Department of Genetics, University of Georgia, Athens, GA, 30677, USA.
BMC Plant Biol. 2018 Feb 6;18(1):30. doi: 10.1186/s12870-018-1249-x.
The chloroplast genomes (plastome) of most plants are highly conserved in structure, gene content, and gene order. Parasitic plants, including those that are fully photosynthetic, often contain plastome rearrangements. These most notably include gene deletions that result in a smaller plastome size. The nature of gene loss and genome structural rearrangement has been investigated in several parasitic plants, but their timing and contributions to the adaptation of these parasites requires further investigation, especially among the under-studied hemi-parasites.
De novo sequencing, assembly and annotation of the chloroplast genomes of five photosynthetic parasites from the family Orobanchaceae were employed to investigate plastome dynamics. Four had major structural rearrangements, including gene duplications and gene losses, that differentiated the taxa. The facultative parasite Aureolaria virginica had the most similar genome content to its close non-parasitic relative, Lindenbergia philippensis, with similar genome size and organization, and no differences in gene content. In contrast, the facultative parasite Buchnera americana and three obligate parasites in the genus Striga all had enlargements of their plastomes, primarily caused by expansion within the large inverted repeats (IRs) that are a standard plastome feature. Some of these IR increases were shared by multiple investigated species, but others were unique to particular lineages. Gene deletions and pseudogenization were also both shared and lineage-specific, with particularly frequent and independent loss of the ndh genes involved in electron recycling.
Five new plastid genomes were fully assembled and compared. The results indicate that plastome instability is common in parasitic plants, even those that retain the need to perform essential plastid functions like photosynthesis. Gene losses were slow and not identical across taxa, suggesting that different lineages had different uses or needs for some of their plastome gene content, including genes involved in some aspects of photosynthesis. Recent repeat region extensions, some unique to terminal species branches, were observed after the divergence of the Buchnera/Striga clade, suggesting that this otherwise rare event has some special value in this lineage.
大多数植物的叶绿体基因组（质体基因组）在结构、基因内容和基因顺序上高度保守。包括完全光合作用在内的寄生植物通常含有质体基因组重排。这些重排最显著的特征是导致较小的质体大小的基因缺失。已经在几种寄生植物中研究了基因丢失和基因组结构重排的性质，但它们的时间和对这些寄生虫适应的贡献需要进一步研究，尤其是在研究较少的半寄生植物中。
利用从头测序、组装和注释五个来自列当科的光合寄生植物的叶绿体基因组，研究了质体基因组的动态。其中四个有主要的结构重排，包括基因复制和基因丢失，使这些分类群得以区分。兼性寄生植物 Aureolaria virginica 与它的近缘非寄生植物 Lindenbergia philippensis 具有最相似的基因组内容，具有相似的基因组大小和组织，基因内容没有差异。相比之下，兼性寄生植物 Buchnera americana 和三个属 Striga 的专性寄生植物的质体基因组都有扩大，主要是由于大反向重复（IR）内的扩张引起的，这是标准质体基因组的一个特征。这些 IR 增加中的一些在多个被研究的物种中共享，但另一些则是特定谱系所特有的。基因缺失和假基因化既在多个谱系中共享，也具有谱系特异性，特别是涉及电子回收的 ndh 基因频繁且独立地缺失。
五个新的质体基因组被完全组装并进行了比较。结果表明，质体不稳定在寄生植物中很常见，即使是那些保留了进行光合作用等基本质体功能的植物也是如此。基因丢失是缓慢的，而且在不同的分类群中并不相同，这表明不同的谱系对它们的质体基因内容有不同的用途或需求，包括参与光合作用某些方面的基因。在 Buchnera/Striga 分支分化后，观察到了最近的重复区扩展，其中一些仅在末端物种分支中出现，这表明这种 otherwise rare event 对该谱系具有特殊价值。
