Ancestral genome reconstruction and the evolution of chromosomal rearrangements in Triticeae

Xueqing Yan; Runxian Yu; Jinpeng Wang; Yuannian Jiao

doi:10.1016/j.jgg.2024.12.017

Ancestral genome reconstruction and the evolution of chromosomal rearrangements in Triticeae

J Genet Genomics. 2024 Dec 31:S1673-8527(24)00370-9. doi: 10.1016/j.jgg.2024.12.017. Online ahead of print.

Authors

Xueqing Yan¹, Runxian Yu¹, Jinpeng Wang², Yuannian Jiao³

Affiliations

¹ State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
² State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063210, China.
³ State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: jiaoyn@ibcas.ac.cn.

PMID: 39746604
DOI: 10.1016/j.jgg.2024.12.017

Abstract

Chromosomal rearrangements (CRs) often cause phenotypic variations. Although several major rearrangements have been identified in Triticeae, a comprehensive study of the order, timing, and breakpoints of CRs has not been conducted. Here, we reconstruct high-quality ancestral genomes for the most recent common ancestor (MRCA) of the Triticeae, and the MRCA of the wheat lineage (Triticum and Aegilops). The protogenes of MRCA of the Triticeae and the wheat lineage are 22,894 and 29,060, respectively, which were arranged in their ancestral order. By partitioning modern Triticeae chromosomes into sets of syntenic regions and linking each to the corresponding protochromosomes, we revisit the rye chromosome structural evolution and propose alternative evolutionary routes. The previously identified 4L/5L reciprocal translocation in rye and Triticum urartu are found to have occurred independently and are unlikely the result of chromosomal introgression following distant hybridization. We also clarify that the 4AL/7BS translocation in tetraploid wheat was a bidirectional rather than unidirectional translocation event. Lastly, we identify several breakpoints in protochromosomes that independently reoccur following Triticeae evolution, representing potential CR hotspots. This study demonstrates that these reconstructed ancestral genomes can serve as special comparative references and facilitate a better understanding of the evolution of structural rearrangements in Triticeae.

Keywords: Ancestral genome reconstruction; Chromosome rearrangement; Evolution; Structure variations; Translocation; Triticeae.