We reconstructed a phylogenetic tree of Chinese vascular plants (Tracheophyta) using sequences of the chloroplast genes atpB, matK, ndhF, and rbcL and mitochondrial matR. We produced a matrix comprising 6098 species and including 13 695 DNA sequences, of which 1803 were newly generated. Our taxonomic sampling spanned 3114 genera representing 323 families of Chinese vascular plants, covering more than 93% of all genera known from China. The comprehensive large phylogeny supports most relationships among and within families recognized by recent molecular phylogenetic studies for lycophytes, ferns (monilophytes), gymnosperms, and angiosperms. For angiosperms, most families in Angiosperm Phylogeny Group IV are supported as monophyletic, except for a paraphyletic Dipterocarpaceae and Santalaceae. The infrafamilial relationships of several large families and monophyly of some large genera are well supported by our dense taxonomic sampling. Our results showed that two species of Eberhardtia are sister to a clade formed by all other taxa of Sapotaceae, except Sarcosperma. We have made our phylogeny of Chinese vascular plants publically available for the creation of subtrees via SoTree (http://www.darwintree.cn/flora/index.shtml), an automated phylogeny assembly tool for ecologists.

Ailanthus altissima (Mill.) Swingle (Simaroubaceae) is a deciduous tree widely distributed throughout temperate regions in China, hence suitable for genetic diversity and evolutionary studies. Previous studies in A. altissima have mainly focused on its biological activities, genetic diversity and genetic structure. However, until now there is no published report regarding genome of this plant species or Simaroubaceae family. Therefore, in this paper, we first characterized A. altissima complete chloroplast genome sequence. The tree of heaven chloroplast genome was found to be a circular molecule 160,815 base pairs (bp) in size and possess a quadripartite structure. The A. altissima chloroplast genome contains 113 unique genes of which 79 and 30 are protein coding and transfer RNA (tRNA) genes respectively and also 4 ribosomal RNA genes (rRNA) with overall GC content of 37.6%. Microsatellite marker detection identified A/T mononucleotides as majority SSRs in all the seven analyzed genomes. Repeat analyses of seven Sapindales revealed a total of 49 repeats in A. altissima, Rhus chinensis, Dodonaea viscosa, Leitneria floridana, while Azadirachta indica, Boswellia sacra, and Citrus aurantiifolia had a total of 48 repeats. The phylogenetic analysis using protein coding genes revealed that A. altissima is a sister to Leitneria floridana and also suggested that Simaroubaceae is a sister to Rutaceae family. The genome information reported here could be further applied for evolution and invasion, population genetics, and molecular studies in this plant species and family.

The gymnosperm Welwitschia mirabilis belongs to the ancient, enigmatic gnetophyte lineage. It is a unique desert plant with extreme longevity and two ever-elongating leaves. We present a chromosome-level assembly of its genome (6.8 Gb/1 C) together with methylome and transcriptome data to explore its astonishing biology. We also present a refined, high-quality assembly of Gnetum montanum to enhance our understanding of gnetophyte genome evolution. The Welwitschia genome has been shaped by a lineage-specific ancient, whole genome duplication (~86 million years ago) and more recently (1-2 million years) by bursts of retrotransposon activity. High levels of cytosine methylation (particularly at CHH motifs) are associated with retrotransposons, whilst long-term deamination has resulted in an exceptionally GC-poor genome. Changes in copy number and/or expression of gene families and transcription factors (e.g. R2R3MYB, SAUR) controlling cell growth, differentiation and metabolism underpin the plant’s longevity and tolerance to temperature, nutrient and water stress.

Gentianales consist of Apocynaceae, Gelsemiaceae, Gentianaceae, Loganiaceae, and Rubiaceae, of which the majority are woody plants in tropical and subtropical areas. Despite extensive efforts in reconstructing the phylogeny of Gentianales based on molecular data, some interfamily and intrafamily relationships remain uncertain. We reconstructed the genus-level phylogeny of Gentianales based on the supermatrix of eight plastid markers (rbcL, matK, atpB, ndhF, rpl16, rps16, the trnL-trnF region, and atpB-rbcL spacer) and one mitochondrial gene (matR) using maximum likelihood. The major clades and their relationships retrieved in the present study concur with those of previous studies. All of the five families of Gentianales are monophyletic with strong support. We resolved Rubiaceae as sister to the remaining families in Gentianales and showed support for the sister relationship between Loganiaceae and Apocynaceae. Our results provide new insights into relationships among intrafamilial clades. For example, within Rubiaceae we found that Craterispermeae were sister to Morindeae þ (Palicoureeae þ Psychotrieae) and that Theligoneae were sister to Putorieae. Within Gentianaceae, our phylogeny revealed that Gentianeae were sister to Helieae and Potalieae, and subtribe Lisianthiinae were sister to Potaliinae and Faroinae. Within Loganiaceae, we found Neuburgia as sister to Spigelieae. Within Apocynaceae, our results supported Amsonieae as sister to Melodineae, and Hunterieae as sister to a clade comprising Plumerieae þ (Carisseae þ APSA). We also confirmed the monophyly of Perplocoideae and the relationships among Baisseeae þ (Secamonoideae þ Asclepiadoideae).

The dove tree, Davidia involucrata Baill. (Davidiaceae), is a relict species endemic to China. Human activities and the strict requirements for seedling recruitments have led to the decline in number of individuals in extant natural populations of this species. In order to provide information for the design of conservation management strategies for D. involucrata, we investigated the phylogeographical pattern of this relict tree. Our sampling included 256 individuals from 32 natural populations of D. involucrata in China and we sequenced six chloroplast DNA (cpDNA) non-coding regions. We distinguished a total of 13 different cpDNA haplotypes. From the cpDNA variation in D. involucrata, we found a very high level of regional differentiation (F ST = 0.812) and a strong phylogeographical pattern (N ST = 0.996 [ G ST = 0.981, P \ 0.05). Phylogenetic analysis reveals three main cpDNA haplotype lineages and four population groups. The split between these geographical groups can be dated back from the late Pliocene to early Pleistocene. Nonoverlapping distribution of chloroplast haplotypes and high genetic differentiation among four distinct geographical groups suggest that D. involucrata probably survives in four separate glacial refugia. Our findings have an important implication for conservation of its genetic diversity. The deduced glacial survival areas for D. involucrata should be recognized as four ''evolutionary significant units'' and be considered as separate targets in conserving its genetic diversity.

To reveal the role of climate oscillations of the Quaternary in forming the contemporary plant diversity in the temperate Sino‐Japanese Floristic Region of mainland China, we assess the phylogeographical patterns of four Sagittaria species in the region using sequence data from plastid DNA non‐coding regions (psbA‐trnH, the rpl16 intron and trnC‐ycf6) and the internal transcribed spacers of nuclear ribosomal DNA (nrITS). Based on both datasets, the divergence time among the four studied species was estimated to fall in the Late Tertiary (plastid DNA: 7.1–13.7 Mya; ITS: 11.1–16.1 Mya). The ancestral distribution analyses revealed that regions with a great diversity in topography, climate and ecological conditions, e.g. the Hengduan Mountains, Central China and East China, were the areas where the endemics originated. Mismatch distribution analyses revealed that each species had experienced a range expansion in response to Quaternary climatic oscillations. Our findings contradict the hypothesis of Quaternary origins of the endemic Sagittaria spp.; we support the view that modern species in the Northern Hemisphere originated mostly during the Tertiary. Range expansion may have profoundly modified the current distribution ranges of Sagittaria species in the Sino‐Japanese Floristic Region.  © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2016, 180, 6–20.

Ailanthus altissima (Mill.) Swingle, a temperate tree species, has a wide distribution in China. To infer its refugia and patterns of migration during past climatic changes in China, genetic variations among different populations were studied. Gene sequences of three chloroplast DNA spacer regions, psbA-trnH, trnL-trnF, and trnD-trnT, were obtained from 440 individuals of 44 populations. The distribution of haplotype and the relationships among them were investigated by haplotype network. In addition, the genetic diversity of the sampled regions was inferred, and the biogeographic history was also reconstructed. Twelve haplotypes were identified, among which, five were unique. The phylogenetic analysis and geographical distribution of haplotypes indicate that multiple glacial refugia existed in mainland China during the Quaternary oscillations. Due to the combined effects of contiguous range expansion and allopatric fragmentation, significant genetic structure was not found in this study. Based on biogeographic and demographic analysis, three main dispersal routes were identified for the major haplotypes, whereas others were more likely localized demographic expansion.

Nymphoides peltata is a distylous aquatic plant. In order to explore the relative importance of clonal growth and sexual reproduction within populations and also to reveal the origin of the commonly occurring one style morph populations in China, we studied the clonal diversity and population genetic structure of this species. By using seven single sequence repeat primer pairs, a total of 192 multilocus genotypes (MLGs) were identified among the 472 samples from the 21 populations analyzed; each population had two or more MLGs. The number of MLGs was lower for the one style morph populations than distylous populations. Analysis of molecular variance showed that a smaller proportion of genetic variation resided among populations (36.8%). A neighbor‐joining tree indicated that there was no significant geographical structure of the genetic variation among populations of N. peltata. The Bottleneck tests indicated that there had been significant bottlenecks in most of the studied populations. The successful sexual recruitment from seeds may have contributed to the high clonal diversity in distylous populations of N. peltata in China. Demographic stochasticity or bottleneck should account for the one style morph population with several MLGs. And also the bottleneck effects or demographic changes caused by human activities occurring randomly in populations should account for the finding of no significant geographical structure of the genetic variation among the investigated populations of N. peltata.