Comparative chloroplast genomes of Dactylicapnos species: insights into phylogenetic relationships.

BACKGROUND: Dactylicapnos is a climbing herbaceous vine, distributed from the Himalayas to southwestern China, and some of the species have important medicinal values. However, the chloroplast genomes of Dactylicapnos have never been investigated. In this study, chloroplast genomes of seven Dactylicapnos species covering all three sections and one informal group of Dactylicapnos were sequenced and assembled, and the detailed comparative analyses of the chloroplast genome structure were provided for the first time. RESULTS: The results showed that the chloroplast genomes of Dactylicapnos have a typical quadripartite structure with lengths from 172,344 bp to 176,370 bp, encoding a total of 133-140 genes, containing 88-94 protein-coding genes, 8 rRNAs and 37-39 tRNAs. 31 codons were identified as relative synonymous codon usage values greater than one in the chloroplast genome of Dactylicapnos genus based on 80 protein-coding genes. The results of the phylogenetic analysis showed that seven Dactylicapnos species can be divided into three main categories. Phylogenetic analysis revealed that seven species form three major clades which should be treated as three sections. CONCLUSIONS: This study provides the initial report of the chloroplast genomes of Dactylicapnos, their structural variation, comparative genomic and phylogenetic analysis for the first time. The results provide important genetic information for development of medical resources, species identification, infrageneric classification and diversification of Dactylicapnos.

The complete plastome sequence of Datisca cannabina L. (Datiscaceae, Cucurbitales).

In this study, we report the first complete plastome sequence of Datisca cannabina (GenBank acc. no. OP432690). The plastome had a typical quadripartite structure. Its size was 162,914 bp, consisting of 90,890 bp large single-copy (LSC), 19,296 bp small single-copy (SSC), and 26,364 bp inverted repeat (IR) regions. It contained 112 genes, including 78 protein-coding, 30 tRNA, and four rRNA genes. The infA gene was pseudogenized. Sixteen genes contain one intron and two genes (clpP and ycf3) had two introns. Our phylogenetic tree showed that D. cannabina formed a close relationship with Begoniaceae. However, further samples are required to determine the phylogenetic placement of Datiscaceae in Cucurbitales.

The complete chloroplast genome sequence of Phlomoides kirghisorum Adylov, Kamelin & Makhmedov 1987 (Lamiaceae), an endemic species of Fergana Valley.

Phlomoides kirghisorum Adylov, Kamelin & Makhmedov 1987 is one of the poorly studied narrow endemics of Fergana Valley, one of Central Asia's most densely human-populated regions. In this study, we sequenced, assembled, and characterized the complete plastome of P. kirghisorum by using high-throughput Illumina reads. The complete chloroplast genome consisted of 151,324 bp, including a large single-copy (LSC) region (82,775 bp), a small single-copy (SSC) region (17,357 bp), and two inverted repeat regions (25,596 bp each). In the chloroplast genome of P. kirghisorum, 133 genes were detected, comprising 88 protein-encoding genes, eight ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. The phylogenetic analysis indicated that the genetic relationship between P. kirghisorum and P. alpina was very close. This study provides basic information to explore the molecular evolution of the Phlomoides genus and the Lamiaceae family.

First comparative analysis of complete chloroplast genomes among six Hedysarum (Fabaceae) species.

Hedysarum is one of the largest genera in the Fabaceae family, mainly distributed in the Northern Hemisphere. Despite numerous molecular studies on the genus Hedysarum, there is still a lack of research aimed at defining the specific characteristics of the chloroplast genome (cp genome) of the genus. Furthermore, the interrelationships between sections in the genus based on the cp genome have not yet been studied. In this study, comprehensive analyses of the complete cp genomes of six Hedysarum species, corresponding to sections Multicaulia, Hedysarum, and Stracheya were conducted. The complete cp genomes of H. drobovii, H. flavescens, and H. lehmannianum were sequenced for this study. The cp genomes of six Hedysarum species showed high similarity with regard to genome size (except for H. taipeicum), gene sequences, and gene classes, as well as the lacking IR region. The whole cp genomes of the six species were found to contain 110 genes ranging from 121,176 bp to 126,738 bp in length, including 76 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. In addition, chloroplast SSRs and repetitive sequence regions were reported for each species. The six Hedysarum species shared 7 common SSRs and exhibited 14 unique SSRs. As well, three highly variable genes (clpP, accD, and atpF) with high Pi values were detected among protein-coding genes. Furthermore, we conducted phylogenetic analyses using the complete cp genomes and 76 protein-coding genes of 14 legume species, including the seven Hedysarum species. The results showed that the Hedysarum species form a monophyletic clade closely related to the genera Onobrychis and Alhagi. Furthermore, both of our phylogenetic reconstructions showed that section Stracheya is more closely related to section Hedysarum than to section Multicaulia. This study is the first comprehensive work to investigate the genome characteristics of the genus Hedysarum, which provides useful genetic information for further research on the genus, including evolutionary studies, phylogenetic relationships, population genetics, and species identification.

Alliumsunhangii - a new species from section Brevidentia F.O.Khass. & Iengal. (Amaryllidaceae) from Southern Pamir-Alay, Uzbekistan.

A new species, Alliumsunhangiisp. nov., of the Middle Asiatic section Brevidentia F.O.Khass. & Iengal., (subgenusAllium, tribe Allioideae, Amaryllidaceae) is described. The species is a small plant from the Babatag Ridge in the Surkhandarya province of Uzbekistan. It is morphologically close to Alliumbrevidens Vved. in having initially dark violet filaments and three-cuspidate inner filaments, but differs by its small size and visibly unequal tepals as well as in the phylogenetic analysis based on ITS data.

Analysis of complete chloroplast genome sequences and insight into the phylogenetic relationships of Ferula L.

BACKGROUND: Ferula L. is one of the largest and most taxonomically complicated genera as well as being an important medicinal plant resource in the family Apiaceae. To investigate the plastome features and phylogenetic relationships of Ferula and its neighboring genera Soranthus Ledeb., Schumannia Kuntze., and Talassia Korovin, we sequenced 14 complete plastomes of 12 species.  RESULTS: The size of the 14 complete chloroplast genomes ranged from 165,607 to 167,013 base pairs (bp) encoding 132 distinct genes (87 protein-coding, 37 tRNA, and 8 rRNA genes), and showed a typical quadripartite structure with a pair of inverted repeats (IR) regions. Based on comparative analysis, we found that the 14 plastomes were similar in codon usage, repeat sequence, simple sequence repeats (SSRs), and IR borders, and had significant collinearity. Based on our phylogenetic analyses, Soranthus, Schumannia, and Talassia should be considered synonymous with Ferula. Six highly divergent regions (rps16/trnQ-UUG, trnS-UGA/psbZ, psbH/petB, ycf1/ndhF, rpl32, and ycf1) were also detected, which may represent potential molecular markers, and combined with selective pressure analysis, the weak positive selection gene ccsA may be a discriminating DNA barcode for Ferula species. CONCLUSION: Plastids contain abundant informative sites for resolving phylogenetic relationships. Combined with previous studies, we suggest that there is still much room for improvement in the classification of Ferula. Overall, our study provides new insights into the plastome evolution, phylogeny, and taxonomy of this genus.

Seed macro- and micromorphology in Allium (Amaryllidaceae) and its phylogenetic significance.

BACKGROUND AND AIMS: Macro- and micromorphology of seeds are diagnostic characteristics of importance in delimiting taxa in Allium (Amaryllidaceae). However, there is no consensus on the phylogenetic significance of testa cell characteristics and whether they reflect the different evolutionary levels recognized in Allium. METHODS: Seeds of 95 species (98 samples) representing 14 subgenera and 58 sections of Allium were examined using scanning electron microscopy (SEM) for such traits as periclinal wall surface area of ten testa cells, distance between testa cells (macromorphology), testa cell shapes, and arrangement and structure of anticlinal and periclinal walls (micromorphology). The data matrix was subjected to cladistic analysis. The produced phylogenetic tree was examined against the molecular tree obtained from publically available ITS sequences. KEY RESULTS: The periclinal wall surface area of ten testa cells and the distance between them, examined for the first time, were found useful for delimitation of species in Allium. Based on seed macro- and micromorphology, we present a taxonomic key and a hypothetical reconstruction of the migration routes during the early stages of evolution of Allium. CONCLUSIONS: The ancestors of Allium originated in an area bounded by the Caucasus, Central Asia and Iran. The seed testa morphology-based evolutionary state of a species is determined by two parameters: the shape of the periclinal walls and curvature of the anticlinal walls.

Oreocharis xieyongii, an unusual new species of Gesneriaceae from western Hunan, China.

A new species, Oreocharis xieyongii T. Deng, D.G. Zhang & H. Sun, from Hunan Province, central China, is described. The combination of purple zygomorphic corolla with longer adaxial lobes and exserted stamens defines the species and discriminates it from all other current Oreocharis species. Morphological traits of the new species were compared to those of two similar species, Oreocharis xiangguiensis and O. rubrostriata. Phylogenetic analysis indicates that the new species is nested within the Oreocharis. Although only half of Oreocharis species were included in our study, evolutionary character analysis indicates that the ancestral states of the genus are likely the purple corolla, longer abaxial lip and inserted stamens. The longer adaxial lip is perhaps an apomorphy and only present in O. xieyongii and O. rubrostriata. Both morphological and molecular evidence suggest that O. xieyongii is a taxon new to science.

Discrimination of the Essential Oils Obtained from Four Apiaceae Species Using Multivariate Analysis Based on the Chemical Compositions and Their Biological Activity.

The chemical composition of the essential oils obtained from the aerial parts of four Apiaceae species, namely Elaeosticta allioides (EA), E. polycarpa (EP), Ferula clematidifolia (FC), and Hyalolaena intermedia (HI), were determined using gas chromatography. Altogether, 100 volatile metabolites representing 78.97, 81.03, 85.78, and 84.49% of the total components present in EA, EP, FC, and HI oils, respectively, were reported. allo-Ocimene (14.55%) was the major component in FC, followed by D-limonene (9.42%). However, in EA, germacrene D (16.09%) was present in a high amount, while heptanal (36.89%) was the predominant compound in HI. The gas chromatographic data were subjected to principal component analysis (PCA) to explore the correlations between these species. Fortunately, the PCA score plot could differentiate between the species and correlate Ferula to Elaeosticta species. Additionally, the antioxidant activity was evaluated in vitro using the 2,2-diphenyl-1-picryl-hydrazyl-hydrate (DPPH), 2,2-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS), and the ferric reducing power (FRAP) assays. In addition, the antimicrobial activity using the agar diffusion method was assessed, and the minimum inhibitory concentrations (MICs) were determined. Furthermore, the cell viability MTT assay was performed to evaluate the cytotoxicity of the essential oils against hepatic (HepG-2) and cervical (HeLa) cancer cell lines. In the DPPH assay, FC exhibited the maximum activity against all the antioxidant assays with IC50 values of 19.8 and 23.0 µg/mL for the DPPH and ABTS assays, respectively. Ferula showed superior antimicrobial and cytotoxic activities as well. Finally, a partial least square regression model was constructed to predict the antioxidant capacity by utilizing the metabolite profiling data. The model showed excellent predictive ability by applying the ABTS assay.

Phylogenomics of Allium section Cepa (Amaryllidaceae) provides new insights on domestication of onion.

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.

Species conservation profile and amended distribution of Cousinia knorringiae (Asteraceae), a narrow endemic of the Western Tian-Shan.

BACKGROUND: Cousinia knorringiae Bornm. (Asteraceae) belongs to C. sect. Subappendiculatae Tscherneva, a group of the species-rich and taxonomically difficult genus Cousinia Cass. This species is narrowly distributed in the Western Tian-Shan and has been known as endemic to Kyrgyzstan. It inhabits bare rocks and screes at elevations of 1200-1500 m above sea level. This species is of conservation interest because of its small population size and limited distribution. NEW INFORMATION: Cousinia knorringiae is reported for the first time from eastern Uzbekistan on the basis of specimens collected on Ungur-Tepa Mt., a south-western outlier of the Bozbu-Too Mts. (Western Tian-Shan). The conservation status of the species is assessed as Endangered (EN), based on criterion D (estimated population size 200-250 mature individuals), according to the IUCN Red List Categories and Criteria (version 3.1). A new distribution map and a line drawing for C. knorringiae are provided and its type locality is clarified. The new knowledge suggests that the species is endemic to the East Fergana botanical hotspot, which includes a transborder territory shared between Kyrgyzstan and Uzbekistan and should, therefore, be subjected to international conservation measures. The southern extension of Ungur-Tepa Mt. harbours important plant species, which cannot be found elsewhere in Uzbekistan and may, therefore, be proposed for legal protection.

The Genus Lagochilus (Lamiaceae): A Review of Its Diversity, Ethnobotany, Phytochemistry, and Pharmacology.

The genus Lagochilus (Lamiaceae) is native to Central, South-Central, and Eastern Asia. It comprises 44 species, which have been commonly used as herbal medicines for the treatments of various ailments for thousands of years, especially in Asian countries. This review aims to summarize the chemical constituents and pharmacological activities of species from the genus Lagochilus to unveil opportunities for future research. In addition, we provide some information about their traditional uses, botany, and diversity. More than 150 secondary metabolites have been reported from Lagochilus, including diterpenes, flavonoids, phenolic compounds, triterpenoids, iridoid glycosides, lignans, steroids, alkaloids, polysaccharides, volatile, non-volatile and aromatic compounds, lipids, carbohydrates, minerals, vitamins, and other secondary metabolites. In vitro and in vivo pharmacological studies on the crude extracts, fractions, and isolated compounds from Lagochilus species showed hemostatic, antibacterial, anti-inflammatory, anti-allergic, cytotoxic, enzyme inhibitory, antispasmodic, hypotensive, sedative, psychoactive, and other activities.

Comparative study on the chemical composition and biological activities of the essential oils of three Lagochilus species collected from Uzbekistan.

Lagochilus species are mainly distributed in Central Asia and widely used in folk medicine as a sedative and haemostatic. The present investigation reports on the extraction by hydrodistillation and the chemical composition of three Lagochilus species (L. gypsaceus, L. inebrians and L. setulosus) essential oils from Uzbekistan. The chemical composition of these essential oils was determined by GC-MS. The results showed that the studied essential oils are made up mainly of linalool (11.97%), ß-ionone (11.75%), trans-chrysanthenyl acetate (7.15%), α-terpineol (7.40%) for L. gypsaceus; trans-chrysanthenyl acetate (9.40%), eugenol (7.01%), trans-verbenol (3.85%), bicyclo[3.1.1]hept-3-en-2-one (3.76%), pinocarvone (3.43%) for L. inebrians; and finally 2,4-bis(1,1-dimethylethyl)phenol (19.78%), bicyclo[3.1.1]hept-2-en-4-ol (5.43%), hexadecanoic acid (5.39%), limonene (5.19%), 2-hexenal (5.03%) for L. setulosus. The best antioxidant and tyrosinase inhibitory activity was observed for the essential oil of L. inebrians. However, L. setulosus essential oil exhibited the strongest inhibitory effect against amylase.

Primula sunhangii (Primulaceae): a new species from Hubei, Central China.

This report provides a description of Primula sunhangii from the Shennongjia Forestry District, Hubei Province in Central China, which is categorized as a new species of the primrose family. Primula sunhangii is morphologically similar to P. involucrata Wall. ex Duby in terms of its simple umbel, efarinose, and prolonged bracts. However, P. sunhangii is distinguished by its glabrous sepal, short petiole (compare with blade) and cylindrical calyx and capsule. Molecular phylogenetic analysis based on nuclear and cpDNA genes demonstrates that P. sunhangii and P. involucrata are closely related. Combining genetic and morphological data, the recognition of P. sunhangii as a unique new species is supported.

Geum sunhangii (Rosaceae), a new species from Hubei Province, China.

Geum sunhangii - first discovered in Shennongjia National Nature Reserve, Hubei Province, China - is described as a new species of Rosaceae. Compared to all known Chinese Geum species, the new species differs by possessing jointed styles, imbricate petals and a reniform radical leaf terminal leaflet. Most significantly, the jointed style is curved at an obtuse or a right angle. In addition, the inclusion of this species within the genus Geum was supported by phylogenetic analysis using the sequence data of a nuclear ribosomal internal transcribed spacer (nrITS) and a chloroplast trnL-trnF intergenic spacer. The new species was found to be closely related to G. rivale and G. aleppicum.

Oxytropis shennongjiaensis (Fabaceae), a new species from Hubei, Central China.

Here we describe Oxytropis shennongjiaensis, a new species of Fabaceae from Central China (Hubei Province). Morphologically, O. shennongjiaensis is closely similar to O. sitaipaiensis, O. melanocalyx and O. kansuensis, but differs in stem characters, with less conspicuous internodes; persistent herbaceous stipules; pale yellow to white corolla; and stipitate legumes, 3-5 mm with a long beak. Phylogenetic analysis, based on the internal transcribed spacers (ITS) and two chloroplast markers (trnL-F and psbA-trnH), also identified O. shennongjiaensis as a new species, which is consistent with our morphological analyses. Considering the morphological data and phylogenetic data presented here, we believe that this evidence satisfies the required diagnostic criteria to identify O. shennongjiaensis as a new species.

Silene sunhangii (Caryophyllaceae), a new species from China.

Silene sunhangii, a new species of Caryophyllaceae known from only three populations in Hubei and Hunan provinces of central China, is described. Both morphological and molecular data were used to assess the taxonomic status and relationships of this species. Morphologically, S. sunhangii is most similar to S. platyphylla Franch. from which it differs most readily in having 3-veined elliptical leaves without pubescence, tasseled catacorolla, pale purple to red petals without a linear lobe or narrow tooth and lanceolate, bifid to one third. A phylogenetic analysis based on nuclear ITS region identified the new species as a well-supported, independent lineage. Our new species is nested within a grade that encompasses species representing a polyphyletic Silene sect. Physolychnis (Benth.) Bocquet. Both the genetic and morphological data support the recognition of Silene sunhangii as a distinct species, although there is inconsistency between these two datasets as to the relationships of the new species.

Translocation of Otostegia bucharica, a highly threatened narrowly distributed relict shrub.

Translocation is a recognized means of rescuing imperiled species but the evidence for the long-term success of translocations is limited. We report the successful translocation of reproductive individuals of a critically endangered shrub Otostegia bucharica from a site facing imminent habitat destruction into a nearby natural population of the species. The relocated plants were visited the year after planting and 13 years later to assess short- and long-term plant survival. Significant percentage of plants that survived transplanting shock and very dry spring following transplanting (around 36%), and further decrease of this number in the next 12 years by only 14%, indicated that O. bucharica is amenable to translocation using reproductive plants. Based on results of species distribution modeling, and failed attempts of ex situ cultivation, we propose introduction of this species into areas with suitable climatic and soil conditions. However, because there is currently no nature reserve in Uzbekistan having suitable conditions for the species under the present climate and that expected in the near future, and because all known habitats of O. bucharica are exposed to the very strong anthropogenic pressure, establishment of a new protected area, awareness building and involvement of local community in conservation activities are required to prevent extinction of this extremely rare species.

Tropical Asian Origin, boreotropical migration and long-distance dispersal in Nettles (Urticeae, Urticaceae).

The tribe Urticeae (Urticaceae), popularly known as Nettles, include 12 genera and ca. 200 species, constituting a diverse and cosmopolitan plant clade centered in tropical Asia, Africa, and South America. The global distribution of this clade makes it an excellent group to test hypotheses regarding the processes underlying tropical intercontinental disjunctions. More specifically, it allows us to test whether current distribution patterns resulted from recent transoceanic long-distance dispersal or ancient vicariance after boreotropical migration. We reconstructed the phylogeny of Nettles with the nuclear ITS and four plastid DNA regions (rbcL, trnL-F, matK and rpl14-rpl36) using Bayesian inference and maximum parsimony approaches. We inferred divergence times using a Bayesian uncorrelated lognormal relaxed molecular clock model and ancestral areas using the divergence-extinction-cladogenesis (DEC) model. Our results indicate a tropical Asian origin for the tribe during the late Paleocene. Migration events to Eurasia, South America and Africa occurred mainly during the Oligocene and Miocene. However, several long-distance dispersal events, including dispersals from Asia to Hawaii or Australasia, were inferred to have occurred from the Miocene onwards. The fleshy fruits and winged diaspores of several taxa are suited for long-distance dispersal.

Prunus sunhangii: A new species of Prunus from central China.

A new species of Rosaceae from Central China, Prunus sunhangii D. G. Zhang & T. Deng, sp. nov. , is described and illustrated. The new species is placed in Prunus subgenus Cerasus by flower and fruit characteristics. It is most similar to Prunus cerasoides, but differs by having longitudinally 2-lobed apical petals, an acuminate leaf apex, 17-25 stamens, white petals, dark black drupes, brown hypanthium, and different phenology. The phylogenetic placement of this species was assessed based on morphological and molecular data. Molecular analysis (cpDNA + ITS) corroborated its placement in subgenus Cerasus, specifically Prunus section Serrula.