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Hepatica  is a small genus of Ranunculaceae with medicinal and horticultural value. We characterized nine complete chloroplast (cp) genomes of  Hepatica , which ranged from 159,549 to 161,081 bp in length and had a typical quadripartite structure with a large single-copy region (LSC; 80,270–81,249 bp), a small single-copy region (SSC; 17,029–17,838 bp), and two copies of inverted repeat (IR; 31,008–31,100 bp). The cp genomes of  Hepatica  possess 76 protein-coding genes (PCGs), 29 tRNAs, and four rRNA genes. Comparative analyses revealed a conserved ca. 5-kb IR expansion in  Hepatica  and other Anemoneae; moreover, multiple inversion events occurred in  Hepatica  and its relatives. Analyses of selection pressure ( dN / dS ) showed that most of the PCGs are highly conserved except for  rpl20  and  rpl22  in  Hepatica falconeri ,  Hepatica americana , and  Hepatica acutiloba.  Two genes ( rps16  and  infA ) were identified as pseudogenes in  Hepatica . In contrast,  rpl32  gene was completely lost. The phylogenetic analyses based on 76 PCGs resolved the phylogeny of  Hepatica  and its related genera. Non-monophyly of  Anemone s.l.  indicates that  Hepatica  should be reclassified as an independent genus. In addition,  Hepatica nobilis  var.  japonica  is not closely related to  H. nobilis.

Phylogenomic Analyses of Hepatica Species and Comparative Analyses Within Tribe Anemoneae (Ranunculaceae)