Combination of Sanger and target-enrichment markers supports revised generic delimitation in the problematic 'Urera clade' of the nettle family (Urticaceae).

Urera Gaudich, s.l. is a pantropical genus comprising c. 35 species of trees, shrubs, and vines. It has a long history of taxonomic uncertainty, and is repeatedly recovered as polyphyletic within a poorly resolved complex of genera in the Urticeae tribe of the nettle family (Urticaceae). To provide generic delimitations concordant with evolutionary history, we use increased taxonomic and genomic sampling to investigate phylogenetic relationships among Urera and associated genera. A cost-effective two-tier genome-sampling approach provides good phylogenetic resolution by using (i) a taxon-dense sample of Sanger sequence data from two barcoding regions to recover clades of putative generic rank, and (ii) a genome-dense sample of target-enrichment data for a subset of representative species from each well-supported clade to resolve relationships among them. The results confirm the polyphyly of Urera s.l. with respect to the morphologically distinct genera Obetia, Poikilospermum and Touchardia. Afrotropic members of Urera s.l. are recovered in a clade sister to the xerophytic African shrubs Obetia; and Hawaiian ones with Touchardia, also from Hawaii. Combined with distinctive morphological differences between Neotropical and African members of Urera s.l., these results lead us to resurrect the previously synonymised name Scepocarpus Wedd. for the latter. The new species epiphet Touchardia oahuensis T.Wells & A.K. Monro is offered as a replacement name for Touchardia glabra non H.St.John, and subgenera are created within Urera s.s. to account for the two morphologically distinct Neotropical clades. This new classification minimises taxonomic and nomenclatural disruption, while more accurately reflecting evolutionary relationships within the group.

Molecular phylogeny and morphology of Elatostema s.l. (Urticaceae): Implications for inter- and infrageneric classifications.

Elatostema s.s. (Urticaceae) comprises approximately 500 species of herbs and subshrubs distributed in tropical and subtropical Asia, Australasia, and Africa. The delimitation of Elatostema s.s. and the closely related genera Elatostematoides, Pellionia, and Procris has long been problematic because of the large number of taxa and presumed homoplasy among diagnostic morphological characters. In the present study, we refer to these four genera together as Elatostema s.l. To evaluate the circumscription of Elatostema s.l. and its generic and subgeneric classification, we conducted phylogenetic analyses of DNA sequence data from the internal transcribed spacer of the nuclear genome (nrITS) and two markers from the plastid genome (psbA-trnH and psbM-trnD) for 126 taxa, representing 88 species of Elatostema s.s., four of Elatostematoides, nine of Pellionia, and five of Procris. Ten selected morphological characters were investigated using ancestral state reconstructions. Our results show that Elatostema s.l. can be divided into three well-supported and morphologically distinct genera: Procris, Elatostematoides, and Elatostema sensu auct. The results of our molecular phylogeny suggest four strongly supported clades within this newly defined Elatostema s.a.: core Elatostema, Pellionia, Weddellia, and an as yet undescribed clade African Elatostema. Homoplasy among the morphological characters used in this study makes it impossible to circumscribe genera using synapomorphies, but combined suites of characters do enable the morphological diagnosis of Elatostema s.a., Elatostematoides, and Procris.

Draft genome sequence of ramie, Boehmeria nivea (L.) Gaudich.

Ramie, Boehmeria nivea (L.) Gaudich, family Urticaceae, is a plant native to eastern Asia, and one of the world's oldest fibre crops. It is also used as animal feed and for the phytoremediation of heavy metal-contaminated farmlands. Thus, the genome sequence of ramie was determined to explore the molecular basis of its fibre quality, protein content and phytoremediation. For further understanding ramie genome, different paired-end and mate-pair libraries were combined to generate 134.31 Gb of raw DNA sequences using the Illumina whole-genome shotgun sequencing approach. The highly heterozygous B. nivea genome was assembled using the Platanus Genome Assembler, which is an effective tool for the assembly of highly heterozygous genome sequences. The final length of the draft genome of this species was approximately 341.9 Mb (contig N50 = 22.62 kb, scaffold N50 = 1,126.36 kb). Based on ramie genome annotations, 30,237 protein-coding genes were predicted, and the repetitive element content was 46.3%. The completeness of the final assembly was evaluated by benchmarking universal single-copy orthologous genes (BUSCO); 90.5% of the 1,440 expected embryophytic genes were identified as complete, and 4.9% were identified as fragmented. Phylogenetic analysis based on single-copy gene families and one-to-one orthologous genes placed ramie with mulberry and cannabis, within the clade of urticalean rosids. Genome information of ramie will be a valuable resource for the conservation of endangered Boehmeria species and for future studies on the biogeography and characteristic evolution of members of Urticaceae.

Urtica spp.: Phenolic composition, safety, antioxidant and anti-inflammatory activities.

Urtica dioica and other less studied Urtica species (Urticaceae) are often used as a food ingredient. Fifteen hydroxycinnamic acid derivatives and sixteen flavonoids, flavone and flavonol-type glycosides were identified in hydroalcoholic extracts from aerial parts of Urtica dioica L., Urtica urens L. and Urtica membranacea using HPLC-PDA-ESI/MSn. Among them, the 4-caffeoyl-5-p-coumaroylquinic acid and three statin-like 3-hydroxy-3-methylglutaroyl flavone derivatives were identified for the first time in Urtica urens and U. membranacea respectively. Urtica membranacea showed the higher content of flavonoids, mainly luteolin and apigenin C-glycosides, which are almost absent in the other species studied. In vitro, Urtica dioica exhibited greater antioxidant activity but Urtica urens exhibited stronger anti-inflammatory potential. Interestingly, statin-like compounds detected in Urtica membranacea have been associated with hypocholesterolemic activity making this plant interesting for future investigations. None of the extracts were cytotoxic to macrophages and hepatocytes in bioactive concentrations (200 and 350µg/mL), suggesting their safety use in food applications.

Pulling the sting out of nettle systematics - A comprehensive phylogeny of the genus Urtica L. (Urticaceae).

The genus Urtica L. is subcosmopolitan, found on all continents (except Antarctica) and most extratropical islands and ranges from Alaska to Patagonia, Spitzbergen to the Cape and Camtschatka to the subantarctic islands. However, throughout its geographical range morphologically nearly indistinguishable species are found alongside morphologically quite disparate species, with the overall diversity of morphological characters extremely limited. The systematics of Urtica have puzzled scientists for the past 200years and no single comprehensive attempt at understanding infrageneric relationships has been published in the past, nor are species delimitations unequivocally established. We here provide the first comprehensive phylogeny of the genus including 61 of the 63 species recognized, represented by 144 ingroup accessions and 14 outgroup taxa. The markers ITS1-5.8S-ITS2, psbA-trnH intergenic spacer, trnL-trnF and trnS-trnG are used. The phylogeny is well resolved. The eastern Asian Zhengyia shennongensis T. Deng, D.G. Zhang & H. Sun is retrieved as sister to Urtica. Within Urtica, a clade comprising the western Eurasian species U. pilulifera L. and U. neubaueri Chrtek is sister to all other species of the genus. The phylogenetic analyses retrieve numerous well-supported clades, suggesting previously unsuspected relationships and implying that classically used taxonomic characters such as leaf morphology and growth habit are highly homoplasious. Species delimitation is problematical, and several accessions assigned to Urtica dioica L. (as subspecies) are retrieved in widely different places in the phylogeny. The genus seems to have undergone numerous dispersal-establishment events both between continents and onto different islands. Three recent species radiations are inferred, one in America centered in the Andes, one in New Zealand, and one in northern Eurasia which includes Urtica dioica s.str. sensu Henning et al. (2014). The present study provides the basis of a critical re-examination of species limits and taxonomy, but also of the dispersal ecology of this widespread plant group and an in-depth study of the three clades with recent radiations.

Identification of small auxin-up RNA (SAUR) genes in Urticales plants: mulberry (Morus notabilis), hemp (Cannabis sativa) and ramie (Boehmeria nivea).

Small auxin-up RNA (SAUR) genes are important gene families in auxin signalling transduction and are commonly used as early auxin responsive markers. Till date, no SAUR gene is identified in Urticales plants despite of the published bioinformation of mulberry, hemp and ramie. In this study, we used Arabidopsis sequences as query to search against mulberry, hemp genomes and ramie transcriptome database. In total, we obtained 62, 56 and 71 SAUR genes in mulberry, hemp and ramie, respectively. Phylogenetic analysis revealed the Urticales specific expansion of SAUR genes. Expression analysis showed 15 randomly selected ramie SAUR genes that were diversely functioned in ramie tissues and revealed a series of IAA-responsive, drought-responsive and high temperature-responsive genes. Moreover, comparison of qRT-PCR data and previous RNA-Seq data suggested the reliability of our work. In this study, we first report the identification of SAUR genes in Urticales plants. These results will provide a foundation for their function validation in Urticales plant growth and development.

Ancestral State Reconstruction Reveals Rampant Homoplasy of Diagnostic Morphological Characters in Urticaceae, Conflicting with Current Classification Schemes.

Urticaceae is a family with more than 2000 species, which contains remarkable morphological diversity. It has undergone many taxonomic reorganizations, and is currently the subject of further systematic studies. To gain more resolution in systematic studies and to better understand the general patterns of character evolution in Urticaceae, based on our previous phylogeny including 169 accessions comprising 122 species across 47 Urticaceae genera, we examined 19 diagnostic characters, and analysed these employing both maximum-parsimony and maximum-likelihood approaches. Our results revealed that 16 characters exhibited multiple state changes within the family, with ten exhibiting >eight changes and three exhibiting between 28 and 40. Morphological synapomorphies were identified for many clades, but the diagnostic value of these was often limited due to reversals within the clade and/or homoplasies elsewhere. Recognition of the four clades comprising the family at subfamily level can be supported by a small number carefully chosen defining traits for each. Several non-monophyletic genera appear to be defined only by characters that are plesiomorphic within their clades, and more detailed work would be valuable to find defining traits for monophyletic clades within these. Some character evolution may be attributed to adaptive evolution in Urticaceae due to shifts in habitat or vegetation type. This study demonstrated the value of using phylogeny to trace character evolution, and determine the relative importance of morphological traits for classification.

Pesticidal and pest repellency activities of a plant derived triterpenoid 2α,3ß,21ß,23,28-penta hydroxyl 12-oleanene against Tribolium castaneum.

BACKGROUND: Tribolium castaneum (Herbst) is a major pest of stored grain-based products, and cause severe damage to cereal grains throughout the world. The present investigation was aimed to determine the pesticidal and pest repellent activities of 2α,3ß,21ß,23,28-penta hydroxyl 12-oleanene against T. castaneum. The compound 2α,3ß,21ß,23,28-penta hydroxyl 12-oleanene is a triterpenoid which was isolated from the roots of Laportea crenulata Gaud. Surface film technique was used for pesticidal screening, whereas, pest repellency property of the triterpenoid was determined by filter paper disc method. RESULTS: At 24 hours of exposure duration, significant mortality records (80% and 86%) were observed at doses 0.88 and 1.77 mg/cm(2). No significant change in mortality records was observed when duration of exposure was increased up to 48 hours. The triterpenoid showed significant repellency activity at doses 0.47 and 0.94 mg/cm(2). CONCLUSION: These data suggest that the triterpenoid 2α,3ß,21ß,23,28-penta hydroxyl 12-oleanene possess both pesticidal and pest repellency activities against T. castaneum and can be used in controlling the pest of grain-based products.

Pesticidal and pest repellency activities of a plant derived triterpenoid 2α, 3ß, 21ß, 23, 28-penta hydroxyl 12-oleanene against Tribolium castaneum

BACKGROUND: Tribolium castaneum (Herbst) is a major pest of stored grain-based products, and cause severe damage to cereal grains throughout the world. The present investigation was aimed to determine the pesticidal and pest repellent activities of 2α,3ß,21ß,23,28-penta hydroxyl 12-oleanene against T. castaneum. The compound 2α,3ß,21ß,23,28-penta hydroxyl 12-oleanene is a triterpenoid which was isolated from the roots of Laportea crenulata Gaud. Surface film technique was used for pesticidal screening, whereas, pest repellency property of the triterpenoid was determined by filter paper disc method. RESULTS: At 24 hours of exposure duration, significant mortality records (80% and 86%) were observed at doses 0.88 and 1.77 mg/cm². No significant change in mortality records was observed when duration of exposure was increased up to 48 hours. The triterpenoid showed significant repellency activity at doses 0.47 and 0.94 mg/cm². CONCLUSION: These data suggest that the triterpenoid 2α,3ß,21ß,23,28-penta hydroxyl 12-oleanene possess both pesticidal and pest repellency activities against T. castaneum and can be used in controlling the pest of grain-based products.

Molecular phylogeny of the nettle family (Urticaceae) inferred from multiple loci of three genomes and extensive generic sampling.

Urticaceae is one of the larger Angiosperm families, but relationships within it remain poorly known. This study presents the first densely sampled molecular phylogeny of Urticaceae, using maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) to analyze the DNA sequence data from two nuclear (ITS and 18S), four chloroplast (matK, rbcL, rpll4-rps8-infA-rpl36, trnL-trnF) and one mitochondrial (matR) loci. We sampled 169 accessions representing 122 species, representing 47 of the 54 recognized genera within Urticaceae, including four of the six sometimes separated as Cecropiaceae. Major results included: (1) Urticaceae including Cecropiaceae was monophyletic; (2) Cecropiaceae was biphyletic, with both lineages nested within Urticaceae; (3) Urticaceae can be divided into four well-supported clades; (4) previously erected tribes or subfamilies were broadly supported, with some additions and alterations; (5) the monophyly of many genera was supported, whereas Boehmeria, Pellionia, Pouzolzia and Urera were clearly polyphyletic, while Urtica and Pilea each had a small genus nested within them; (6) relationships between genera were clarified, mostly with substantial support. These results clarify that some morphological characters have been overstated and others understated in previous classifications of the family, and provide a strong foundation for future studies on biogeography, character evolution, and circumscription of difficult genera.

[Study on phylogenetic relationships of urticaceae based on rbcL sequence].

The sequences of rbcL from four species of Boehmeria were analyzed in this study by PCR amplification and directly sequencing. The sequences of PCR products were about 1,370 bp. RbcL sequences of nine generas were chosen from GenBank, then the rbcL of 13 species were sequenced with clustal X1.83. After sequencing, the length of rbcL was 1,428 bp and has 1,263 conserved sites, 165 variable sites and 71 information sites. By using MEGA3.1, MP tree and NJ tree of Urticaceae were constructed. Based on the difference in rbcL squence, the genetic distances among species were calculated. With these informations, we can further analyze the genetic relationships of Urticaceae. In result, Pellionia, Poikilospermum, Procris, Elatostema and Pilea formed a monophyletic group; Parietaria and Boehmeria formed another monophyletic group. However, Urtica formed a single group, suggesting it had the most distant relationship to the other genus of Urticaceae.