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Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat
- Source :
- Huo, Naxin; Vogel, John P.; Lazo, Gerard R.; You, Frank M.; Ma, Yaqin; McMahon, Stephanie; et al.(2009). Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat. Plant Molecular Biology: An International Journal on Molecular Biology, Molecular Genetics and Biochemistry, 70(1), pp 47-61. doi: 10.1007/s11103-009-9456-3. Retrieved from: http://www.escholarship.org/uc/item/7ss61705
- Publication Year :
- 2009
- Publisher :
- Springer Science and Business Media LLC, 2009.
-
Abstract
- Brachypodium distachyon (Brachypodium) has been recently recognized as an emerging model system for both comparative and functional genomics in grass species. In this study, 55,221 repeat masked Brachypodium BAC end sequences (BES) were used for comparative analysis against the 12 rice pseudomolecules. The analysis revealed that approximately 26.4% of BES have significant matches with the rice genome and 82.4% of the matches were homologous to known genes. Further analysis of paired-end BES and approximately 1.0 Mb sequences from nine selected BACs proved to be useful in revealing conserved regions and regions that have undergone considerable genomic changes. Differential gene amplification, insertions/deletions and inversions appeared to be the common evolutionary events that caused variations of microcolinearity at different orthologous genomic regions. It was found that approximately 17% of genes in the two genomes are not colinear in the orthologous regions. Analysis of BAC sequences also revealed higher gene density (approximately 9 kb/gene) and lower repeat DNA content (approximately 13.1%) in Brachypodium when compared to the orthologous rice regions, consistent with the smaller size of the Brachypodium genome. The 119 annotated Brachypodium genes were BLASTN compared against the wheat EST database and deletion bin mapped wheat ESTs. About 77% of the genes retrieved significant matches in the EST database, while 9.2% matched to the bin mapped ESTs. In some cases, genes in single Brachypodium BACs matched to multiple ESTs that were mapped to the same deletion bins, suggesting that the Brachypodium genome will be useful for ordering wheat ESTs within the deletion bins and developing specific markers at targeted regions in the wheat genome.
- Subjects :
- Chromosomes, Artificial, Bacterial
Genome evolution
Colinearity
DNA, Plant
Genomics
Plant Science
Repetitive DNA elements
Biology
Genes, Plant
Poaceae
Synteny
Genome
Evolution, Molecular
Gene density
Genetics
Conserved Sequence
Triticum
Expressed Sequence Tags
Comparative genomics
Brachypodium distachyon
Plant Sciences
Life Sciences
food and beverages
Oryza
Sequence Analysis, DNA
General Medicine
Plant Pathology
biology.organism_classification
Biochemistry, general
Brachypodium
Sequence Alignment
Agronomy and Crop Science
Genome, Plant
Subjects
Details
- ISSN :
- 15735028 and 01674412
- Volume :
- 70
- Database :
- OpenAIRE
- Journal :
- Plant Molecular Biology
- Accession number :
- edsair.doi.dedup.....e3a59463dd224502347efbc75fb96873