New Insights into Phylogenetic Relationship of Hydrocotyle (Araliaceae) Based on Plastid Genomes.

Hydrocotyle, belonging to the Hydrocotyloideae of Araliaceae, consists of 95 perennial and 35 annual species. Due to the lack of stable diagnostic morphological characteristics and high-resolution molecular markers, the phylogenetic relationships of Hydrocotyle need to be further investigated. In this study, we newly sequenced and assembled 13 whole plastid genomes of Hydrocotyle and performed comparative plastid genomic analyses with four previously published Hydrocotyle plastomes and phylogenomic analyses within Araliaceae. The plastid genomes of Hydrocotyle exhibited typical quadripartite structures with lengths from 152,659 bp to 153,669 bp, comprising a large single-copy (LSC) region (83,958-84,792 bp), a small single-copy (SSC) region (18,585-18,768 bp), and a pair of inverted repeats (IRs) (25,058-25,145 bp). Each plastome encoded 113 unique genes, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Comparative analyses showed that the IR boundaries of Hydrocotyle plastomes were highly similar, and the coding and IR regions exhibited more conserved than non-coding and single-copy (SC) regions. A total of 2932 simple sequence repeats and 520 long sequence repeats were identified, with specificity in the number and distribution of repeat sequences. Six hypervariable regions were screened from the SC region, including four intergenic spacers (IGS) (ycf3-trnS, trnS-rps4, petA-psbJ, and ndhF-rpl32) and two coding genes (rpl16 and ycf1). Three protein-coding genes (atpE, rpl16, and ycf2) were subjected to positive selection only in a few species, implying that most protein-coding genes were relatively conserved during the plastid evolutionary process. Plastid phylogenomic analyses supported the treatment of Hydrocotyle from Apiaceae to Araliaceae, and topologies with a high resolution indicated that plastome data can be further used in the comprehensive phylogenetic research of Hydrocotyle. The diagnostic characteristics currently used in Hydrocotyle may not accurately reflect the phylogenetic relationships of this genus, and new taxonomic characteristics may need to be evaluated and selected in combination with more comprehensive molecular phylogenetic results.

Comparative genomics and phylogenetic relationships of two endemic and endangered species (Handeliodendron bodinieri and Eurycorymbus cavaleriei) of two monotypic genera within Sapindales.

BACKGROUND: Handeliodendron Rehder and Eurycorymbus Hand.-Mazz. are the monotypic genera in the Sapindaceae family. The phylogenetic relationship of these endangered species Handeliodendron bodinieri (Lévl.) Rehd. and Eurycorymbus cavaleriei (Lévl.) Rehd. et Hand.-Mazz. with other members of Sapindaceae s.l. is not well resolved. A previous study concluded that the genus Aesculus might be paraphyletic because Handeliodendron was nested within it based on small DNA fragments. Thus, their chloroplast genomic information and comparative genomic analysis with other Sapindaceae species are necessary and crucial to understand the circumscription and plastome evolution of this family. RESULTS: The chloroplast genome sizes of Handeliodendron bodinieri and Eurycorymbus cavaleriei are 151,271 and 158,690 bp, respectively. Results showed that a total of 114 unique genes were annotated in H. bodinieri and E. cavaleriei, and the ycf1 gene contained abundant SSRs in both genomes. Comparative analysis revealed that gene content, PCGs, and total GC content were remarkably similar or identical within 13 genera from Sapindaceae, and the chloroplast genome size of four genera was generally smaller within the family, including Acer, Dipteronia, Aesculus, and Handeliodendron. IR boundaries of the H. bodinieri showed a significant contraction, whereas it presented a notable expansion in E. cavaleriei cp genome. Ycf1, ndhC-trnV-UAC, and rpl32-trnL-UAG-ccsA were remarkably divergent regions in the Sapindaceae species. Analysis of selection pressure showed that there are a few positively selected genes. Phylogenetic analysis based on different datasets, including whole chloroplast genome sequences, coding sequences, large single-copy, small single-copy, and inverted repeat regions, consistently demonstrated that H. bodinieri was sister to the clade consisting of Aesculus chinensis and A. wangii and strongly support Eurycorymbus cavaleriei as sister to Dodonaea viscosa. CONCLUSION: This study revealed that the cp genome size of the Hippocastanoideae was generally smaller compared to the other subfamilies within Sapindaceae, and three highly divergent regions could be used as the specific DNA barcodes within Sapindaceae. Phylogenetic results strongly support that the subdivision of four subfamilies within Sapindaceae, and Handeliodendron is not nested within the genus Aesculus.

Tracking temporal shifts in area, biomes, and pollinators in the radiation of Salvia (sages) across continents: leveraging anchored hybrid enrichment and targeted sequence data.

PREMISE OF THE STUDY: A key question in evolutionary biology is why some clades are more successful by being widespread geographically, biome diverse, or species-rich. To extend understanding of how shifts in area, biomes, and pollinators impact diversification in plants, we examined the relationships of these shifts to diversification across the mega-genus Salvia. METHODS: A chronogram was developed from a supermatrix of anchored hybrid enrichment genomic data and targeted sequence data for over 500 of the nearly 1000 Salvia species. Ancestral areas and biomes were reconstructed using BioGeoBEARS. Pollinator guilds were scored, ancestral pollinators determined, shifts in pollinator guilds identified, and rates of pollinator switches compared. KEY RESULTS: A well-resolved phylogenetic backbone of Salvia and updated subgeneric designations are presented. Salvia originated in Southwest Asia in the Oligocene and subsequently dispersed worldwide. Biome shifts are frequent from a likely ancestral lineage utilizing broadleaf and/or coniferous forests and/or arid shrublands. None of the four species diversification shifts are correlated to shifts in biomes. Shifts in pollination system are not correlated to species diversification shifts, except for one hummingbird shift that precedes a major shift in diversification near the crown of New World subgen. Calosphace. Multiple reversals back to bee pollination occurred within this hummingbird clade. CONCLUSIONS: Salvia diversified extensively in different continents, biomes, and with both bee and bird pollinators. The lack of tight correlation of area, biome, and most pollinator shifts to the four documented species diversification shifts points to other important drivers of speciation in Salvia.

Phylogeny and staminal evolution of Salvia (Lamiaceae, Nepetoideae) in East Asia.

Background and Aims: Salvia is the largest genus within Lamiaceae, with about 980 species currently recognized. East Asia, with approx. 100 species, is one of the three major biodiversity centres of Salvia. However, relationships within this lineage remain unclear, and the staminal lever mechanism, which may represent a key innovation within the genus, has been understudied. By using six genetic markers and nearly comprehensive taxon sampling, this study attempts to elucidate relationships and examine evolutionary trends of staminal development within the East Asia (EA) Salvia clade. Methods: Ninety-one taxa of EA Salvia were sampled and 34 taxa representing all other major lineages of Salvia were included for analysis. Two nuclear [internal transcribed spacer (ITS) and external transcribed spacer (ETS)] and four chloroplast (psbA-trnH, ycf1-rps15, trnL-trnF and rbcL) DNA markers were used for phylogenetic analysis employing maximum parsimony (MP), maximum likelihood (ML) and BEAST, with the latter also used to estimate divergence times. Key Results: All Salvia species native to East Asia form a clade, and eight major subclades (A-G) were recognized. Subclade A, comprising two limestone endemics (S. sonchifolia and S. petrophila), is sister to the remainder of EA Salvia. Six distinct stamen types were observed within the EA clade. Stamen type A, with two fully fertile posterior thecae, only occurs in S. sonchifolia and may represent the ancestral stamen type within EA Salvia. Divergence time estimates showed that the crown of EA Salvia began to diversify approx. 17.4 million years ago. Conclusions: This study supports the adoption of a broadly defined Salvia and treats EA Salvia as a subgenus, Glutinaria, recognizing eight sections within this subgenus. Stamen type A is ostensibly plesiomorphic within EA Salvia, and the other five types may have been derived from it. Staminal morphology has evolved in parallel within the EA Salvia, and staminal structure alone is inadequate to delimit infrageneric categories.

The complete chloroplast genome of Chrysoglossum ornatum (Epidendroideae, Orchidaceae) and its phylogenetic analysis.

Chrysoglossum ornatum Blume, the type species of Chrysoglossum Blume, belongs to the tribe Collabieae of the subfamily Epidendroideae of Orchidaceae. In this study, we sequenced, assembled, and analyzed the complete chloroplast genome of C. ornatum. The result showed that the complete chloroplast genome of C. ornatum was 158,175 bp in size, consisting of a large single-copy (LSC) region of 87,235 bp, a small single-copy (SSC) region of 18,384 bp, and a pair of inverted repeats (IRs) of 26,278 bp. The chloroplast genome encoded 113 unique genes, comprising 80 protein-coding genes, 29 tRNA genes, and four rRNA genes. Phylogenetic analysis inferred from the complete chloroplast genome indicated that Chrysoglossum was closely related to Collabium Blume. This study provides genomic resources helpful for further phylogenetic and biodiversity research on Chrysoglossum.

Oxalisxishuiensis (Oxalidaceae), a new species from Danxia landforms in Guizhou, China.

Oxalisxishuiensis, a new species of Oxalidaceae from Danxia landforms of Xishui County, Guizhou, China, is described and illustrated. It is morphologically similar to O.wulingensis by the two lateral leaflets arranged at about 180° angle and oblong pink petals with lilac veins, but clearly differs from the latter by leaflets almost as long as wide, obliquely obcordate lateral leaflets, shorter peduncles, longer capsule (1.2-1.5 cm vs. 0.5-0.7 cm) and alveolate seeds.

Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution.

Introduction: The recently established Linderniaceae, separated from the traditionally defined Scrophulariaceae, is a taxonomically complicated family. Although previous phylogenetic studies based on a few short DNA markers have made great contributions to the taxonomy of Linderniaceae, limited sampling and low resolution of the phylogenetic tree have failed to resolve controversies between some generic circumscriptions. The plastid genome exhibits a powerful ability to solve phylogenetic relationships ranging from shallow to deep taxonomic levels. To date, no plastid phylogenomic studies have been carried out in Linderniaceae. Methods: In this study, we newly sequenced 26 plastid genomes of Linderniaceae, including eight genera and 25 species, to explore the phylogenetic relationships and genome evolution of the family through plastid phylogenomic and comparative genomic analyses. Results: The plastid genome size of Linderniaceae ranged from 152,386 bp to 154,402 bp, exhibiting a typical quartile structure. All plastomes encoded 114 unique genes, comprising 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The inverted repeat regions were more conserved compared with the single-copy regions. A total of 1803 microsatellites and 1909 long sequence repeats were identified, and five hypervariable regions (petN-psbM, rps16-trnQ, rpl32-trnL, rpl32, and ycf1) were screened out. Most protein-coding genes were relatively conserved, with only the ycf2 gene found under positive selection in a few species. Phylogenomic analyses confirmed that Linderniaceae was a distinctive lineage and revealed that the presently circumscribed Vandellia and Torenia were non-monophyletic. Discussion: Comparative analyses showed the Linderniaceae plastomes were highly conservative in terms of structure, gene order, and gene content. Combining morphological and molecular evidence, we supported the newly established Yamazakia separating from Vandellia and the monotypic Picria as a separate genus. These findings provide further evidence to recognize the phylogenetic relationships among Linderniaceae and new insights into the evolution of the plastid genomes.

The complete chloroplast genome sequence of Heteropolygonatum ginfushanicum (Asparagaceae) and phylogenetic analysis.

Heteropolygonatum ginfushanicum is an endemic epiphytic herb in China. The complete chloroplast (cp) genome of H. ginfushanicum is reported in this study. The total length of the cp genome is 155,508 bp with a typical quadripartite structure consisting of a large single copy region (LSC) of 84,552 bp and a small single copy region (SSC) of 18,528 bp, separated by a pair of 26,214 bp inverted repeats (IRs). It encodes a total of 113 unique genes, including 79 protein-coding, 30 tRNA, and four rRNA genes. Phylogenetic analysis indicated that H. ginfushanicum is sister to Heteropolygonatum marmoratum within subfamily Nolinoideae.

Rediscovery of Pogostemon dielsianus (Lamiaceae, Lamioideae), a rare endemic species from southwestern China, after one century.

Pogostemon dielsianus (Lamiaceae) was described in 1913 based on a single gathering from northwestern Yunnan of China collected in 1905, and thereafter no further collections were observed until 2019. We rediscovered the rare endemic species in Lushui County, Yunnan. Molecular phylogenetic analyses based on four cpDNA markers (rbcL, rps16, psbA-trnH, and trnL-trnF) and the nuclear ribosomal internal transcribed spacer (ITS) region confirmed its infrageneric placement within subg. Pogostemon. Based on observations of the rediscovered population of P. dielsianus, we updated its morphological description, provided an illustration, and discussed its distribution. Under IUCN criteria, the species was categorized as "Critically Endangered (CR)".

Comparative plastomic analysis and insights into the phylogeny of Salvia (Lamiaceae).

Salvia is the largest genus of Lamiaceae, with almost 1000 species, and has been divided into 11 subgenera. Salvia subg. Glutinaria, native to East Asia, is particularly important because of its potential medicinal value. However, the interspecific relationships of this subgenus have not been resolved and the plastomes of Salvia have rarely been studied. In the current study, we compared plastid genome structure and organization of 19 species of Salvia (14 newly sequenced and 5 previously published). Our comparative analysis showed that all Salvia plastomes examined have a quadripartite structure typical of most angiosperms and contain an identical set of 114 unique genes (80 protein-coding genes, 4 rRNA genes, and 30 tRNA genes). The plastome structure of all Salvia species is highly conserved like other Lamiaceae plastomes. Gene content, gene order, and GC content were highly similar in these plastomes. The inverted repeats/single copy region (IR/SC) boundaries of Salvia are highly conserved, and IR contraction only occurred in two species (Salvia mekongensis and S. rosmarinus). In Salvia, sequence divergence was higher in non-coding regions than in coding regions. We found that using large single copy (LSC) and small single copy regions (SSC) with exclusion of the rapidly evolving sites produced the highest resolution in phylogenetic analysis of Salvia, suggesting that using suitable informative sites to build trees is more conducive in phylogenetic research. This study assembled a powerful matrix data set for studying the phylogeny of Salvia, resolving the interspecific relationship of Salvia subg. Glutinaria. The newly sequenced plastid genomes will also enrich the plastome database of Salvia, providing the scientific basis for the development and utilization of germplasm resources of this large and important genus.

The complete plastome sequence of Tanakaea radicans (Saxifragaceae) and its phylogenetic analysis.

Tanakaea radicans is classified in the monotypic genus Tanakaea in the Saxifragaceae. It is a small, evergreen plant with a disjunct distribution in Japan and China. Here, we report and characterize for the first time the complete plastid genome sequence of T. radicans. The chloroplast genome is 155,265 bp in length and contains a pair of inverted repeats (25,794 bp) separated by a large single copy (86,289 bp) and a small single copy (17,388 bp). A total of 113 unique genes, including 79 protein-coding, 30 tRNA, and four rRNA genes, were annotated. Phylogenetic analysis showed that T. radicans was sister to Leptarrhena pyrolifolia within Huecheroids linage of Saxifragaceae.

The Complete Chloroplast Genome of the Vulnerable Oreocharis esquirolii (Gesneriaceae): Structural Features, Comparative and Phylogenetic Analysis.

Oreocharis esquirolii, a member of Gesneriaceae, is known as Thamnocharis esquirolii, which has been regarded a synonym of the former. The species is endemic to Guizhou, southwestern China, and is evaluated as vulnerable (VU) under the International Union for Conservation of Nature (IUCN) criteria. Until now, the sequence and genome information of O. esquirolii remains unknown. In this study, we assembled and characterized the complete chloroplast (cp) genome of O. esquirolii using Illumina sequencing data for the first time. The total length of the cp genome was 154,069 bp with a typical quadripartite structure consisting of a pair of inverted repeats (IRs) of 25,392 bp separated by a large single copy region (LSC) of 85,156 bp and a small single copy region (SSC) of18,129 bp. The genome comprised 114 unique genes with 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Thirty-one repeat sequences and 74 simple sequence repeats (SSRs) were identified. Genome alignment across five plastid genomes of Gesneriaceae indicated a high sequence similarity. Four highly variable sites (rps16-trnQ, trnS-trnG, ndhF-rpl32, and ycf 1) were identified. Phylogenetic analysis indicated that O. esquirolii grouped together with O. mileensis, supporting resurrection of the name Oreocharis esquirolii from Thamnocharisesquirolii. The complete cp genome sequence will contribute to further studies in molecular identification, genetic diversity, and phylogeny.

Synergistic Effects of Boron Nitride (BN) Nanosheets and Silver (Ag) Nanoparticles on Thermal Conductivity and Electrical Properties of Epoxy Nanocomposites.

Polymer composites, with both high thermal conductivity and high electrical insulation strength, are desirable for power equipment and electronic devices, to sustain increasingly high power density and heat flux. However, conventional methods to synthesize polymer composites with high thermal conductivity often degrade their insulation strength, or cause a significant increase in dielectric properties. In this work, we demonstrate epoxy nanocomposites embedded with silver nanoparticles (AgNPs), and modified boron nitride nanosheets (BNNSs), which have high thermal conductivity, high insulation strength, low permittivity, and low dielectric loss. Compared with neat epoxy, the composite with 25 vol% of binary nanofillers has a significant enhancement (~10x) in thermal conductivity, which is twice of that filled with BNNSs only (~5x), owing to the continuous heat transfer path among BNNSs enabled by AgNPs. An increase in the breakdown voltage is observed, which is attributed to BNNSs-restricted formation of AgNPs conducting channels that result in a lengthening of the breakdown path. Moreover, the effects of nanofillers on dielectric properties, and thermal simulated current of nanocomposites, are discussed.

Decomposition Characteristics of SF6 under Flashover Discharge on the Epoxy Resin Surface.

In this paper, the flashover discharging experiment was carried out on epoxy resin surface in an SF6 atmosphere under pin-plate electrodes, with the electrodes distance from 5 mm to 9 mm. The concentration of seven characteristic gases was detected, indicating that the concentration of SOF2 and CF4 was the two highest, followed by SO2, CO2, SO2F2, CS2, and H2S. Based on the changes in the concentration of the characteristic gases, a preliminary rule was proposed to predict the occurrence of flashover discharge on epoxy resin: When the concentration of SOF2 reaches twice of CF4 concentration, and the total concentration of both SOF2 and CF4 is much higher than that of H2S, a possible flashover discharge on the epoxy resin surface in SF6-infused electrical equipment occurs. Through the simulation of decomposition of epoxy resin, it has been revealed that H2O has different generation paths that can facilitate the formation of SOF2, finally influencing the concentration variation of the seven characteristic gases.

The complete chloroplast genome of the threatened Dipentodon sinicus (Dipentodontaceae).

Dipentodon is a monotypic genus of Dipentodontaceae and the only species, Dipentodon sinicus, is scattered in southwest China as well as adjacent Myanmar, northeast India and northern Vietnam. This species was evaluated as vulnerable in 'China Species Red List'. Here, we assembled and characterized the complete chloroplast (cp) genome of D. sinicus using Illumina sequencing data for the first time. The complete cp genome was 158,795 bp in length, consisting of a pair of inverted repeats of 26,587 bp, a large single-copy region of 87,233 bp and a small single-copy region of 18,388 bp. The genome encoded 113 unique genes, including 79 protein-coding genes, 30 tRNA genes and four rRNA genes. Phylogenetic analysis based on 16 complete cp genome sequences indicated that D. sinicus is a member of Huerteales, consistent with its position in the latest classification of flowering plants (AGP IV).

The implications of ritual practices and ritual plant uses on nature conservation: a case study among the Naxi in Yunnan Province, Southwest China.

BACKGROUND: Conservation of biodiversity is primary important of today's critically vulnerable environment. Efficient conservation can be possible only with the long-term participation and understanding of the communities. Ritual beliefs of the indigenous people are one of the important tools to understand the local communities and aid the nature conservation. In this paper, we documented contemporary ritual practices and ritual plant uses among the Naxi people and discussed the importance of traditional knowledge on ritual practice in the conservation of plants in the mountains presenting a case study of the Dongba culture. METHODS: This study was carried out from July in 2013 to July in 2014. To document and analyze the present state of the ritual plant used by the Naxi people we conducted an ethnobotanical survey. We interviewed local people including Dongba priests using the semi-structured questionnaire. During the field study, we participated in the local religious activities to witness the use of different plants in ritual activities of the Naxi people. We interviewed twenty-two key informants and eleven of them were male. All the specimens of documented species were collected and deposited at the herbarium of Kunming Institute of Botany. RESULTS: The survey results revealed the Naxi people possessed sound knowledge of the traditional ritual plants and great diversity of plants used in many of Naxi rituals and festivals. From the survey, we documented 32 ritual plant species belonging to 24 genera of 17 families used in various ritual activities. The ritual plants were grouped into two categories, namely those burned as incense, and those used for decoration. The incense plants like Olea europaea subsp. cuspidata and Pistacia weinmanniifolia were probably promising natural aromatic resource. Plants of genus Quercus were the most frequently used species. The places for ritual activities were diverse, such as the incense burners inside and outside the house and sacred trees at the Baishuitai. Local people except the young generation had an abundant of traditional knowledge. CONCLUSIONS: Our study shows the live ritual activities and the beliefs of the residents are keeping the plant diversity and the entire forest preserved as sacred mountains. Our study emphasizes traditional belief and an alternative view of conservation that is not led mainly by governmental policies, as local practices and ritual plants uses play as constant reminders to the Naxi on nature conservation. However, further research is recommended for in-depth understanding the role of traditional belief in biodiversity conservation.

Prioritizing fodder species based on traditional knowledge: a case study of mithun (Bos frontalis) in Dulongjiang area, Yunnan Province, Southwest China.

BACKGROUND: Livestock rearing is one of the oldest and most important types of smallholder farming worldwide. The sustainability of livestock production depends on the efficient utilization of locally available resources. Some traditional methods of raising livestock may offer valuable lessons in this regard. This study documented and evaluated local knowledge of wild forage plants in the Dulongjiang area in Southwest China in the context of rearing mithun (Bos frontalis) in order to provide a sound evidence base for tree fodder selection and the establishment of integrated tree-crop-livestock systems. METHODS: The snowball technique was used to identify key informants with specific knowledge about the topic. Free listing and semi-structured interviews were conducted with 58 households. Participatory investigation and transit walks were used to investigate potential fodder species. Ethnobotanical information was collected, documented and organized. RESULTS: Overall, 142 wild forage plants from 58 families and 117 genera were identified. Species of the Poaceae, Rosaceae and Urticaceae families were most abundant, with 16, 14 and 11 species respectively identified as fodder plants. Our results indicated that tree/shrub forage plays a major role in the diet of mithun, unlike that of other ruminants. Mithun prefers to browse and move around the forest in search of food, particularly rough and even barbed leaves. Tree species like Debregeasia orientalis, Saurauia polyneura and Rubus species were identified as being important fodder sources. Farmers in this area have traditionally relied on common property resources such as community-managed forests and grasslands to feed their livestock. Farmers have strong incentive to raise mithuns rather than other livestock species due to Dulong people's cultural preferences. CONCLUSIONS: The wide variety of plants cited by the informants demonstrate the importance of traditional knowledge in gathering information about forage resources. This diversity also offers the prospect of identifying promising species which could be used as fodder plants. Identifying such species and tree fodder species in particular could help smallholder farmers to integrate trees, livestock and crops as part of a sustainable farming system.