AUTHOR=Huang Yuling , Li Xiaojuan , Yang Zhenyan , Yang Chengjin , Yang Junbo , Ji Yunheng 

TITLE=Analysis of Complete Chloroplast Genome Sequences Improves Phylogenetic Resolution in Paris (Melanthiaceae)

JOURNAL=Frontiers in Plant Science

VOLUME=7

YEAR=2016

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2016.01797

DOI=10.3389/fpls.2016.01797

ISSN=1664-462X

ABSTRACT=<p>The genus <italic>Paris</italic> in the broad concept is an economically important group in the monocotyledonous family Melanthiaceae (tribe Parideae). The phylogeny of <italic>Paris</italic> was controversial in previous morphology-based classification and molecular phylogeny. Here, the complete cp genomes of eleven <italic>Paris</italic> taxa were sequenced, to better understand the evolutionary relationships among these plants and the mutation patterns in their chloroplast (cp) genomes. Comparative analyses indicated that the overall cp genome structure among the <italic>Paris</italic> taxa is quite similar. The triplication of <italic>trn</italic>I-CAU was found only in the cp genomes of <italic>P. quadrifolia</italic> and <italic>P. verticillata</italic>. Phylogenetic analyses based on the complete cp genomes did not resolve <italic>Paris</italic> as a monophyletic group, instead providing evidence supporting division of the twelve taxa into two segregate genera: <italic>Paris sensu strict</italic> and <italic>Daiswa</italic>. The sister relationship between <italic>Daiswa</italic> and <italic>Trillium</italic> was well supported. We recovered two fully supported lineages with divergent distribution in <italic>Daiswa</italic>; however, none of the previously recognized sections in <italic>Daiswa</italic> was resolved as monophyletic using plastome data, suggesting that the infrageneric relationships and biogeography of <italic>Daiswa</italic> species require further investigation. Ten highly divergent DNA regions, suitable for species identification, were detected among the 12 cp genomes. This study is the first successful attempt to provide well-supported evolutionary relationships in <italic>Paris</italic> based on phylogenomic analyses. The findings highlight the potential of the whole cp genomes for improving resolution in phylogeny as well as species identification in phylogenetically and taxonomically difficult plant genera.</p>