Complete chloroplast genomes of Archiclematis, Naravelia and Clematis (Ranunculaceae), and their phylogenetic implications

Abstract

Archiclematis and Naravelia were considered to be two small genera closely related to the large cosmopolitan genus Clematis. They have been included into Clematis s.l. in recent years according to molecular phylogenetic evidence. There is still little genomic information available for Archiclematis and Naravelia species. In this study, six complete chloroplast genomes from Archiclematis, Naravelia and Clematis were reported based on Illumina sequencing. The gene order and organization of the chloroplast genomes of Archiclematis and Naravelia are the same with that of Clematis. Analysis of eight complete chloroplast genomes showed that the plastomes of Clematis s.l. are typically circular, with a total length ranging from 159,513 bp to 159,783 bp. The total number of genes is identical within the broadly defined genus Clematis. We also identified variation hotspots, plastid repeats and SSRs for Clematis s.l. species. Our plastid phylogenomic analyses recovered the inclusion of Archiclematis and Naravelia into Clematis. The present study provides important phylogenomic data of Ranunculaceae and illuminates the phylogenetic relationships among Clematis species.

Comparative Analysis of Complete Chloroplast Genomes of Anemoclema, Anemone, Pulsatilla, and Hepatica Revealing Structural Variations Among Genera in Tribe Anemoneae (Ranunculaceae)

“…The tribe Anemoneae (as defined by Tamura, 1995 ) traditionally includes three subtribes (Kingdoniinae, Anemoninae, and Clematidinae), based on previous molecular phylogenetic studies that did not include the subtribe Kingdoniinae (Hoot et al, 2012 ; Jiang et al, 2017a ). For subtribe Clematidinae, almost all satellite genera of Clematis (such as Naravelia and Archiclematis ) were nested within Clematis by previous studies (Miikeda et al, 2006 ; Xie et al, 2011 ; Lehtonen et al, 2016 ; Jiang et al, 2017a ; Liu et al, 2018 ). In subtribe Anemoninae, Hoot et al ( 2012 ) reduced Hepatica, Pulsatilla, Oreithales, Knowltonia , and Barneoudia to the genus Anemone using molecular phylogenetic results inferred from nrITS and atpB-rbcL regions.…”

“…Vouchers were deposited at the Beijing Forestry University (BJFC) Herbarium. In our previous study (Liu et al, 2018 ), complete chloroplast genome sequences of Clematis, Archiclematis , and Naravelia were reported. Thus, in this study, we included samples representing all of the major clades ( Hepatica clade, Anemone s.l .…”

“…Chloroplast genome structural rearrangements and inversions in Anemone and other related genera have been previously reported based on genetic mapping by restriction enzyme site methods (Hoot and Palmer, 1994 ; Johansson, 1999 ). In recent years, several complete chloroplast genomes of Ranunculaceae have been published (Chen et al, 2015 ; Park et al, 2015 , 2017 ; Li et al, 2016 ; Park and Park, 2016 ; Jiang et al, 2017b ; Lim et al, 2017 ; Szczecinska et al, 2017 ; Liu et al, 2018 ). Recently, Jiang et al ( 2017b ) and Liu et al ( 2018 ) published plastome sequences of Anemoclema and Clematis s.l .…”

“…In recent years, several complete chloroplast genomes of Ranunculaceae have been published (Chen et al, 2015 ; Park et al, 2015 , 2017 ; Li et al, 2016 ; Park and Park, 2016 ; Jiang et al, 2017b ; Lim et al, 2017 ; Szczecinska et al, 2017 ; Liu et al, 2018 ). Recently, Jiang et al ( 2017b ) and Liu et al ( 2018 ) published plastome sequences of Anemoclema and Clematis s.l . (including Archiclematis, Clematis , and Naravelia ; Liu et al, 2018 ), and they also discovered striking structural rearrangements in plastome sequence of the reported genera comparing to that of other Ranunculaceae genera.…”

“…Recently, Jiang et al ( 2017b ) and Liu et al ( 2018 ) published plastome sequences of Anemoclema and Clematis s.l . (including Archiclematis, Clematis , and Naravelia ; Liu et al, 2018 ), and they also discovered striking structural rearrangements in plastome sequence of the reported genera comparing to that of other Ranunculaceae genera. However, structural variation of tribe Anemoneae plastomes were not discussed in detail by previous studies.…”