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Analysis of Brachypodium genomes with genome-wide optical maps

Journal Article · · Genome
 [1];  [2];  [1];  [1];  [1];  [3];  [4];  [1]
  1. Univ. of California, Davis, CA (United States)
  2. Univ. of California, Davis, CA (United States); China Agricultural Univ., Beijing (China)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. China Academy of Sciences, Beijing (China)
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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.
Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1544007
Journal Information:
Genome, Journal Name: Genome Journal Issue: 8 Vol. 61; ISSN 0831-2796
Country of Publication:
United States
Language:
English

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Cited By (3)

Sequencing a Juglans regia × J. microcarpa hybrid yields high-quality genome assemblies of parental species journal March 2019
Procedurally Generated Artworks Based on Multiple Sequence Alignment of Orthologous Gene Copies journal May 2019
Accessing a Russian Wheat Aphid Resistance Gene in Bread Wheat by Long‐Read Technologies journal June 2019

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