| Summary: | <i>Symplocarpus</i>, a skunk cabbage genus, includes two sister groups, which are drastically different in life history traits and thermogenesis, as follows: The nonthermogenic summer flowering <i>S. nipponicus</i> and thermogenic early spring flowering <i>S. renifolius</i>. Although the molecular basis of thermogenesis and complete chloroplast genome (plastome) of thermogenic <i>S. renifolius</i> have been well characterized, very little is known for that of <i>S. nipponicus</i>. We sequenced the complete plastomes of <i>S. nipponicus</i> sampled from Japan and Korea and compared them with that of <i>S. renifolius</i> sampled from Korea. The nonthermogenic <i>S. nipponicus</i> plastomes from Japan and Korea had 158,322 and 158,508 base pairs, respectively, which were slightly shorter than the thermogenic plastome of <i>S. renifolius</i>. No structural or content rearrangements between the species pairs were found. Six highly variable noncoding regions (<i>psbC/trnS</i>, <i>petA/psbJ</i>, <i>trnS/trnG</i>, <i>trnC/petN</i>, <i>ycf4/cemA</i>, and <i>rpl3/rpl22</i>) were identified between <i>S. nipponicus</i> and <i>S. renifolius</i> and 14 hot-spot regions were also identified at the subfamily level. We found a similar total number of SSR (simple sequence repeat) motifs in two accessions of <i>S. nipponicus</i> sampled from Japan and Korea. Phylogenetic analysis supported the basal position of subfamily Orontioideae and the monophyly of genus <i>Symplocarpus</i>, and also revealed an unexpected evolutionary relationship between <i>S. nipponicus</i> and <i>S. renifolius</i>.
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