GBE Plastid Phylogenomic Analyses Resolve Tofieldiaceae as the Root of the Early Diverging Monocot Order Alismatales Yang Luo1,2,3,y, Peng-Fei Ma1,2,y, Hong-Tao Li2, Jun-Bo Yang2, Hong Wang1,2,*, and De-Zhu Li1,2,* 1Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China 2Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China 3Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, China yThese authors contributed equally to this work. *Corresponding author: E-mail:
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[email protected]. Accepted: December 23, 2015 Data deposition: The genomes sequences have been deposited at GenBank under the accession numbers KT89950–KT89952. Abstract The predominantly aquatic order Alismatales, which includes approximately 4,500 species within Araceae, Tofieldiaceae, and the core alismatid families, is a key group in investigating the origin and early diversification of monocots. Despite their importance, phylogenetic ambiguity regarding the root of the Alismatales tree precludes answering questions about the early evolution of the order. Here, we sequenced the first complete plastid genomes from three key families in this order: Potamogeton perfoliatus (Potamogetonaceae), Sagittaria lichuanensis (Alismataceae), and Tofieldia thibetica (Tofieldiaceae). Each family possesses the typical quadripartite structure, with plastid genome sizes of 156,226, 179,007, and 155,512 bp, respectively. Among them, the plastid genome of S. lichuanensis is the largest in monocots and the second largest in angiosperms. Like other sequenced Alismatales plastid genomes, all three families generally encode the same 113 genes with similar structure and arrangement.