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. 2025 Aug 1;14(15):2361. doi: 10.3390/plants14152361

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© 2025 by the authors.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).

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Inference of the ancestral chromosomes in gymnosperms. Collinearity blocks between pairs of gymnosperm species were identified to construct proto-chromosomes of AGK1 to AGK12, such as (A) AGK1, AGK2, and AGK10 from G. biloba (Gbil) vs. P. tabulaeformis (Ptab). (B) AGK11, AGK6, and AGK12 from G. biloba (Gbil) vs. C. panzhihuaensis (Cpan). (C) AGK5 from G. biloba (Gbil) vs. C. panzhihuaensis (Cpan) and P. tabulaeformis (Ptab). (D) AGK8 from G. biloba (Gbil) vs. C. panzhihuaensis (Cpan) and P. tabulaeformis (Ptab). (E) AGK9 from G. biloba (Gbil) vs. C. panzhihuaensis (Cpan) and T. grandis (Tgra). AGK3, AGK4, and AGK7 from G. biloba (Gbil) vs. M. glyptostroboides (Mgly) (F) and P. tabulaeformis (Ptab) (G). AGK1 to AGK12: the inferred gymnosperm proto-chromosomes were color-coded with 12 distinct colors to differentiate the chromosomes (SteelBlue, ForestGreen, GoldEnrod, OrangeRed, Crimson, DarkOrchid, Tan, IndianRed, OliveDrab, DarkTurquoise, LightSteelBlue, and SlateGray). Numbers with circular symbols represented ancestral chromosomes, and boxes of dotted lines were used to represent blocks involved in the construction of ancestral chromosomes.