Maianthemum is a genus with more than 35 species from the tribe Polygonateae (Asparagaceae), widely distributed between North to Central Americas and eastern Asiawithhigh diversity in the eastern Himalayas to the Hengduan Mountains of SW China. Although most species from SW China form a well-supported clade, phylogenetic relationships within this clade remain unclear. With a broad level of taxon sampling and an extensive character sampling from eight DNA regions, this study intends to revisit the phylogeny and biogeography of the genus to better understand the divergence patterns of species from SW China. Phylogenetic results suggested the monophyly of Maianthemum with recognition of nine strongly supported clades, but backbone relationships among these clades remained largely uncertain. For the SW China clade, individuals from the same species are grouped into different lineages. Our results revealed that the fast radiation of the SW China clade was occurred in the eastern Himalayas, followed by subsequent radiation in the Hengduan Mountains in the Pliocene. Intercontinental disjunctions of Maianthemum in the Northern Hemisphere appear to have occurred multiple times during the late Miocene to the Pliocene, likely resulted by a combination of both vicariance and long-distance dispersal events.

Allium sect. Cepa (Amaryllidaceae) comprises economically important plants, yet resolving the phylogenetic relationships within the section has been difficult as nuclear and chloroplast-based phylogenetic trees have been incongruent. Until now, phylogenetic studies of the section have been based on a few genes. In this study, we sequenced the complete chloroplast genome (plastomes) of four central Asian species of sect. Cepa: Allium oschaninii, A. praemixtum, A. pskemense and A. galanthum. Their chloroplast (cp) genomes included 114 unique genes of which 80 coded proteins. Seven protein-coding genes were highly variable and therefore promising for future phylogenetic and phylogeographic studies. Our plastome-based phylogenetic tree of Allium sect. Cepa revealed two separate clades: one comprising the central Asian species A. oschaninii, A. praemixtum, and A. pskemense, and another comprising A. galanthum, A. altaicum, and two cultivated species, A. cepa and A. fistulosum. These findings contradict previously reported phylogenies that relied on ITS and morphology. Possible explanations for this discrepancy are related to interspecific hybridization of species ancestral to A. galanthum and A. cepa followed by chloroplast capture; however, this is impossible to prove without additional data. Our results suggest that the central Asian Allium species did not play a role in the domestication of the common onion. Among the chloroplast genes, rpoC2 was identified as a gene of choice in further phylogeographical studies of the genus Allium.

The species composition of plant communities is determined by a number of factors, including current environmental conditions as well as biogeographical and evolutionary history. Despite evidence that plant diversity decreases and species relatedness increases along latitudinal and environmental gradients (e.g., low temperatures), it remains unclear whether these same patterns occur along elevational gradients, especially in the subtropical mountainous areas harboring rich biodiversity. In this study, we explored the pattern of phylogenetic relatedness of woody angiosperm assemblages and examined the effects of temperature variables on the phylogenetic relatedness among angiosperm woody plants using generalized linear model in subtropical forest communities along a broad elevational gradient in the Dulong Valley of Yunnan Province, China. Our results showed that woody angiosperm species in local forest plots tend to be more phylogenetically related at higher elevations and in areas with lower temperatures. Additionally, winter average temperature, rather than mean annual temperature, is a major predictor of the pattern of increasing phylogenetic relatedness with increasing elevation. This finding is consistent with the prediction of ‘Tropical Niche Conservatism’ hypothesis, which highlights the role of niche constraints in driving phylogenetic community assembly along an elevational gradient.

Madagascar, a globally renowned biodiversity hotspot characterized by high rates of endemism, is one of the few remaining refugia for many plants and animal species. However, global climate change has greatly affected the natural ecosystem and endemic species living in Madagascar, and will likely continue to influence species distribution in the future. Madagascar is home to six endemic baobab (Adansonia spp., Bombacoideae [Malvaceae]) species (Adansonia grandidieri, A. suarezensis, A. madagascariensis, A. perrieri, A. rubrostipa, A. za), which are remarkable and endangered plants. This study aimed to model the current distribution of suitable habitat for each baobab species endemic to Madagascar and determine the effect that climate change will have on suitable baobab habitat by the years 2050 and 2070. The distribution was modeled using MaxEnt based on locality information of 245 occurrence sites of six species from both online database and our own field work. A total of seven climatic variables were used for the modeling process. The present distribution of all six Madagascar's baobabs was largely influenced by temperature-related factors. Although both expansion and contraction of suitable habitat are predicted for all species, loss of original suitable habitat is predicted to be extensive. For the most widespread Madagascar baobab, A. za, more than 40% of its original habitat is predicted to be lost because of climate change. Based on these findings, we recommend that areas predicted to contract in response to climate change should be designated key protection regions for baobab conservation.

Two varieties of Bouteloua aristidoides have been recognized, the widespread var. aristidoides and the more narrowly distributed var. arizonica. The two varieties differ in inflorescence form even more than that seen between many other closely related species of Bouteloua. We therefore asked whether these taxa might be better regarded as distinct species. A total of 93 vouchers were studied by using morphometry (principal components analysis and statistical tests), leaf micromorphology, ancestral state reconstruction, and/or molecular (ITS, trnC-rpoB and trnT-L-F) phylogenetic analyses. Except from the ITS tree, all results supported elevation of B. aristidoides var. arizonica to the rank of species, thus the new combination Bouteloua arizonica (M.E. Jones) L.F. Cuellar & Columbus comb. nov. et stat. nov., is proposed. Chloroplast and combined chloroplast-nuclear molecular trees depicted var. arizonica as monophyletic (even in sympatric populations with var. aristidoides) and reveals phylogenetic structure within var. aristidoides for which the presence of new undescribed varieties of B. aristidoides (different from B. arizonica) is addressed. B. arizonica differs from B. aristidoides in having fewer branches per inflorescence, a bigger branch with more spikelets, and a shorter branch extension. Scanning electron microscopy revealed the presence of papillae on leaves of B. arizonica as a clear synapomorphy. Growing mature plants of B. arizonica from seeds in a greenhouse revealed a strong cleistogamous nature for this species for which gene flow in sympatric populations with B. aristidoides seems unlikely. A taxonomic treatment and distribution map for identification of B. arizonica is provided.

Of all types of interactions between humans and plants, the utilization of plants by people is the most direct and influential. China has a long history of using native plants and a large body of recorded knowledge on uses. Here, we present an inventory of plant uses in China based on an extensive survey of the literature. Twelve categories of usage are recognized (medicinal, edible, etc.), these categories being chosen according to an integration of various current standards. A total of 50,521 use-citations were recorded, covering 10,808 species and infraspecies, representing 28% of the Chinese flora. Additional information is included in the dataset on taxonomy and endangerment status. Analysis of the data reveals that the eight plant families with the greatest numbers of species used in China, namely Asteraceae, Fabaceae, Rosaceae, Ranunculaceae, Poaceae, Lamiaceae, Orchidaceae, and Liliaceae, are also the top eight most species-rich Chinese plant families. However, there are some families that are overrepresented or under-representation in certain use categories, compared with their relative abundance in the total flora. There are indications that rare and endangered species are being subject to some degree of over-exploitation. A disproportionately high number of used species are Chinese endemics (3552 species, representing over 33% of used species). A total of 20% of used species have been classified as threatened nationally or globally, according to at least one of the various threat assessments that have been made for the Chinese flora. This comprehensive inventory of the useful plants of China, with relevant ethnobotanical information included, provides a baseline for further studies of plant resources. It will be useful in follow-up research. The scientific dataset it contains will be useful for the protection and sustainable utilization of plant resources in China.

Compressed materials of fossil foliage described here as Itea polyneura sp. nov. (Iteaceae) were collected from the Oligocene of Wenshan, Yunnan Province, southwestern China. The identification is based on the following characters: eucamptodromous secondary veins, strict scalariform tertiary veins, irregular tooth with setaceous apex. The leaf morphology of all modern and fossil species was compared with the new species from Wenshan and show that I. polyneura is most similar to the extant East Asian species Itea omeiensis, which inhabits subtropical forests of southern China. This discovery represents the first unambiguous leaf fossil record of Itea in East Asia. Together with other species in the Wenshan flora and evidence from several other flora in southern China, these findings demonstrate that Itea from East Asia arose with the Paleogene modernization.

Stress-associated proteins (SAPs) are known as response factors to multiple abiotic and biotic stresses in plants. However, the potential physiological and molecular functions of SAPs remain largely unclear. Castor bean (Ricinus communis L.) is one of the most economically valuable non-edible woody oilseed crops, able to be widely cultivated in marginal lands worldwide because of its broad adaptive capacity to soil and climate conditions. Whether SAPs in castor bean plays a key role in adapting diverse soil conditions and stresses remains unknown. In this study, we used the castor bean genome to identify and characterize nine castor bean SAP genes (RcSAP). Structural analysis showed that castor bean SAP gene structures and functional domain types vary greatly, differing in intron number, protein sequence, and functional domain type. Notably, the AN1-C2H2-C2H2 zinc finger domain within RcSAP9 has not been often observed in other plant families. High throughput RNA-seq data showed that castor bean SAP gene profiles varied among different tissues. In addition, castor bean SAP gene expression varied in response to different stresses, including salt, drought, heat, cold and ABA and MeJA, suggesting that the transcriptional regulation of castor bean SAP genes might operate independently of each other, and at least partially independent from ABA and MeJA signal pathways. Cis-element analyses for each castor bean SAP gene showed that no common cis-elements are shared across the nine castor bean SAP genes. Castor bean SAPs were localized to different regions of cells, including the cytoplasm, nucleus, and cytomembrane. This study provides a comprehensive profile of castor bean SAP genes that advances our understanding of their potential physiological and molecular functions in regulating growth and development and their responses to different abiotic stresses.

Manganese (Mn) contamination limits the production and quality of crops, and affects human health by disrupting the food chain. Arabis paniculata is a pioneer species of Brassicaceae found in mining areas, and has the ability to accumulate heavy metals. However, little is known about the genetic mechanisms of Mn tolerance in A. paniculata. In this study, we found that Mn tolerance and ability to accumulate Mn were higher in A. paniculata than in Arabidopsis thaliana. The mechanisms underlying the response and recovery of A. paniculata to Mn toxicity were further investigated using transcriptome analysis. A total of 69,862,281 base pair clean reads were assembled into 61,627 high-quality unigenes, of which 41,591 (67.5%) and 39,297 (63.8%) were aligned in the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO), respectively. In response to Mn toxicity, genes were expressed in twelve distinct patterns, which can be divided into four general categories: initial, stable, dose-dependent, and lineage. Genes that were differentially expressed during Mn response and recovery belong to several dominant KEGG pathways. An early response to Mn toxicity in A. paniculata includes the upregulation of genes involved in glutathione metabolism. ATP-binding cassette (ABC) transporter proteins were up-regulated during the entire response phase, and genes involved in glycerophospholipid metabolism were upregulated during the late phase of the Mn response. Genes in the phenylpropanoid pathway were differentially expressed in the repair process after Mn treatment. These findings reveal ideal material and genetic resources for phytoremediation in Mn-contaminated areas and highlight new knowledge and theoretical perspectives on the mechanisms of Mn tolerance.

Roses are important horticultural plants with enormous diversity in flowers and flowering behavior. However, molecular regulation of flowering time variation in roses remains poorly characterized. Here, we report an expansion of the FAR1/FRS-like genes that correlates well with the switch to prostrate-toerect growth of shoots upon flowering in Rosa wichuraiana ‘Basye's Thornless’ (BT). With the availability of the high-quality chromosome-level genome assembly for BT that we developed recently, we identified 91 RwFAR1/FRS-like genes, a significant expansion in contrast to 52 in Rosa chinensis ‘Old Blush’ (OB), a founder genotype in modern rose domestication. Rose FAR1/FRS-like proteins feature distinct variation in protein domain structures. The dispersed expansion of RwFAR1/FRS-like genes occurred specifically in clade I and Ⅱ and is significantly associated with transposon insertion in BT. Most of the RwFAR1/FRS-like genes showed relatively higher expression level than their corresponding orthologs in OB. FAR1/FRS-like genes regulate light-signaling processes, shade avoidance, and flowering time in Arabidopsis thaliana. Therefore, the expansion and duplication of RwFAR1/FRS-like genes, followed by diversification in gene expression, might offer a novel leverage point for further understanding the molecular regulation of the variation in shoot-growth behavior and flowering time in roses.