title: Sequencing and comparative analyses of Aegilops tauschii chromosome arm 3DS reveal rapid evolution of Triticeae genomes.
abstract: Bread wheat (Triticum aestivum, AABBDD) is an allohexaploid species derived from two rounds of interspecific hybridizations. A high-quality genome sequence assembly of diploid Aegilops tauschii, the donor of the wheat D genome, will provide a useful platform to study polyploid wheat evolution. A combined approach of BAC pooling and next-generation sequencing technology was employed to sequence the minimum tiling path (MTP) of 3176 BAC clones from the short arm of Ae. tauschii chromosome 3 (At3DS). The final assembly of 135 super-scaffolds with an N50 of 4.2 Mb was used to build a 247-Mb pseudomolecule with a total of 2222 predicted protein-coding genes. Compared with the orthologous regions of rice, Brachypodium, and sorghum, At3DS contains 38.67% more genes. In comparison to At3DS, the short arm sequence of wheat chromosome 3B (Ta3BS) is 95-Mb large in size, which is primarily due to the expansion of the non-centromeric region, suggesting that transposable element (TE) bursts in Ta3B likely occurred there. Also, the size increase is accompanied by a proportional increase in gene number in Ta3BS. We found that in the sequence of short arm of wheat chromosome 3D (Ta3DS), there was only less than 0.27% gene loss compared to At3DS. Our study reveals divergent evolution of grass genomes and provides new insights into sequence changes in the polyploid wheat genome.
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China.
authors.forename: Jingzhong
authors.initials: J
authors.lastname: Xie
authors.affiliation: USDA-ARS West Regional Research Center, Albany, CA 94710, USA; Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA.
authors.forename: Naxin
authors.initials: N
authors.lastname: Huo
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China.
authors.forename: Shenghui
authors.initials: S
authors.lastname: Zhou
authors.affiliation: USDA-ARS West Regional Research Center, Albany, CA 94710, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Wang
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China.
authors.forename: Guanghao
authors.initials: G
authors.lastname: Guo
authors.affiliation: Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA.
authors.forename: Karin R
authors.initials: KR
authors.lastname: Deal
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China.
authors.forename: Shuhong
authors.initials: S
authors.lastname: Ouyang
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Liang
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China.
authors.forename: Zhenzhong
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA.
authors.forename: Lichan
authors.initials: L
authors.lastname: Xiao
authors.affiliation: Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA.
authors.forename: Tingting
authors.initials: T
authors.lastname: Zhu
authors.affiliation: USDA-ARS West Regional Research Center, Albany, CA 94710, USA.
authors.forename: Tiezhu
authors.initials: T
authors.lastname: Hu
authors.affiliation: Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
authors.forename: Vijay
authors.initials: V
authors.lastname: Tiwari
authors.affiliation: Arizona Genomics Institute, School of Plant Science, University of Arizona, Tucson, AZ 85721, USA.
authors.forename: Jianwei
authors.initials: J
authors.lastname: Zhang
authors.affiliation: USDA-ARS West Regional Research Center, Albany, CA 94710, USA.
authors.forename: Hongxia
authors.initials: H
authors.lastname: Li
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China.
authors.forename: Zhongfu
authors.initials: Z
authors.lastname: Ni
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China.
authors.forename: Yingyin
authors.initials: Y
authors.lastname: Yao
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China.
authors.forename: Huiru
authors.initials: H
authors.lastname: Peng
authors.affiliation: USDA-ARS West Regional Research Center, Albany, CA 94710, USA.
authors.forename: Shengli
authors.initials: S
authors.lastname: Zhang
authors.affiliation: USDA-ARS West Regional Research Center, Albany, CA 94710, USA.
authors.forename: Olin D
authors.initials: OD
authors.lastname: Anderson
authors.affiliation: Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA.
authors.forename: Patrick E
authors.initials: PE
authors.lastname: McGuire
authors.affiliation: Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA. Electronic address: jdvorak@ucdavis.edu.
authors.forename: Jan
authors.initials: J
authors.lastname: Dvorak
authors.affiliation: Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA. Electronic address: mcluo@ucdavis.edu.
authors.forename: Ming-Cheng
authors.initials: MC
authors.lastname: Luo
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China. Electronic address: zyliu@genetics.ac.cn.
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Liu
authors.affiliation: USDA-ARS West Regional Research Center, Albany, CA 94710, USA. Electronic address: yong.gu@ars.usda.gov.
authors.forename: Yong Q
authors.initials: YQ
authors.lastname: Gu
authors.affiliation: State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China. Electronic address: qxsun@cau.edu.cn.
authors.forename: Qixin
authors.initials: Q
authors.lastname: Sun
mesh_terms: D032461:Chromosomes, Plant / Q000235:genetics*; D019143:Evolution, Molecular; D018745:Genome, Plant / Q000235:genetics*; D054643:INDEL Mutation; D006109:Poaceae / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017421:Sequence Analysis; D026801:Synteny; D014908:Triticum / Q000235:genetics*
keywords: Aegilops tauschii; Comparative genomics; Genome sequencing; Grass evolution; Sequence assembly