Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence
- Scott Ferguson1,4,
- Ashley Jones1,4,
- Kevin Murray1,2,
- Rose Andrew3,
- Benjamin Schwessinger1 and
- Justin Borevitz1
- 1Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia;
- 2Weigel Department, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany;
- 3Botany & N.C.W. Beadle Herbarium, School of Environmental and Rural Science, University of New England, Armidale, New South Wales 2351, Australia
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↵4 These authors contributed equally to this work.
Abstract
Genomes have a highly organized architecture (nonrandom organization of functional and nonfunctional genetic elements within chromosomes) that is essential for many biological functions, particularly gene expression and reproduction. Despite the need to conserve genome architecture, a high level of structural variation has been observed within species. As species separate and diverge, genome architecture also diverges, becoming increasingly poorly conserved as divergence time increases. However, within plant genomes, the processes of genome architecture divergence are not well described. Here we use long-read sequencing and de novo assembly of 33 phylogenetically diverse, wild and naturally evolving Eucalyptus species, covering 1–50 million years of diverging genome evolution to measure genome architectural conservation and describe architectural divergence. The investigation of these genomes revealed that following lineage divergence, genome architecture is highly fragmented by rearrangements. As genomes continue to diverge, the accumulation of mutations and the subsequent divergence beyond recognition of rearrangements become the primary driver of genome divergence. The loss of syntenic regions also contribute to genome divergence but at a slower pace than that of rearrangements. We hypothesize that duplications and translocations are potentially the greatest contributors to Eucalyptus genome divergence.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.277999.123.
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Freely available online through the Genome Research Open Access option.
- Received April 19, 2023.
- Accepted March 22, 2024.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
