title: Analysis of Complete Chloroplast Genome Sequences Improves Phylogenetic Resolution inParis(Melanthiaceae).
abstract: The genusParisin the broad concept is an economically important group in the monocotyledonous family Melanthiaceae (tribe Parideae). The phylogeny ofPariswas controversial in previous morphology-based classification and molecular phylogeny. Here, the complete cp genomes of elevenParistaxa 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 theParistaxa is quite similar. The triplication oftrnI-CAU was found only in the cp genomes ofP. quadrifoliaandP. verticillata. Phylogenetic analyses based on the complete cp genomes did not resolveParisas a monophyletic group, instead providing evidence supporting division of the twelve taxa into two segregate genera:Paris sensu strictandDaiswa. The sister relationship betweenDaiswaandTrilliumwas well supported. We recovered two fully supported lineages with divergent distribution inDaiswa; however, none of the previously recognized sections inDaiswawas resolved as monophyletic using plastome data, suggesting that the infrageneric relationships and biogeography ofDaiswaspecies 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 inParisbased 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.
authors.affiliation: Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China; University of Chinese Academy of SciencesBeijing, China.
authors.forename: Yuling
authors.initials: Y
authors.lastname: Huang
authors.affiliation: Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China; University of Chinese Academy of SciencesBeijing, China.
authors.forename: Xiaojuan
authors.initials: X
authors.lastname: Li
authors.affiliation: Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences Kunming, China.
authors.forename: Zhenyan
authors.initials: Z
authors.lastname: Yang
authors.affiliation: Chinese Medicinal Resources Co. Ltd, Yunnan Baiyao Group Kunming, China.
authors.forename: Chengjin
authors.initials: C
authors.lastname: Yang
authors.affiliation: Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences Kunming, China.
authors.forename: Junbo
authors.initials: J
authors.lastname: Yang
authors.affiliation: Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences Kunming, China.
authors.forename: Yunheng
authors.initials: Y
authors.lastname: Ji
keywords: Daiswa; Melanthiaceae; Paris; chloroplast genome; comparative genomics; phylogeny