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Luo, M.C.* ; Gu, Y.Q.* ; You, F.M.* ; Deal, K.R.* ; Ma, Y.* ; Hu, Y.* ; Huo, N.* ; Wang, Y.* ; Wang, J.* ; Chen, S.* ; Jorgensen, C.M.* ; Zhang, Y.* ; McGuire, P.E.* ; Pasternak, S.* ; Stein, J.C.* ; Ware, D.* ; Kramer, M.* ; McCombie, W.R.* ; Kianian, S.F.* ; Martis, M.M. ; Mayer, K.F.X. ; Sehgal, S.K.* ; Li, W.* ; Gill, B.S.* ; Bevan, M.W.* ; Šimková, H.* ; Dolezel, J.* ; Weining, S.* ; Lazo, G.R.* ; Anderson, O.D.* ; Dvorak, J.*

A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor.

Proc. Natl. Acad. Sci. U.S.A. 110, 7940-7945 (2013)
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The current limitations in genome sequencing technology require the construction of physical maps for high-quality draft sequences of large plant genomes, such as that of Aegilops tauschii, the wheat D-genome progenitor. To construct a physical map of the Ae. tauschii genome, we fingerprinted 461,706 bacterial artificial chromosome clones, assembled contigs, designed a 10K Ae. tauschii Infinium SNP array, constructed a 7,185-marker genetic map, and anchored on the map contigs totaling 4.03 Gb. Using whole genome shotgun reads, we extended the SNP marker sequences and found 17,093 genes and gene fragments. We showed that collinearity of the Ae. tauschii genes with Brachypodium distachyon, rice, and sorghum decreased with phylogenetic distance and that structural genome evolution rates have been high across all investigated lineages in subfamily Pooideae, including that of Brachypodieae. We obtained additional information about the evolution of the seven Triticeae chromosomes from 12 ancestral chromosomes and uncovered a pattern of centromere inactivation accompanying nested chromosome insertions in grasses. We showed that the density of noncollinear genes along the Ae. tauschii chromosomes positively correlates with recombination rates, suggested a cause, and showed that new genes, exemplified by disease resistance genes, are preferentially located in high-recombination chromosome regions.
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Publication type Article: Journal article
Document type Scientific Article
Keywords Single nucleotide polymorphism; Synteny; Gene density; Oryza; BAC contig coassembly; Single Nucleotide Polymorphisms ; Artificial Chromosome Libraries ; Brachypodium-distachyon ; Sequence Composition ; Plants ; Genes ; Recombination ; Organization ; Divergence ; Triticeae
Language english
Publication Year 2013
HGF-reported in Year 2013
ISSN (print) / ISBN 0027-8424
e-ISSN 1091-6490
Journal Proceedings of the National Academy of Sciences of the United States of America
Quellenangaben Volume: 110, Issue: 19, Pages: 7940-7945 Article Number: , Supplement: ,
Publisher National Academy of Sciences
Reviewing status Peer reviewed
Institute(s) Institute of Bioinformatics and Systems Biology (IBIS)
POF-Topic(s) 20402 - Sustainable Plant Production
Research field(s) Enabling and Novel Technologies
PSP Element(s) G-503790-001
PubMed ID 23610408
DOI 10.1073/pnas.1219082110
WOS ID WOS:000319327700088
Scopus ID 84877344186
Erfassungsdatum 2013-04-26
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