1. Analysis of Brachypodium genomes with genome-wide optical maps
- Author
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Jan Dvorak, Zhiyong Liu, Karin R. Deal, Tingting Zhu, Ming-Cheng Luo, Juan C Rodriguez, Zhaorong Hu, and John P. Vogel
- Subjects
0301 basic medicine ,Sequence assembly ,Genome ,Chromosomes, Plant ,Evolution, Molecular ,Polyploidy ,Structural variation ,03 medical and health sciences ,Species Specificity ,Polyploid ,Genetic model ,Genetics ,Molecular Biology ,Phylogeny ,biology ,General Medicine ,biology.organism_classification ,Diploidy ,030104 developmental biology ,Evolutionary biology ,Brachypodium ,Brachypodium distachyon ,Ploidy ,Biotechnology - Abstract
Brachypodium distachyon (n = 5) is a diploid and has been widely used as a genetic model. Brachypodium stacei (n = 10) and B. hybridum (n = 15) are species that are related to B. distachyon, leading to an hypothesis that they are part of a polyploid series based on x = 5. Several lines of evidence suggest that this hypothesis is incorrect and that the genomes of the three taxa may have evolved by a more complex process. We constructed an optical whole-genome BioNano genome (BNG) map for each species and did pairwise alignment of the BNG maps. The maps showed that B. distachyon and B. stacei are both diploid, in spite of B. stacei having twice as many chromosomes as B. distachyon, and that B. hybridum is an allopolyploid formed from hybridization between B. distachyon and B. stacei. This study also demonstrated the use of BNG maps in the detection and quantification of structural variants among the genomes.
- Published
- 2018