Plastid Genomes of Five Species of Riverweeds (Podostemaceae): Structural Organization and Comparative Analysis in Malpighiales
Plastid Genomes of Five Species of Riverweeds (Podostemaceae): Structural Organization and Comparative Analysis in Malpighiales
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DOI：
10.3389/fpls.2019.01035
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发表时间：
2019-08-20
影响因子：
5.6
通讯作者：
Olmstead, Richard G.
中科院分区：
文献类型：
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作者：
Bedoya, Ana M.;Ruhfel, Bradley R.;Olmstead, Richard G.
随着下一代测序技术的出现，全质体数据可以作为植物基因组DNA的低覆盖测序的副产品获得。这提供了一个机会，研究质体进化的群体，以及测试类群之间的系统发育关系。在Malpighiales目（类似于16，000种）中，Podostemaceae（300 spp.）它们因其独特的习性而脱颖而出，生活在快速流动的水生栖息地的岩石上，并显示出高度修饰的形态，这使我们对其分类，生物学和进化的理解变得混乱。在这项研究中，我们使用基因组略读数据组装的全质体基因组的5种Podostemaceae。我们在Malpighiales内的比较框架中分析了我们的数据，以确定该科质体的结构、基因含量和重排。Podostemaceae有一个最小的质体基因组报告到目前为止的Malpighiales，可能是由于长度的变化反向重复序列（IR）区域，基因丢失，和基因间区域的变化。我们还检测到一个大的单拷贝区域独特的家庭的主要反转。在被子植物和一般的陆地植物中，ycf1和ycf2的不常见的损失或假基因化也被认为是Podostemaceae的特征，但补偿机制和影响，accD，rp122和clpP的假基因化和rps16的损失仍有待解释。此外，我们估计了一个系统发育树之间的选择种在Malpighiales。我们的研究结果表明，Podostemaceae是一个独特的血统与长的分支，这表明更快的速度在该组的质体的进化，与其他类群的顺序。本研究为今后该家系的基因组学研究奠定了基础。
With the advent of next-generation sequencing technologies, whole-plastome data can be obtained as a byproduct of low-coverage sequencing of the plant genomic DNA. This provides an opportunity to study plastid evolution across groups, as well as testing phylogenetic relationships among taxa. Within the order Malpighiales (similar to 16,000 spp.), the Podostemaceae (similar to 300 spp.) stand out for their unique habit, living attached to rocks in fast-flowing aquatic habitats, and displaying highly modified morphologies that confound our understanding of their classification, biology, and evolution. In this study, we used genome skimming data to assemble the full plastid genome of 5 species within Podostemaceae. We analyzed our data in a comparative framework within Malpighiales to determine the structure, gene content, and rearrangements in the plastomes of the family. The Podostemaceae have one of the smallest plastid genomes reported so far for the Malpighiales, possibly due to variation in length of inverted repeat (IR) regions, gene loss, and intergenic region variation. We also detected a major inversion in the large single-copy region unique to the family. The uncommon loss or pseudogenization of ycf1 and ycf2 in angiosperms and in land plants in general is also found to be characteristic of Podostemaceae, but the compensatory mechanisms and implications of this and of the pseudogenization of accD, rpl22, and clpP and loss of rps16 remain to be explained in this group. In addition, we estimated a phylogenetic tree among selected species in Malpighiales. Our findings indicate that the Podostemaceae are a distinct lineage with long branches that suggest faster rates of evolution in the plastome of the group, compared with other taxa in the order. This study lays the foundations for future phylogenomic studies in the family.