Analysis of Brachypodium genomes with genome-wide optical maps.

Autor: Zhu T; a Department of Plant Sciences, University of California, Davis, CA 95616, USA., Hu Z; a Department of Plant Sciences, University of California, Davis, CA 95616, USA.; b State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), China Agricultural University, Beijing, 100193, China., Rodriguez JC; a Department of Plant Sciences, University of California, Davis, CA 95616, USA., Deal KR; a Department of Plant Sciences, University of California, Davis, CA 95616, USA., Dvorak J; a Department of Plant Sciences, University of California, Davis, CA 95616, USA., Vogel JP; c DOE Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, CA 94598, USA., Liu Z; d State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China., Luo MC; a Department of Plant Sciences, University of California, Davis, CA 95616, USA.
Jazyk: angličtina
Zdroj: Genome [Genome] 2018 Aug; Vol. 61 (8), pp. 559-565. Date of Electronic Publication: 2018 Jun 08.
DOI: 10.1139/gen-2018-0013
Abstrakt: 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.
Databáze: MEDLINE
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