ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Systematics and Evolution
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1673127
This article is part of the Research TopicEvolutionary Dynamics, Functional Variation and Application of Plant Organellar GenomeView all 30 articles
Dispersed repeats and Inverted Repeat expansion drive major plastomic rearrangements in Calliandra haematocephala (Leguminosae: Mimoseae)
Provisionally accepted
- Kunming Institute of Botany Chinese Academy of Sciences, Kunming, China
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Structural variations in legume plastomes impact phylogenetic and evolutionary studies. In this study, we focus on the tribe Mimoseae by integrating a newly assembled plastome of Calliandra haematocephala (from PacBio sequencing data) with 15 previously published plastomes representing major lineages, to analyze structural rearrangements, repeat sequences, and selection pressures. The plastome of C. haematocephala revealed extensive structural rearrangements and a ca. 14-kb expansion of the inverted repeats (IRs) into the large single copy (LSC) region, resulting in IRs of 42,069 bp. It also contained a high abundance of clustered dispersed repeats (> 90 bp). These features potentially contribute to significant plastome rearrangements, making it the largest plastome (200,623 bp) recorded to date in Mimoseae and, more broadly, in Leguminosae. Nucleotide diversity (Pi) analysis identified several highly variable regions (Pi > 0.03), including the genes accD, rps18, clpP, and multiple non-coding loci, suggesting their potential as molecular markers. Selection pressure analyses detected positive selection (dN/dS > 1) in clpP, ycf2, and rps17, suggesting possible roles in adaptive evolution. Branch-specific positive selection was also found in genes such as rpoC1 and atpA within the Calliandra clade, indicating lineage-specific adaptive pressures. This study highlights the dynamic evolution of plastomes in Mimoseae and offers new insights into their structural diversity and adaptive evolution.
Keywords: Plastome evolution, Inverted repeat expansion, rearrangement, Nucleotide diversity, positive selection
Received: 25 Jul 2025; Accepted: 12 Sep 2025.
Copyright: © 2025 Zhao, An, Gu, Lu, Dingjie, Xiahou, Zhang and Yi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Rong Zhang, Kunming Institute of Botany Chinese Academy of Sciences, Kunming, China
Ting-Shuang Yi, Kunming Institute of Botany Chinese Academy of Sciences, Kunming, China
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