PDF(Pubmed)
Abstract：
BACKGROUND: The Polygonaceae is a family well-known for its weeds, and edible plants, Fagopyrum (buckwheat) and Rheum (rhubarb), which are primarily herbaceous and temperate in distribution. Yet, the family also contains a number of lineages that are principally distributed in the tropics and subtropics. Notably, these lineages are woody, unlike their temperate relatives. To date, full-genome sequencing has focused on the temperate and herbaceous taxa. In an effort to increase breadth of genetic knowledge of the Polygonaceae, we here present six fully assembled and annotated chloroplast genomes from six of the tropical, woody genera: Coccoloba rugosa (a narrow and endangered Puerto Rican endemic), Gymnopodium floribundum, Neomillspaughia emarginata, Podopterus mexicanus, Ruprechtia coriacea, and Triplaris cumingiana.
RESULTS: These assemblies represent the first publicly-available assembled and annotated plastomes for the genera Podopterus, Gymnopodium, and Neomillspaughia, and the first assembled and annotated plastomes for the species Coccoloba rugosa, Ruprechtia coriacea, and Triplaris cumingiana. We found the assembled chloroplast genomes to be above the median size of Polygonaceae plastomes, but otherwise exhibit features typical of the family. The features of greatest sequence variation are found among the ndh genes and in the small single copy (SSC) region of the plastome. The inverted repeats show high GC content and little sequence variation across genera. When placed in a phylogenetic context, our sequences were resolved within the Eriogonoideae.
CONCLUSIONS: These six plastomes from among the tropical woody Polygonaceae appear typical within the family. The plastome assembly of Ruprechtia coriacea presented here calls into question the sequence identity of a previously published plastome assembly of R. albida.
RESULTS: These assemblies represent the first publicly-available assembled and annotated plastomes for the genera Podopterus, Gymnopodium, and Neomillspaughia, and the first assembled and annotated plastomes for the species Coccoloba rugosa, Ruprechtia coriacea, and Triplaris cumingiana. We found the assembled chloroplast genomes to be above the median size of Polygonaceae plastomes, but otherwise exhibit features typical of the family. The features of greatest sequence variation are found among the ndh genes and in the small single copy (SSC) region of the plastome. The inverted repeats show high GC content and little sequence variation across genera. When placed in a phylogenetic context, our sequences were resolved within the Eriogonoideae.
CONCLUSIONS: These six plastomes from among the tropical woody Polygonaceae appear typical within the family. The plastome assembly of Ruprechtia coriacea presented here calls into question the sequence identity of a previously published plastome assembly of R. albida.
摘要：
背景：虎杖科是一个以杂草闻名的家族，和可食用的植物，苦参（荞麦）和大黄（大黄），主要是草本和温带分布。然而，该家族还包含许多主要分布在热带和亚热带的血统。值得注意的是,这些血统是木质的，不像他们温和的亲戚。迄今为止,全基因组测序集中在温带和草本类群。为了增加对the科遗传知识的广度，我们在这里展示了六个完全组装和注释的叶绿体基因组，来自六个热带，木本属：Coccolobarugosa（一种狭窄且濒临灭绝的波多黎各特有物种），绞股蓝，emarginataNeomillspaughia,墨西哥Podopterus,Ruprechtiacoriacea,还有三叶草.
结果：这些组件代表了Podopterus属的第一个公开可用的组装和注释的质体，体操，和Neomillspaughia,和第一个组装和注释的硬体，Ruprechtiacoriacea,还有三叶草.我们发现组装的叶绿体基因组高于虎杖科质体的中位数大小，但在其他方面表现出典型的家庭特征。在ndh基因和质体的小单拷贝（SSC）区域中发现了最大的序列变异特征。反向重复序列显示出高GC含量和跨属的小序列变异。当放置在系统发育环境中时，我们的序列在Eriogonoideae中得到了解析。
结论：这六个来自热带木本虎杖科的质体在该科中具有典型性。此处介绍的Ruprechtiacoriacea的质体组装质疑先前发表的R.albida的质体组装的序列同一性。
结果：这些组件代表了Podopterus属的第一个公开可用的组装和注释的质体，体操，和Neomillspaughia,和第一个组装和注释的硬体，Ruprechtiacoriacea,还有三叶草.我们发现组装的叶绿体基因组高于虎杖科质体的中位数大小，但在其他方面表现出典型的家庭特征。在ndh基因和质体的小单拷贝（SSC）区域中发现了最大的序列变异特征。反向重复序列显示出高GC含量和跨属的小序列变异。当放置在系统发育环境中时，我们的序列在Eriogonoideae中得到了解析。
结论：这六个来自热带木本虎杖科的质体在该科中具有典型性。此处介绍的Ruprechtiacoriacea的质体组装质疑先前发表的R.albida的质体组装的序列同一性。
