Phylogenomics and phylogeography of <i>Menispermum</i> (Menispermaceae)

<h4>Introduction</h4>Phylogenomics have been widely used to resolve ambiguous and controversial evolutionary relationships among plant species and genera, and the identification of unique indels in plastomes may even help to understand the evolution of some plant families. <i>Menispermum</i> L. (Menispermaceae) consists of three species, <i>M. dauricum</i> DC., <i>M. canadense</i> L., and <i>M. mexicanum</i> Rose, which are disjuncly distributed among East Asia, Eastern North America and Mexico. Taxonomists continue to debate whether <i>M. mexicanum</i> is a distinct species, a variety of <i>M. dauricum</i>, or simply a synonym of <i>M. canadense</i>. To date, no molecular systematics studies have included this doubtful species in phylogenetic analyses.<h4>Methods</h4>In this study, we examined phylogenomics and phylogeography of <i>Menispermum</i> across its entire range using 29 whole plastomes of Menispermaceae and 18 ITS1&ITS2 sequences of Menispermeae. We reconstructed interspecific relationships of <i>Menispermum</i> and explored plastome evolution in Menispermaceae, revealing several genomic hotspot regions for the family.<h4>Results and discussion</h4>Phylogenetic and network analyses based on whole plastome and ITS1&ITS2 sequences show that <i>Menispermum</i> clusters into two clades with high support values, Clade A (<i>M. dauricum</i>) and Clade B (<i>M. canadense</i> + <i>M. mexicanum</i>). However, <i>M. mexicanum</i> is nested within <i>M. canadense</i> and, as a result, we support that <i>M. mexicanum</i> is a synonym of <i>M. canadense</i>. We also identified important molecular variations in the plastomes of Menispermaceae. Several indels and consequently premature terminations of genes occur in Menispermaceae. A total of 54 regions were identified as the most highly variable plastome regions, with nucleotide diversity (<i>Pi</i>) values > 0.05, including two coding genes (<i>mat</i>K, <i>ycf</i>1), four introns (<i>trn</i>K intron, <i>rpl16</i> intron, <i>rps</i>16 intron, <i>ndh</i>A intron), and 48 intergenic spacer (IGS) regions. Of these, four informative hotspot regions (<i>trn</i>H-<i>psb</i>A, <i>ndh</i>F-<i>rpl</i>32, <i>trn</i>K-<i>rps</i>16, and <i>trn</i>P-<i>psa</i>J) should be especially useful for future studies of phylogeny, phylogeography and conservation genetics of Menispermaceae.