Data Sheet 3_Dispersed repeats and inverted repeat expansion drive major plastomic rearrangements in Calliandra haematocephala (Leguminosae: Mimoseae).zip

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。本研究以含羞草族（Mimoseae）为研究对象，将基于PacBio测序数据新组装的朱缨花（Calliandra haematocephala）质体基因组，与15个已发表的代表主要演化支的质体基因组进行整合，以分析结构重排、重复序列以及选择压力。朱缨花的质体基因组展现出广泛的结构重排，且其反向重复序列（inverted repeats, IRs）向大单拷贝区（large single copy, LSC）发生了约14kb的扩张，使得反向重复序列长度达到42069 bp。该质体基因组还包含大量长度大于90 bp的成簇散布重复序列。上述特征可能促成了显著的质体基因组重排，使其成为目前含羞草族乃至更广范围豆科（Leguminosae）中已记录的最大质体基因组（全长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等基因以及多个非编码基因座，表明这些区域有望作为分子标记。选择压力分析检测到clpP、ycf2和rps17基因存在正选择（dN/dS＞1），暗示这些基因可能在适应性进化中发挥作用。在朱缨花演化支内，rpoC1、atpA等基因还检测到分支特异性正选择，表明该演化支存在谱系特异性的适应性选择压力。本研究凸显了含羞草族质体基因组的动态演化，并为其结构多样性与适应性进化提供了新的见解。