PDF(Pubmed)
Abstract：
The orchid genus Dipodium R.Br. (Epidendroideae) comprises leafy autotrophic and leafless mycoheterotrophic species, with the latter confined to sect. Dipodium. This study examined plastome degeneration in Dipodium in a phylogenomic and temporal context. Whole plastomes were reconstructed and annotated for 24 Dipodium samples representing 14 species and two putatively new species, encompassing over 80% of species diversity in sect. Dipodium. Phylogenomic analysis based on 68 plastid loci including a broad outgroup sampling across Orchidaceae found that sect. Leopardanthus is the sister lineage to sect. Dipodium. Dipodium ensifolium, the only leafy autotrophic species in sect. Dipodium, was found to be a sister to all leafless, mycoheterotrophic species, supporting a single evolutionary origin of mycoheterotrophy in the genus. Divergence-time estimations found that Dipodium arose ca. 33.3 Ma near the lower boundary of the Oligocene and that crown diversification commenced in the late Miocene, ca. 11.3 Ma. Mycoheterotrophy in the genus was estimated to have evolved in the late Miocene, ca. 7.3 Ma, in sect. Dipodium. The comparative assessment of plastome structure and gene degradation in Dipodium revealed that plastid ndh genes were pseudogenised or physically lost in all Dipodium species, including in leafy autotrophic species of both Dipodium sections. Levels of plastid ndh gene degradation were found to vary among species as well as within species, providing evidence of relaxed selection for retention of the NADH dehydrogenase complex within the genus. Dipodium exhibits an early stage of plastid genome degradation, as all species were found to have retained a full set of functional photosynthesis-related genes and housekeeping genes. This study provides important insights into plastid genome degradation along the transition from autotrophy to mycoheterotrophy in a phylogenomic and temporal context.
摘要：
兰花属DipodiumR.Br.（Epidendroideae）包括多叶自养和无叶杂种，后者仅限于教派。Dipodium.这项研究在系统基因组和时间背景下检查了Dipodium中的质体退化。重建并注释了24个Dipodium样品，代表14个物种和两个假定的新物种，涵盖了80%以上的物种多样性。Dipodium.基于68个质体基因座的系统基因组分析，包括整个兰科的广泛外群采样，发现了该教派。豹纹是教派的姊妹血统。Dipodium.Dipodiumentifolium,sect中唯一的多叶自养物种。Dipodium,被发现是所有无叶的姐妹，异养真菌，支持该属中杂种的单一进化起源。发散时间估计发现Dipodium出现了大约。33.3Ma靠近渐新世的下边界，并且冠层的多样化始于上新世晚期，CA.11.3毫安。据估计，该属的杂种营养是在上世纪晚期进化的，CA.7.3Ma,在教派中。Dipodium.对Dipodium中的质体结构和基因降解的比较评估表明，在所有Dipodium物种中，质体ndh基因都被假成因化或物理丢失，包括两个Dipodium切片的多叶自养物种。发现质体ndh基因降解的水平在物种之间以及物种内都有所不同，提供了在属内保留NADH脱氢酶复合物的放松选择的证据。Dipodium表现出质体基因组降解的早期阶段，因为发现所有物种都保留了全套功能性光合作用相关基因和管家基因。这项研究为在系统发育和时间背景下从自养到杂养的过渡过程中质体基因组降解提供了重要见解。
