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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. 2013 May 07; 110(19):7940-5.PN

Abstract

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.

Authors+Show Affiliations

Department of Plant Sciences, University of California, Davis, CA 95616, USA.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

23610408

Citation

Luo, Ming-Cheng, et al. "A 4-gigabase Physical Map Unlocks the Structure and Evolution of the Complex Genome of Aegilops Tauschii, the Wheat D-genome Progenitor." Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 19, 2013, pp. 7940-5.
Luo MC, Gu YQ, You FM, et al. 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. 2013;110(19):7940-5.
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., ... Dvorak, J. (2013). A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. Proceedings of the National Academy of Sciences of the United States of America, 110(19), 7940-5. https://doi.org/10.1073/pnas.1219082110
Luo MC, et al. 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. 2013 May 7;110(19):7940-5. PubMed PMID: 23610408.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. AU - Luo,Ming-Cheng, AU - Gu,Yong Q, AU - You,Frank M, AU - Deal,Karin R, AU - Ma,Yaqin, AU - Hu,Yuqin, AU - Huo,Naxin, AU - Wang,Yi, AU - Wang,Jirui, AU - Chen,Shiyong, AU - Jorgensen,Chad M, AU - Zhang,Yong, AU - McGuire,Patrick E, AU - Pasternak,Shiran, AU - Stein,Joshua C, AU - Ware,Doreen, AU - Kramer,Melissa, AU - McCombie,W Richard, AU - Kianian,Shahryar F, AU - Martis,Mihaela M, AU - Mayer,Klaus F X, AU - Sehgal,Sunish K, AU - Li,Wanlong, AU - Gill,Bikram S, AU - Bevan,Michael W, AU - Simková,Hana, AU - Dolezel,Jaroslav, AU - Weining,Song, AU - Lazo,Gerard R, AU - Anderson,Olin D, AU - Dvorak,Jan, Y1 - 2013/04/22/ PY - 2013/4/24/entrez PY - 2013/4/24/pubmed PY - 2013/7/20/medline KW - BAC contig coassembly KW - Oryza KW - gene density KW - single nucleotide polymorphism KW - synteny SP - 7940 EP - 5 JF - Proceedings of the National Academy of Sciences of the United States of America JO - Proc Natl Acad Sci U S A VL - 110 IS - 19 N2 - 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. SN - 1091-6490 UR - https://www.unboundmedicine.com/medline/citation/23610408/A_4_gigabase_physical_map_unlocks_the_structure_and_evolution_of_the_complex_genome_of_Aegilops_tauschii_the_wheat_D_genome_progenitor_ L2 - http://www.pnas.org/cgi/pmidlookup?view=long&pmid=23610408 DB - PRIME DP - Unbound Medicine ER -