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. 2021 Aug 19;5(10):1382–1393. doi: 10.1038/s41559-021-01523-y

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© The Author(s) 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a, Diagram of resynthesized allotetraploids and natural A. suecica (Asu). Allo733 and Allo738 are two stable A. suecica-like allotetraploids derived from tetraploid A. thaliana (Ath, Ler4) and A. arenosa (Aar, Care-1)¹¹. Natural Asu was formed ~300,000 years ago. b, Genomic synteny of A. thaliana Col genome (Col-T), A (Aar-related) subgenome of Allo738, sT and sA subgenomes of Asu and A. lyrata (Aly). Syntenic blocks with 30 or more genes are shown. c, Rearrangements between sT (1–5) and sA (1–8) subgenomes of natural Asu and extant progenitors, A. thaliana (Col, T1–T5) and A. arenosa (A subgenome of Allo738, A1–A8). Ribbons indicate translocation between subgenomes (TLb, black), within a subgenome (TLs, blue) and transposition in the same chromosomes (TP, red). d, A large (~5 Mb) translocation is present between sT1 and sA1 relative to T1 and A1 chromosomes, which was validated by chromatin contact (Hi-C) maps. e, Proportion of sequence variation in sA and sT subgenomes of Asu relative to extant progenitors. INV, inversion; TP, transpositions; TLs, translocations within a subgenome; TLb, translocations between subgenomes. f, Boxplots of the estimated time for intact LTR insertion (million years ago, Ma) in A (Aar-related) subgenome of 738, Col genome (Col-T), sT and sA subgenomes of Asu, diploid Ler genome (Ler2-T), T (Ler4) subgenome of Allo738 and A. lyrata (Aly) genome. Single and double asterisks indicate statistical significance levels of P < 0.05 and 0.01, respectively (permutation test using 1,000 permutations).

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