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Title: Analysis of Brachypodium genomes with genome-wide optical maps

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.

Authors:
 [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)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1544007
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Genome
Additional Journal Information:
Journal Volume: 61; Journal Issue: 8; Journal ID: ISSN 0831-2796
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biotechnology & Applied Microbiology; Genetics & Heredity

Citation Formats

Zhu, Tingting, Hu, Zhaorong, Rodriguez, Juan C., Deal, Karin R., Dvorak, Jan, Vogel, John P., Liu, Zhiyong, and Luo, Ming-Cheng. Analysis of Brachypodium genomes with genome-wide optical maps. United States: N. p., 2018. Web. doi:10.1139/gen-2018-0013.
Zhu, Tingting, Hu, Zhaorong, Rodriguez, Juan C., Deal, Karin R., Dvorak, Jan, Vogel, John P., Liu, Zhiyong, & Luo, Ming-Cheng. Analysis of Brachypodium genomes with genome-wide optical maps. United States. https://doi.org/10.1139/gen-2018-0013
Zhu, Tingting, Hu, Zhaorong, Rodriguez, Juan C., Deal, Karin R., Dvorak, Jan, Vogel, John P., Liu, Zhiyong, and Luo, Ming-Cheng. Fri . "Analysis of Brachypodium genomes with genome-wide optical maps". United States. https://doi.org/10.1139/gen-2018-0013. https://www.osti.gov/servlets/purl/1544007.
@article{osti_1544007,
title = {Analysis of Brachypodium genomes with genome-wide optical maps},
author = {Zhu, Tingting and Hu, Zhaorong and Rodriguez, Juan C. and Deal, Karin R. and Dvorak, Jan and Vogel, John P. and Liu, Zhiyong and Luo, Ming-Cheng},
abstractNote = {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.},
doi = {10.1139/gen-2018-0013},
url = {https://www.osti.gov/biblio/1544007}, journal = {Genome},
issn = {0831-2796},
number = 8,
volume = 61,
place = {United States},
year = {2018},
month = {6}
}

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