1 Department of Plant Sciences, University of California, Davis, CA, USA.
2 Department of Statistics, University of California, Davis, CA, USA.
3 Department of Plant Breeding, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
4 Crop Improvement & Genetics Research, USDA-ARS, Albany, CA, USA.
5 Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
6 School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.
7 Institute of Plant Breeding, Genetics and Genomics (Department of Crop & Soil Sciences), University of Georgia, Athens, GA, USA.
8 Department of Plant Biology, University of Georgia, Athens, GA, USA.
9 Agriculture & Agri-Food Canada, Morden, MB, Canada.
10 Department of Biology, Concordia University, Montreal, QC, Canada.

Structural variation and rates of genome evolution in the grass family seen through comparison of sequences of genomes greatly differing in size.

Plant J. 2018 08;95(3):487-503

Authors: Dvorak J, Wang L, Zhu T, Jorgensen CM, Deal KR, Dai X, Dawson MW, Müller HG, Luo MC, Ramasamy RK, Dehghani H, Gu YQ, Gill BS, Distelfeld A, Devos KM, Qi P, You FM, Gulick PJ, McGuire PE

Abstract

Homology was searched with genes annotated in the Aegilops tauschii pseudomolecules against genes annotated in the pseudomolecules of tetraploid wild emmer wheat, Brachypodium distachyon, sorghum and rice. Similar searches were performed with genes annotated in the rice pseudomolecules. Matrices of collinear genes and rearrangements in their order were constructed. Optical BioNano genome maps were constructed and used to validate rearrangements unique to the wild emmer and Ae. tauschii genomes. Most common rearrangements were short paracentric inversions and short intrachromosomal translocations. Intrachromosomal translocations outnumbered segmental intrachromosomal duplications. The densities of paracentric inversion lengths were approximated by exponential distributions in all six genomes. Densities of collinear genes along the Ae. tauschii chromosomes were highly correlated with meiotic recombination rates but those of rearrangements were not, suggesting different causes of the erosion of gene collinearity and evolution of major chromosome rearrangements. Frequent rearrangements sharing breakpoints suggested that chromosomes have been rearranged recurrently at some sites. The distal 4 Mb of the short arms of rice chromosomes Os11 and Os12 and corresponding regions in the sorghum, B. distachyon and Triticeae genomes contain clusters of interstitial translocations including from 1 to 7 collinear genes. The rates of acquisition of major rearrangements were greater in the large wild emmer wheat and Ae. tauschii genomes than in the lineage preceding their divergence or in the B. distachyon, rice and sorghum lineages. It is suggested that synergy between large quantities of dynamic transposable elements and annual growth habit have been the primary causes of the fast evolution of the Triticeae genomes.

PMID: 29770515 [PubMed - in process]