Table 1_Dispersed repeats and inverted repeat expansion drive major plastomic rearrangements in Calliandra haematocephala (Leguminosae: Mimoseae).xlsx

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.

豆科质体基因组（plastome）的结构变异会对系统发育与进化研究产生影响。本研究聚焦含羞草族（Mimoseae），将基于PacBio测序数据新组装的朱缨花（Calliandra haematocephala）质体基因组，与15个代表主要演化分支的已发表质体基因组进行整合，以此分析结构重排、重复序列与选择压力。朱缨花的质体基因组存在广泛的结构重排，且反向重复序列（inverted repeats，IRs）向大单拷贝区（large single copy，LSC）发生约14 kb的扩张，使得反向重复序列长度达到42069 bp；该基因组同时富含长度大于90 bp的成簇分散重复序列。上述特征可能促成了显著的质体基因组重排，使其成为含羞草族乃至更广范围豆科（Leguminosae）中迄今记录到的最大质体基因组（200623 bp）。核苷酸多样性（nucleotide diversity，Pi）分析鉴定出多个高变异区域（Pi>0.03），包括accD、rps18、clpP基因及多个非编码位点，提示这些区域可作为潜在的分子标记。选择压力分析检测到clpP、ycf2和rps17基因受到正向选择（dN/dS>1），表明其可能在适应性进化中发挥作用。此外，在朱缨花演化枝内的rpoC1、atpA等基因中发现了分支特异性正向选择，暗示存在分支特异性的适应性选择压力。本研究揭示了含羞草族质体基因组的动态演化过程，为其结构多样性与适应性进化提供了新的研究视角。