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bioRxiv · 10.64898/2026.03.16.711854

Short repeats rewrite plant mitochondrial evolution: Genomic expansion and hybridization signatures in a taxonomically complex radiation

Zhang, F.·Gao, L.-Z.
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Abstract

Plant mitochondrial genomes are paradoxical: structurally dynamic yet functionally conserved. In hybrid-prone lineages like Camellia (Theaceae), the forces shaping mitogenome evolution remain unclear. Here, we assemble mitogenomes of eight Camellia species and an outgroup. We show that short repeats (<100 bp) drive genome expansion (PGLS: R{superscript 2} = 0.97, P = 6.3 x 10-), overturning the long-repeat paradigm. Multichromosomal architectures and extensive horizontal transfer (up to 25.5% plastid DNA) characterize hybrid lineages. Stark phylogenomic conflicts among mitochondrial, chloroplast and nuclear genomes expose genome-wide hybridization signatures. Mitochondria thus act as recorders of historical gene flow, capturing repeat explosions triggered by introgression. This work redefines plant mitogenome evolution and provides a framework to resolve taxonomic complexities in rapidly radiating angiosperms.

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Zhang, F., Gao, L.-Z.. 2026-03-18. Short repeats rewrite plant mitochondrial evolution: Genomic expansion and hybridization signatures in a taxonomically complex radiation. https://doi.org/10.64898/2026.03.16.711854

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