Table_1_The Complete Chloroplast Genome Sequence of Ampelopsis: Gene Organization, Comparative Analysis, and Phylogenetic Relationships to Other Angiosperms.DOCX

Ampelopsis brevipedunculata is an economically important plant that belongs to the Vitaceae family of angiosperms. The phylogenetic placement of Vitaceae is still unresolved. Recent phylogenetic studies suggested that it should be placed in various alternative families including Caryophyllaceae, asteraceae, Saxifragaceae, Dilleniaceae, or with the rest of the rosid families. However, these analyses provided weak supportive results because they were based on only one of several genes. Accordingly, complete chloroplast genome sequences are required to resolve the phylogenetic relationships among angiosperms. Recent phylogenetic analyses based on the complete chloroplast genome sequence suggested strong support for the position of Vitaceae as the earliest diverging lineage of rosids and placed it as a sister to the remaining rosids. These studies also revealed relationships among several major lineages of angiosperms; however, they highlighted the significance of taxon sampling for obtaining accurate phylogenies. In the present study, we sequenced the complete chloroplast genome of A. brevipedunculata and used these data to assess the relationships among 32 angiosperms, including 18 taxa of rosids. The Ampelopsis chloroplast genome is 161,090 bp in length, and includes a pair of inverted repeats of 26,394 bp that are separated by small and large single copy regions of 19,036 bp and 89,266 bp, respectively. The gene content and order of Ampelopsis is identical to many other unrearranged angiosperm chloroplast genomes, including Vitis and tobacco. A phylogenetic tree constructed based on 70 protein-coding genes of 33 angiosperms showed that both Saxifragales and Vitaceae diverged from the rosid clade and formed two clades with 100% bootstrap value. The position of the Vitaceae is sister to Saxifragales, and both are the basal and earliest diverging lineages. Moreover, Saxifragales forms a sister clade to Vitaceae of rosids. Overall, the results of this study will contribute to better support of the evolution, molecular biology and genetic improvement of the plant Ampelopsis.

白蔹（Ampelopsis brevipedunculata）是一种兼具重要经济价值的被子植物（angiosperms），隶属于葡萄科（Vitaceae）。目前葡萄科的系统发育位置尚未明确。近期相关系统发育研究提出，该类群可被归入石竹科（Caryophyllaceae）、菊科（Asteraceae）、虎耳草科（Saxifragaceae）、五桠果科（Dilleniaceae）等多个替代类群，或是与其余蔷薇类（rosids）类群归为同一演化支。然而，此类分析的支持强度较弱，原因在于仅基于单个基因位点开展研究。因此，亟需完整叶绿体基因组（chloroplast genome）序列以厘清被子植物间的系统发育关系。近期基于完整叶绿体基因组序列的系统发育分析，为葡萄科作为蔷薇类最早分化支系的位置提供了强支持，并将其定为其余蔷薇类的姊妹群。此类研究同时揭示了被子植物多个主要支系间的亲缘关系，但也凸显了类群采样对于获得准确系统发育树的重要性。本研究对白蔹（Ampelopsis brevipedunculata）的完整叶绿体基因组进行了测序，并利用所得数据评估了32种被子植物的亲缘关系，其中包含18个蔷薇类类群。白蔹属（Ampelopsis）叶绿体基因组全长161090 bp，包含一对长度为26394 bp的反向重复序列（inverted repeats），二者分别由长89266 bp的大单拷贝区（large single copy, LSC）与长19036 bp的小单拷贝区（small single copy, SSC）分隔。该属的基因组成与基因排布与多种未发生重排的被子植物叶绿体基因组一致，包括葡萄属（Vitis）植物与烟草（tobacco）。基于33种被子植物的70个蛋白质编码基因（protein-coding genes）构建的系统发育树显示，虎耳草目（Saxifragales）与葡萄科均从蔷薇类演化支（clade）中分化而来，并形成了两个自举支持值（bootstrap value）为100%的演化支。葡萄科与虎耳草目互为姊妹群，二者均为基部且最早分化的支系。此外，虎耳草目与蔷薇类类群中的葡萄科构成姊妹演化支。综上，本研究结果可为白蔹（Ampelopsis brevipedunculata）的演化、分子生物学研究及遗传改良提供更有力的支撑。