachypodium genome, a total of 2,185 BAC end sequences (BES), representing 1.3 Mb of random genomic sequence, were compared with the NCBI GenBank database and the GIRI repeat database. Using a cutoff expectation E value < 10-10, only 3.3% of the BESs show similarity to repetitive sequences in the existing database, while 40.0% have matches to the sequences in the EST database, suggesting that a considerable portion of the genome is likely transcribed. When the BESs were compared with individual EST databases, more matches hit wheat than maize although their EST collections are of a similar size, further supporting the close relationship between Brachypodium and the Triticeae. Additionally, our results suggest that the development of a BAC-based physical map for Brachypodium can be greatly facilitated by anchoring BAC end sequences to the rice genome.

Last Modified: 9/2/2014