Table 2_Comparative organellar genomics of Arundina graminifolia: mitochondrial complexity and plastid conservation in Orchidaceae.xlsx

Orchidaceae is one of the largest and most diverse angiosperm families, exhibiting remarkable morphological and ecological diversity. Organellar genomes, including mitochondrial and plastid genomes, play essential roles in energy metabolism, photosynthesis, and adaptive evolution, yet their structural evolution in orchids remains unclear. In this study, the mitochondrial and plastid genomes of Arundina graminifolia were assembled and compared with 15 representative orchid species to investigate genome architecture, repeat content, gene composition, and evolutionary dynamics. The mitochondrial genome of A. graminifolia displayed a complex multi-circular structure with extensive rearrangements and abundant repeats, including simple sequence repeats and long repeats, contributing to genome expansion and structural complexity. In contrast, the plastid genome was highly conserved, exhibiting a typical quadripartite structure. Plastid-to-mitochondrion DNA transfers (MTPTs) varied among orchid species in both number and composition, mainly involving complete plastid genes associated with photosynthesis and translation. Analyses of selection pressure and nucleotide diversity revealed strong purifying selection and low sequence variability in mitochondrial genes, whereas plastid genes exhibited higher diversity and evolutionary rates. Phylogenetic analyses based on conserved single-copy genes from both organellar genomes yielded congruent topologies, with A. graminifolia clustering closely with Bletilla striata. Synteny analysis indicated low conservation of mitochondrial genome organization across lineages, particularly in mycoheterotrophic orchids, reflecting dynamic genome evolution. Gene loss and duplication further enhanced genome plasticity and potential functional redundancy. Overall, this study highlights contrasting evolutionary constraints and structural dynamics between mitochondrial and plastid genomes in orchids, providing valuable genomic resources for understanding organelle genome evolution and phylogenetic relationships in Orchidaceae.

兰科（Orchidaceae）是被子植物中物种多样性最高、类群最丰富的科之一，展现出显著的形态与生态多样性。细胞器基因组（organellar genome）包括线粒体基因组与质体基因组（plastid genome），在能量代谢、光合作用及适应性进化中发挥关键作用，但兰科植物细胞器基因组的结构演化机制仍不明晰。本研究组装了竹叶兰（Arundina graminifolia）的线粒体与质体基因组，并与15个代表性兰科物种开展比较分析，以探究其基因组结构、重复序列组成、基因构成及演化动态。竹叶兰的线粒体基因组呈现复杂的多环状结构，伴随大规模重排与丰富的重复序列，包括简单序列重复（simple sequence repeats）与长重复序列，这些特征推动了基因组扩张并增加了结构复杂度。与之形成鲜明对比的是，质体基因组高度保守，呈现典型的四分体结构。质体向线粒体DNA转移（Plastid-to-mitochondrion DNA transfers，MTPTs）在兰科物种间的数量与组成上均存在差异，转移序列主要涉及与光合作用及翻译过程相关的完整质体基因。选择压力与核苷酸多样性分析显示，线粒体基因受到强烈的净化选择，序列变异度较低；而质体基因则表现出更高的多样性与演化速率。基于两类细胞器基因组的保守单拷贝基因开展的系统发育分析得到了一致的拓扑结构，其中A. graminifolia与白及（Bletilla striata）聚为紧密分支。共线性分析（synteny analysis）表明，不同兰科谱系间的线粒体基因组组织保守性较低，在菌异养兰科植物中尤为显著，反映出动态的基因组演化过程。基因丢失与复制进一步增强了基因组可塑性（genome plasticity）与潜在的功能冗余。总体而言，本研究揭示了兰科植物线粒体与质体基因组间截然不同的演化约束与结构动态，为理解兰科细胞器基因组演化及系统发育关系提供了宝贵的基因组资源。