Investigating the Path of Plastid Genome Degradation in an Early-Transitional Clade of Heterotrophic Orchids, and Implications for Heterotrophic Angiosperms
Investigating the Path of Plastid Genome Degradation in an Early-Transitional Clade of Heterotrophic Orchids, and Implications for Heterotrophic Angiosperms
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DOI：
10.1093/molbev/msu252
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发表时间：
2014-12-01
影响因子：
10.7
通讯作者：
Santos, Cristian
中科院分区：
文献类型：
--
作者：
Barrett, Craig F.;Freudenstein, John V.;Santos, Cristian
寄生生物体的形态和基因组的减少。一些异养、寄生植物由于对光合功能的选择压力放松而导致质体基因组急剧减少和降解。然而，很少有研究涉及含有光合和非光合物种的群体中质体降解的初始阶段。珊瑚根属是一种无叶、异养的兰花属，包含绿色的光合物种和非绿色的非光合物种，并代表了一个理想的系统，在其中评估过渡到“最小质体组”的开始。“使用Illumina对基因组DNA进行配对末端测序，为珊瑚根属的9个分类群生成完整的质体，以评估分类群之间的降解程度，并与被子植物之间的一般降解模型进行比较。总叶绿素的定量表明，非绿色珊瑚根仍然产生叶绿素，但在10倍的浓度比绿色同系物。完整的质体和部分核rDNA顺反子产生了一个完全解析树珊瑚根，至少有两个独立的光合作用损失，证明了在Co. striata和nongreen Co. maculata的基因缺失和假基因。所有珊瑚根都显示出NAD（P）H脱氢酶复合物基因降解的证据。在开放阅读框的基因中，光合作用相关基因显示出非绿色珊瑚根中性进化的证据，而ATP合酶复合体的基因显示出这些相同群体中正选择的一些证据，尽管原因不明。珊瑚根跨越了质体降解的一般模型的早期阶段，并为理解异养被子植物质体进化的过程增加了重要的见解。
Parasitic organisms exemplify morphological and genomic reduction. Some heterotrophic, parasitic plants harbor drastically reduced and degraded plastid genomes resulting from relaxed selective pressure on photosynthetic function. However, few studies have addressed the initial stages of plastome degradation in groups containing both photosynthetic and nonphotosynthetic species. Corallorhiza is a genus of leafless, heterotrophic orchids that contains both green, photosynthetic species and nongreen, putatively nonphotosynthetic species, and represents an ideal system in which to assess the beginning of the transition to a "minimal plastome." Complete plastomes were generated for nine taxa of Corallorhiza using Illumina paired-end sequencing of genomic DNA to assess the degree of degradation among taxa, and for comparison with a general model of degradation among angiosperms. Quantification of total chlorophyll suggests that nongreen Corallorhiza still produce chlorophyll, but at 10-fold lower concentrations than green congeners. Complete plastomes and partial nuclear rDNA cistrons yielded a fully resolved tree for Corallorhiza, with at least two independent losses of photosynthesis, evidenced by gene deletions and pseudogenes in Co. striata and nongreen Co. maculata. All Corallorhiza show some evidence of degradation in genes of the NAD(P)H dehydrogenase complex. Among genes with open reading frames, photosynthesis-related genes displayed evidence of neutral evolution in nongreen Corallorhiza, whereas genes of the ATP synthase complex displayed some evidence of positive selection in these same groups, though for reasons unknown. Corallorhiza spans the early stages of a general model of plastome degradation and has added critical insight for understanding the process of plastome evolution in heterotrophic angiosperms.