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Background: The family Geminiviridae contains plant viruses commonly referred to as geminiviruses, which cause diseases in numerous important plants. Geminiviridae is one of the most important family of plant-infecting viruses that has been divided into fourteen recognized genera. Amongst these, the genus Begomovirus is the largest and economically most important one, viruses of the genus are further categorized into bipartite (two genomic components called DNA-A and DNA-B) and monopartite (single genomic component or DNA-A) begomoviruses. Method: The genomic DNA was extracted from symptomatic plant samples and both the DNA-(B and A) components of a bipartite begomovirus were amplified via rolling circular amplification (RCA) and PCR. The amplified DNA-A and DNA-B were cloned and sequenced by Primer walking, Sanger sequencing, and Illumina sequencing methods. The phylogenetic and biogeographic analyses of both components were performed by various bioinformatics tools. Results: DNA-A (accession number MW722701) and DNA-B (accession number MW722782) of begomoviruses that were sequenced shared >95% sequence similarity with the bipartite begomovirus known as Tomato Leaf Curl New Delhi virus (TLCuNDV). Phylogenetic and biogeographic analyses proposed several possible ancestors, and multiple dispersal and vicariance events may be involved in the evolution of this virus. Conclusions: This is the first time a bipartite begomovirus has been found to infect a plant in the study area (District Swat, Pakistan). The existence of ToLCNDV may pose a major danger to other important crops in the region. [ABSTRACT FROM AUTHOR]

The inedible parts of nuts and stone fruits are low‐cost and lignin‐rich feedstock for more sustainable production of aromatic chemicals in comparison with the agricultural and forestry residues. However, the depolymerization performances on food‐related biomass remains unclear, owing to the broad physicochemical variations from the edible parts of the fruits and plant species. In this study, the monomer production potentials of ten major fruit and nutshell biomass were investigated with comprehensive numerical information derived from instrumental analysis, such as plant cell wall chemical compositions, syringyl/guaiacyl (S/G ratios, and contents of lignin substructure linkages (β‐O‐4, β–β, β‐5). A standardized one‐pot reductive catalytic fractionation (RCF) process was applied to benchmark the monomer yields, and the results were statistically analyzed. Among all the tested biomass, mango endocarp provided the highest monolignol yields of 37.1 % per dry substrates. Positive S‐lignin (70–84 %) resulted in higher monomer yield mainly due to more cleavable β‐O‐4 linkages and less condensed C−C linkages. Strong positive relationships were identified between β‐O‐4 and S‐lignin and between β‐5 and G‐lignin. The analytical, numerical, and experimental results of this study shed lights to process design of lignin‐first biorefinery in food‐processing industries and waste management works. [ABSTRACT FROM AUTHOR]

Specialisation in food resource use is a crucial process that fosters species coexistence in plant–animal networks, contributing to the maintenance of biodiversity, ecological complexity, and community stability. Notably, although there is a vast literature on ecological specialisation in pollination systems, the evolutionary similarity among the plant species visited by particular pollinators has been largely ignored. Here, we apply a robust phylogenetic approach to analyse whether the evolutionary relatedness of plant species is a significant factor in mediating pollinator visits and how it relates to the morphology of interacting species. We quantified ecological and clade specialisation of hummingbird and insect species in three mutualistic networks from the Costa Rican highlands and associated these metrics with species traits. We found that hummingbirds were overall ecologically more specialised than insects (i.e. visited a less diverse set of plant species). However, when evaluating the phylogenetic relatedness among the visited plant species, all hummingbird species and most insects had overdispersed diets, which indicates they visited phylogenetically distant plant species in the community. Moreover, a great proportion of these clade generalists visited plant species with a great variation in corolla length, showing a lack of preference for this morphological trait. Altogether, our results demonstrate that by incorporating plant phylogeny to network analysis, pollinator species were generalists and that corolla length weakly influences plant–pollinator interactions in the three studied networks. A phylogenetic perspective should occupy a central role in the study of specialisation since it contributes to understanding the interplay between ecological and evolutionary processes in mutualistic networks. Future research should focus on evaluating whether the phylogenetic structure of animal diets mediates patterns of interactions in different types of mutualisms and environmental contexts, linking these patterns to other floral traits. This knowledge may be valuable for deepening our comprehension of the underlying mechanisms shaping ecological networks. [ABSTRACT FROM AUTHOR]

Species morphological and behavioural traits are key determinants of which pollinator species interact with which plant species. However, individuals within species are not identical in their traits and this diversity could help us understand plant–pollinator interaction patterns.Using three independent data sets, we assessed whether bee intraspecific body size variation (ITV) and sociality influenced pollinator interaction specialisation, intraspecific niche partitioning, centrality in the interaction network and phylogenetic diversity of the plants visited.We found that solitary pollinators were more specialised in their interactions with plants and had lower intraspecific niche partitioning compared to social pollinators. Furthermore, solitary pollinators with higher ITV had higher centrality in the network and visited a higher phylogenetic diversity of plants compared to solitary species with lower ITV, whereas the opposite pattern emerged for social pollinators. Pollinator ITV did not differ between social and solitary bee species.Our findings show that the effect of pollinator body size variation on plant–pollinator interactions depends on pollinator species sociality. Specifically, solitary pollinators with higher ITV and social pollinators with lower ITV seem to be the most important contributors to maintaining the evolutionary diversity of the plant community, and also the species with the largest potential to affect (via cascade effects) the entire plant–pollinator network. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

The pear is an economic fruit that is widely planted around the world and is loved by people for its rich nutritional value. Autophagy is a self-protection mechanism in eukaryotes, and its occurrence often accompanied by the degradation of damaged substances in cells and the recycling of nutrients. Autophagy is one of the mechanisms through which plants respond to environmental stress and plays an important role in plant development and stress resistance. Functional studies of autophagy-related genes (ATGs) have been performed on a variety of plant species, but little information is available on the ATG family in pear (Pyrus bretschneideri Rehd). Therefore, we analyzed the evolutionary dynamics and performed a genome-wide characterization of the PbrATG gene family. A total of 28 PbrATG members were identified. Phylogenetic analysis showed that PbrATGs were more closely related to ATGs of European pear and apple. Evolutionary analysis revealed that whole-genome duplication (WGD) and dispersed duplication events were the main driving forces of PbrATG family expansion. Expression analysis of different pear tissues showed that all the genes were expressed in different pear tissues, and different PbrATGs are expressed at different times and in different locations. Moreover, all PbrATGs also responded to different abiotic stresses, especially salt and drought stress, which elicited the highest expression levels. Pear seedlings were subsequently infected with Botryosphaeria dothidea (B. dothidea). The results showed that different PbrATGs had different expression patterns at different infection stages. According to the gene expression data, PbrATG1a was selected as a key autophagy gene for further analysis. Silencing of PbrATG1a reduced the resistance of pear to B. dothidea, which resulted in increased lesions, reactive oxygen species (ROS) contents, antioxidant enzyme activity, and gene expression levels in the silenced pear seedlings after B. dothidea inoculation. In this study, a comprehensive bioinformatic analysis of ATGs was conducted, and the functions of PbrATGs in pear development and in response to stress were elucidated, which laid a foundation for further study of the molecular mechanism of autophagy and a new strategy for pear resistance breeding. [ABSTRACT FROM AUTHOR]

Taxus cuspidata is a rare plant with important medicinal and ornamental value. Aiming at the obvious differences between wild and cultivated populations of T. cuspidata from Northeast China, a total of 61 samples, that is, 33 wild yews and 28 cultivated yews were used to analyze the differences and correlations of the kinship, genetic diversity, and genetic structure between them by specific length amplified fragment sequencing (SLAF-seq). Finally, 470725 polymorphic SLAF tags and 58622 valid SNP markers were obtained. Phylogenetic analysis showed that 61 samples were classified into 2 clusters: wild populations and cultivated populations, and some wild yews were categorized into the cultivated populations; the genetic diversity analysis showed that the Nei diversity index of wild populations (0.4068) was smaller than that of cultivated populations (0.4414), and the polymorphic information content (PIC) of wild populations (0.2861) was smaller than that of cultivated populations (0.3309). The genetic differentiation analysis showed that the total populations of gene diversity (Ht) of cultivated and wild populations were respectively 0.8159 and 0.5685, the coefficient of gene differentiation (Gst) of cultivated and wild populations was respectively 0.3021 and 0.1068, and the gene flow (Nm) (2.4967) of wild populations was larger than cultivated populations (0.8199). The molecular variance (AMOVA) revealed that inter-population variation accounted for 29.57% of the total genetic variation, while intra-population variation accounted for 70.42% of the total genetic variation (p < 0.001), this suggested that the genetic variation in the T. cuspidata is mainly attributed to within-population factors. In conclusion, the genetic distance between geographical ecological groups of wild populations was generally smaller than that of cultivated populations, and the degree of genetic diversity and genetic differentiation was smaller than that of cultivated populations. As evident, the utilization of SLAF-seq technology enables efficient and accurate development of SNP markers suitable for genetic analysis of T. cuspidata species. These developed SNP markers can provide a molecular foundation for T. cuspidata breeding, construction of genetic maps, variety identification, and association analysis of agronomic traits. [ABSTRACT FROM AUTHOR]

β-ketoacyl-CoA synthase (KCS) is an important enzyme that catalyzes the biosynthesis of very-long-chain fatty acids (VLCFAs). In this study, the genome-wide analysis and functional characterization of the KCS gene family members in common bean (Phaseolus vulgaris L.) plants were conducted, and the response of the identified gene family to abiotic stresses was evaluated. In this study, 19 KCS genes were identified and characterized in the P. vulgaris genome. The molecular weights of these KCS proteins ranged from 49.14 kDa to 60.57 kDa, their amino acid lengths varied from 437 to 534, and their pI values ranged from 8.81 to 9.47, indicating a basic nature. Segmental and tandem duplications were observed in the Pvul-KCS gene family. Phylogenetic analysis revealed that Pvul-KCS proteins clustered into three main groups with Arabidopsis thaliana and Glycine max species. Comparative mapping analysis was also conducted with A. thaliana and G. max. Expression profile comparisons indicated that these genes had different expression levels in common bean varieties and played a role in the plant's response to biotic and abiotic stresses. This study provides important insights into the biological functions of KCS genes in Phaseolus vulgaris and offers valuable information for improving drought and salt stress tolerance in common beans. [ABSTRACT FROM AUTHOR]

As a vital component of biodiversity, phyllosphere bacteria in forest canopy play a critical role in maintaining plant health and influencing the global biogeochemical cycle. There is limited research on the community structure of phyllosphere bacteria in natural forests, which creates a gap in our understanding of whether and/or how phyllosphere bacteria are connected to leaf traits of their host. In this study, we investigated the bacterial diversity and composition of the canopy leaves of six dominant tree species in deciduous broad-leaved forests in northeastern China, using high-throughput sequencing. We then compare the differences in phyllosphere bacterial community structure and functional genes of dominant tree species. Fourteen key leaf functional traits of their host trees were also measured according to standard protocols to investigate the relationships between bacterial community composition and leaf functional traits. Our result suggested that tree species with closer evolutionary distances had similar phyllosphere microbial alpha diversity. The dominant phyla of phyllosphere bacteria were Proteobacteria, Actinobacteria, and Firmicutes. For these six tree species, the functional genes of phyllosphere bacteria were mainly involved in amino acid metabolism and carbohydrate metabolism processes. The redundancy and envfit analysis results showed that the functional traits relating to plant nutrient acquisition and resistance to diseases and pests (such as leaf area, isotope carbon content, and copper content) were the main factors influencing the community structure of phyllosphere bacteria. This study highlights the key role of plant interspecific genetic relationships and plant attributes in shaping phyllosphere bacterial diversity. [ABSTRACT FROM AUTHOR]

The root-associated soil microbiome contributes immensely to support plant health and performance against abiotic and biotic stressors. Understanding the processes that shape microbial assembly in root-associated soils is of interest in microbial ecology and plant health research. In this study, 37 plant species were grown in the same soil mixture for 10 months, whereupon the root-associated soil microbiome was assessed using amplicon sequencing. From this, the contribution of direct and indirect plant effects on microbial assembly was assessed. Plant species and plant-induced changes in soil physicochemistry were the most significant factors that accounted for bacterial and fungal community variation. Considering that all plants were grown in the same starting soil mixture, our results suggest that plants, in part, shape the assembly of their root-associated soil microbiome via their effects on soil physicochemistry. With the increase in phylogenetic ranking from plant species to class, we observed declines in the degree of community variation attributed to phylogenetic origin. That is, plant-microbe associations were unique to each plant species, but the phylogenetic associations between plant species were not important. We observed a large degree of residual variation (> 65%) not accounted for by any plant-related factors, which may be attributed to random community assembly. [ABSTRACT FROM AUTHOR]

Background: Bruguiera hainesii C.G. Rogers 1919, a true mangrove tree is a critically endangered species (CR) in Vietnam. This species is restricted to the Con Dao National Park, Ba Ria-Vung Tau province, where it occurs in very tiny populations. However, the exploration of the chloroplast genome of B. hainesii in Vietnam has a serious lack of information. It is extremely challenging to promote the conservation of B. hainesii. Therefore, urgently required to discover and comprehend the chloroplast genome of B. hainesii. Methods: To detect evolutionary analysis between mangroves, we sequenced the complete chloroplast genome of B. hainesii using next-generation sequencing technology (Illumina Hiseq X Ten). Results: We sequenced and assembled the complete chloroplast genome of B. hainesii, which was deposited in GenBank as accession number OR086085. The DNA was circular with 164,305 bp length, comprising 37% GC. The genome contained a large single-copy region of 91,724 bp, inverted repeat regions of 26,360 bp, and a short single-copy region of 19,861 bp. Furthermore, it contained 130 genes, consisting of 83 protein-coding genes, 37 tRNAs, and 8 rRNAs. We detected 131 single-sequence repeats, including 119 mononucleotides, 11 dinucleotides, and one trinucleotide. Phylogenetic analysis showed strong support that B. hainesii was sister to B. cylindrica. Conclusions: The findings in this study provide a foundation for species identification, evolutionary genetics, and the conservation of endangered B. hainesii in Vietnam. [ABSTRACT FROM AUTHOR]

Soil functioning is closely linked to the interactions between biological communities with the physical environment. Yet, the impact of plant community attributes on metabolic processes promoting soil nutrient cycling remains largely unknown. We hypothesized that the plant community acts as a regulating agent of nutrient mobilization in soils according to the phylogenetic and morpho-functional traits of plant species of which it is composed. Rhizosphere soils were collected in autumn and spring under 32 tree and shrub species in two Mediterranean mixed forests (four plots in each) located in southern Spain, and nine soil enzymatic activities related to C, N and P mobilization were assessed. Phylogeny and morpho-functional traits of plant species were recorded and their imprint in soil enzymatic activities across forests was determined. The results showed a plant phylogenetic signal for N mobilization in both forests, while it varied across forests for non-labile C and P mobilization. The plant phylogenetic signals were primarily driven by lineages that diversified through the Miocene, about 25 Myr ago. In addition, leaf traits and plant's mycorrhizal type explained soil enzymatic activities independently from phylogeny. C and P mobilization increased under ectomycorrhizal plants, whilst enhanced N mobilization did occur under arbuscular mycorrhizal ones. The plant community composition led to a different carbon and nutrient mobilization degree, which in turn was mediated by distinct microbial communities mirroring differentiated resource-acquisition strategies of plants. Our results highlight the role of plant traits and mycorrhizal interactions in modulating carbon and nutrient cycling in Mediterranean mixed forest soils. [ABSTRACT FROM AUTHOR]

Leaf photosynthetic nitrogen‐use efficiency (PNUE) diversified significantly among C3 species. To date, the morpho‐physiological mechanisms and interrelationships shaping PNUE on an evolutionary time scale remain unclear. In this study, we assembled a comprehensive matrix of leaf morpho‐anatomical and physiological traits for 679 C3 species, ranging from bryophytes to angiosperms, to comprehend the complexity of interrelationships underpinning PNUE variations. We discovered that leaf mass per area (LMA), mesophyll cell wall thickness (Tcwm), Rubisco N allocation fraction (PR), and mesophyll conductance (gm) together explained 83% of PNUE variations, with PR and gm accounting for 65% of those variations. However, the PR effects were species‐dependent on gm, meaning the contribution of PR on PNUE was substantially significant in high‐gm species compared to low‐gm species. Standard major axis (SMA) and path analyses revealed a weak correlation between PNUE and LMA (r2 = 0.1), while the SMA correlation for PNUE–Tcwm was robust (r2 = 0.61). PR was inversely related to Tcwm, paralleling the relationship between gm and Tcwm, resulting in the internal CO2 drawdown being only weakly proportional to Tcwm. The coordination of PR and gm in relation to Tcwm constrains PNUE during the course of evolution. Summary Statement: Leaf photosynthetic nitrogen‐use efficiency (PNUE) varies significantly among major phylogenetic clades and species. Numerous studies have examined the variations in PNUE among major plant groups, attributing these variations to leaf habits or height‐related economic spectra, microhabitat acclimations, or unknown fundamental differences. Results from a comprehensive matrix of leaf morpho‐anatomical and physiological traits for 679 C3 species discovered that cell wall thickness (Tmcw) has phylogenetically consistent effects on PNUE of terrestrial plants. [ABSTRACT FROM AUTHOR]

For the purpose of functional validation, the mung bean (Vigna radiata) VrPR gene was cloned and overexpressed in Arabidopsis thaliana. The findings revealed that the ORF of VrPR contained 1200 bp, in which 399 amino acids were encoded. Bioinformatics analysis showed that the VrPR protein belonged to the NADB Rossmann superfamily, which was one of the non-transmembrane hydrophilic proteins. VrPR was assumed to have 44 amino acid phosphorylation sites and be contained in chloroplasts. The VrPR secondary structure comprised of random coil, α helix, β angle, and extended chain, all of which were quite compatible with the anticipated tertiary structure. Moreover, analysis of the phylogenetic tree indicated that the soybean PR (Glyma.12G222200) and VrPR were closely related. Furthermore, chlorophyll content in leaves is markedly increased in Arabidopsis when VrPR is overexpressed. Our findings will serve as a reference for more functional studies on the PR genes in mung bean. [ABSTRACT FROM AUTHOR]

WRKY transcription factors play an important role in the immune system and the innate defense response of plants. WRKY transcription factors have great feedback on nitrogen stress. In this study, bioinformatics was used to detect the WRKYs of Panax notoginseng (PnWRKYs). The response of PnWRKYs under nitrogen stress was also well studied. PnWRKYs were distributed on 11 chromosomes. According to PnWRKY and Arabidopsis thaliana WRKY (AtWRKY) domains, these PnWRKY proteins were divided into three groups by phylogenetic analysis. MEME analysis showed that almost every member contained motif 1 and motif 2. PlantCARE online predicted the cis-acting elements of the promoter. PnWRKY gene family members obtained 22 pairs of repeat fragments by collinearity analysis. The expression levels of PnWRKYs in different parts (roots, flowers, and leafs) were analyzed by the gene expression pattern. They reflected tissue-specific expressions. The qRT-PCR experiments were used to detect 74 PnWRKYs under nitrogen stress. The results showed that the expression levels of 8 PnWRKYs were significantly induced. The PnWRKY gene family may be involved in biotic/abiotic stresses and hormone induction. This study will not only lay the foundation to explore the functions of PnWRKYs but also provide candidate genes for the future improvement of P. notoginseng. [ABSTRACT FROM AUTHOR]

Rising atmospheric CO2 concentration triggers an emergent phenomenon called plant photosynthetic acclimation to elevated CO2 (PAC). PAC is often characterized by a reduction in leaf photosynthetic capacity (Asat), which varies dramatically along the continuum of plant phylogeny. However, it remains unclear whether the mechanisms responsible for PAC are also different across plant phylogeny, especially between gymnosperms and angiosperms. Here, by compiling a dataset of 73 species, we found that although leaf Asat increased significantly from gymnosperms to angiosperms, there was no phylogenetic signal in the PAC magnitude along the phylogenetic continuum. Physio‐morphologically, leaf nitrogen concentration (Nm), photosynthetic nitrogen‐use efficiency (PNUE), and leaf mass per area (LMA) dominated PAC for 36, 29, and 8 species, respectively. However, there was no apparent difference in PAC mechanisms across major evolutionary clades, with 75% of gymnosperms and 92% of angiosperms regulated by the combination of Nm and PNUE. There was a trade‐off between Nm and PNUE in driving PAC across species, and PNUE dominated the long‐term changes and inter‐specific differences in Asat under elevated CO2. These findings indicate that nitrogen‐use strategy drives the acclimation of leaf photosynthetic capacity to elevated CO2 across terrestrial plant species. [ABSTRACT FROM AUTHOR]

Phylogenetic analysis for plants can be very helpful in determining species identification or taxonomic status morphologically. rbcL and matK are widely used as genetic markers in constructing seed plant phylogenies. Different identification and new collection during the re-inventory from the previous study were found in two and four types of rare fruits in Sibohe Forest, West Kalimantan. The six types include pisang karok (Musa sp.) and Kandis (Garcinia sp.), as well as nubik (Artocarpus sp.), tehengan (Artocarpus sp.), smallest arok (Ficus sp.), and amok (Alpinia sp.). This study aimed to analyze the phenetic relationship of six rare fruits from Kalimantan based on rbcL and matK genes. DNA samples were obtained from dried body parts of the previous study and amplified by PCR using both forward and reverse primers for rbcL and matK genes. Amplification was observed on electrophoresis gel for rbcL gene of nubik, tehengan, smallest arok, amok, and pisang karok, while only pisang karok in matK gene. However, matK gene sequence was also obtained for amok even though the band was not seen on the gel. Phylogenetic analysis using the two genes confirmed the morphological identification reported in the previous study; however, using matK as a single gene for taxonomic confirmation must be reconsidered. The information of rbcL and matK sequences of six rare fruits from West Kalimantan could be the first information for building the DNA barcodes of the rare fruits in West Kalimantan. [ABSTRACT FROM AUTHOR]

Azalea is a general designation of Rhododendron in the Ericaceae family. Rhododendron not only has high ornamental value but also has application value in ecological protection, medicine, and scientific research. In this study, we used Illumina and PacBio sequencing to assemble and annotate the entire chloroplast genomes (cp genomes) of four Rhododendron species. The chloroplast genomes of R. concinnum, R. henanense subsp. lingbaoense, R. micranthum, and R. simsii were assembled into 207,236, 208,015, 207,233, and 206,912 bp, respectively. All chloroplast genomes contain eight rRNA genes, with either 88 or 89 protein-coding genes. The four cp genomes were compared and analyzed by bioinformatics, and the phylogenetic analysis based on chloroplast genomes of 26 species of Ericaceae, Actinidiaceae, and Primulaceae under Ericales was conducted. A comparison of the linear structure of cp genomes of four Rhododendron showed that there were substantial sequence similarities in coding regions, but high differences in non-coding regions. A phylogenetic analysis, based on chloroplast whole genome sequences, showed that all Rhododendron species are in the clade Ericaceae. This study provides valuable genetic information for the study of population genetics and evolutionary relationships in Rhododendron and other azalea species. [ABSTRACT FROM AUTHOR]

Background: Light is an important environmental factor affecting the growth and survival of plants in forest communities. The competition for light resources and divergent responses to light may affect plant species coexistence in natural forests through niche partitioning and environmental filtering, respectively. Methods: In the present study, sequences of light-response-related functional genes were extracted from transcriptomic data of 99 tree species in a subtropical forest and average and nearest taxon phylogenetic diversity of adult (A_Apd', A_NTpd') and seedling neighbors (S_Apd', S_NTpd') around each focal seedling were calculated to evaluate effects of differentiation in light-response-related genes on community assembly processes. Results: The results showed that seedling survival was related to S_NTpd', S_ Apd' and A_Apd' of two chlorophyll ab-binding proteins involved in the assembly of photosystem II and two genes responsive to light intensity, indicating seedlings surrounded by neighbors with distinct light responses tended to have high survival rates. Conclusions: Our results indicated that niche partitioning due to competition for light resources between plants may act as the key mechanism in determining seedling dynamics in subtropical forests. [ABSTRACT FROM AUTHOR]

The development of allometric biomass models is important process in biomass estimation because the reliability of forest biomass and carbon estimations largely depends on the accuracy and precision of such models. National Forest Inventories (NFI) are detailed assessments of forest resources at national and regional levels that provide valuable data for forest biomass estimation. However, the lack of biomass allometric equations for each tree species in the NFI currently hampers the estimation of national-scale forest biomass. The main objective of this study was to develop allometric biomass regression equations for each tree species in the NFI of China based on limited biomass observations. These equations optimally grouped NFI and biomass observation species according to their phylogenetic relationships. Significant phylogenetic signals demonstrated phylogenetic conservation of the crown-to-stem biomass ratio. Based on phylogenetic relationships, we grouped and matched NFI and biomass observation species into 22 categories. Allometric biomass regression models were developed for each of these 22 species categories, and the models performed successfully (R² = 0.97, root mean square error (RMSE) = 12.9 t.ha-1, relative RMSE = 11.5%). Furthermore, we found that phylogeny-based models performed more effectively than wood density-based models. The results suggest that grouping species based on their phylogenetic relationships is a reliable approach for the development and selection of accurate allometric equations. [ABSTRACT FROM AUTHOR]

The phylogenetic diversity (PD) can be used as a proxy for measures of functional diversity (FD); this relationship between PD and FD is premised on the reasonable assumption that evolutionary diversification has generated trait diversification, which in turn may result in greater niche complementarity. Functional traits have been used in various applications, from assemblage ecology looking at the relationship between functional diversity, environmental filtering, and assemblage structure. We used a trait-based approach, quantifying variations in the leaf-height-seed (LHS) scheme and functional and phylogenetic indices in semi-arid communities from three different habitats (grasslands, shrubland, and mixed habitats). To do so, three functional traits including specific leaf area (SLA), vegetation height (VH), and seed mass (SM) were measured in three habitats. We calculated at the plot scale, community weighted means (CWM) for each trait, species richness, Faith's phylogenetic diversity index (PD), functional richness (Frich), functional and phylogenetic mean pairwise dissimilarities (MPD), and nutrient concentration. The results showed that the first Soil_PCA axis (explaining 37.1% of the total variance) showed a high loading of soil nutrients (N, P, K, OM) and pH, while the second axis (which explained 22.1% 224 of the variance) exhibited a high loading of pH at the top and K at the bottom. Also, the higher soil nutrient concentration and pH were significant and positively related with species and functional richness and Faith's phylogenetic diversity. [ABSTRACT FROM AUTHOR]

As a vital component of biodiversity, phyllosphere bacteria in forest canopy play a critical role in maintaining plant health and influencing the global biogeochemical cycle. There is limited research on the community structure of phyllosphere bacteria in natural forests, which creates a gap in our understanding of whether and/or how phyllosphere bacteria are connected to leaf traits of their host. In this study, we investigated the bacterial diversity and composition of the canopy leaves of six dominant tree species in deciduous broad-leaved forests in northeastern China, using high-throughput sequencing. We then compare the differences in phyllosphere bacterial community structure and functional genes of dominant tree species. Fourteen key leaf functional traits of their host trees were also measured according to standard protocols to investigate the relationships between bacterial community composition and leaf functional traits. Our result suggested that tree species with closer evolutionary distances had similar phyllosphere microbial alpha diversity. The dominant phyla of phyllosphere bacteria were Proteobacteria, Actinobacteria, and Firmicutes. For these six tree species, the functional genes of phyllosphere bacteria were mainly involved in amino acid metabolism and carbohydrate metabolism processes. The redundancy and envfit analysis results showed that the functional traits relating to plant nutrient acquisition and resistance to diseases and pests (such as leaf area, isotope carbon content, and copper content) were the main factors influencing the community structure of phyllosphere bacteria. This study highlights the key role of plant interspecific genetic relationships and plant attributes in shaping phyllosphere bacterial diversity.

Abstract Background Plant nitrogen use efficiency (NUE) is an important ecological indicator that reflects the capacity of a plant to transform nitrogen into production, which is essential for further elucidating plant growth and terrestrial ecosystem productivity. Although there are a growing number of studies that address NUE changes at local scales, the variations of NUE over large spatial scales remain unclear. In this study, we analyzed the geographic patterns of NUE and explored its phylogenic and environmental drivers across 1452 species at 1102 sites in China. Results NUE tended to decrease with latitude (r = − 0.56), whereas it increased with longitude (r = 0.54), and varied widely in different ecosystems and plant life forms. Furthermore, NUE was negatively correlated with plant foliar phosphorus concentration (r = − 0.53), soil pH (r = − 0.10), soil total phosphorus (r = − 0.13) and available phosphorus (r = − 0.05), but positively with the mean annual temperature (r = 0.32), annual precipitation (r = 0.27), and aridity index (r = 0.26). NUE was significantly altered with phylogeny and evolved toward a lower value (r = − 0.28), which may have been due to increasing nitrogen deposition and fixation in biogeochemical evolution. Overall, the combination of foliar phosphorus concentration, phylogeny, climate, and soil properties accounted for 52.7% of the total variations of NUE. In particular, foliar phosphorus concentration was the most important factor, whereas plant evolutionary history was second in contributing to NUE variations. Conclusions Our study emphasizes the pivotal role of plant stoichiometry and phylogeny in nitrogen cycling and suggests incorporating them into earth system models to better understanding plant growth and nitrogen cycling in the context of environmental changes.

Studies investigating the mechanisms underlying the variation of photosynthesis along plant phylogeny and especially during domestication are of great importance, and may provide new insights to further improve crop photosynthesis. In the present study, we compiled a database including 542 sets of data of leaf gas exchange parameters and leaf structural and chemical traits in ferns and fern allies, gymnosperms, non-crop angiosperms, and crops. We found that photosynthesis was dramatically improved from ferns and fern allies to non-crop angiosperms, and further increased in crops. The improvement of photosynthesis during phylogeny and domestication was related to increases in carbon dioxide diffusional capacities and, to a lesser extent, biochemical capacity. Cell wall thickness rather than chloroplast surface area facing intercellular airspaces drives the variation of mesophyll conductance. The variation of the maximum carboxylation rate was not related to leaf nitrogen content. The slope of the relationship between mass-based photosynthesis and nitrogen was lower in crops than in non-crop angiosperms. These findings suggest that the manipulation of cell wall thickness is the most promising approach to further improve crop photosynthesis, and that an increase of leaf nitrogen will be less efficient in improving photosynthesis in crops than in non-crop angiosperms. [ABSTRACT FROM AUTHOR]

The Darwinian shortfall, i.e. the lack of knowledge of phylogenetic relationships, significantly impedes our understanding of evolutionary drivers of global patterns of biodiversity. Spatial bias in the Darwinian shortfall, where phylogenetic knowledge in some regions is more complete than others, could undermine eco‐ and biogeographic inferences. Yet, spatial biases in phylogenetic knowledge for major groups – such as plants – remain poorly understood. Using data for 337 023 species (99.7%) of seed plants (Spermatophyta), we produced a global map of phylogenetic knowledge based on regional data and tested several potential drivers of the observed spatial variation. Regional phylogenetic knowledge was defined as the proportion of the regional seed plant flora represented in GenBank's nucleotide database with phylogenetically relevant data. We used simultaneous autoregressive models to explain variation in phylogenetic knowledge based on three biodiversity variables (species richness, range size and endemism) and six socioeconomic variables representing funding and accessibility. We compared observed patterns and relationships to established patterns of the Wallacean shortfall (the lack of knowledge of species distributions). We found that the Darwinian shortfall is strongly and significantly related to the macroecological distribution of species' range sizes. Small‐ranged species were significantly less likely to have phylogenetic data, leading to a concentration of the Darwinian shortfall in species‐rich, tropical countries where range sizes are small on average. Socioeconomic factors were less important, with significant but quantitatively small effects of accessibility and funding. In conclusion, reducing the Darwinian shortfall and smoothen its spatial bias will require increased efforts to sequence the world's small‐ranged (endemic) species. [ABSTRACT FROM AUTHOR]

Plant phylogeny sometimes predicts interspecific variation in pollinator composition better than floral features, and its predictive value seems to differ among major groups of insect pollinators. Earlier findings suggesting that pollination by Plant phylogeny sometimes predicts interspecific variation in pollinator composition better than gross floral features, and its predictive value seems to differ among major groups of insect pollinators. Pollination by beetles exhibits the strongest phylogenetic signal and the strongest phylogenetic conservatism, which is particularly intriguing given that beetles were probably the pollinators of early angiosperms. We examine in this paper the relationship between plant phylogeny and flower visitation by nitidulid beetles (Coleoptera: Nitidulidae), an old monophyletic group of flower specialists and pollinators of gymnosperms and angiosperms. Using quantitative data on pollinator composition for 251 plant species (belonging to 167 genera in 46 families) from well-preserved Mediterranean montane habitats from southeastern Spain, the following questions were addressed: Is pollination by nitidulids correlated with plant phylogeny in the large species sample studied, and if it does, which are the relative importances of plant phylogeny, floral characteristics, and environmental features as predictors of nitidulid pollination in the plant assemblage studied ? Nitidulids were recorded in flowers of 25% of the plant species considered. Their distribution was significantly related to plant phylogeny, being clustered on certain lineages (Ranunculales, Malvales, Rosales, Asterales) and remarkably absent from others (e.g., Fabales, Lamiales). None of the environmental (habitat type, elevation) or macroscopic floral features considered (perianth type and color, flower mass) predicted nitidulid visitation after statistically accounting for the effect of plant phylogeny. We theorize that nitidulid beetles use characters of plants that track plant phylogeny at least as deep as the early radiation of the eudicots, imaginably characters such as the chemical signatures of pollen.

Background: Stevia rebaudiana is a perennial semi-shrub plant which comes from the Asteraceae family, with an approximate height of around 30 cm. The leaves of Stevia are small, elliptic, and serrated, measuring 2 to 4 cm long. It has been used commercially as a natural sweetener in Japan due to the steviol glycosides (SGs) content in the leaves. The stevioside content is 300 times sweeter than sucrose. It has non-nutritive values, which is good for diabetes and obesity patients. The SGs content in Stevia can be improved by increasing light exposure (long day condition). The Senescence Associated Gene 21 (SAG21) gene is one of the interesting genes to be identified and discovered in Stevia. Aims and Objectives: The objectives of this research were to identify and characterise the SAG21 gene using in silico analysis. Materials and Methods: These data analyses were obtained using ExPASy, blastP, InterPro, Pfam, TMHMM, ProtParam, and MEGA software. Results: Putative SAG21 MS007 showed high homology with the SAG21 gene in Helianthus annuus with a high percentage of identity, which was 80.90%. It also confirmed that the putative SAG21 MS007 protein contained the domain LEA_3. It was usually found in land plants and accumulated heavily in the last stage of seed formation. ProtParam analysis found that the putative SAG21 protein was a stable globular protein. TMHMM analysis predicted that this protein is a hydrophilic protein and is located outside of transmembrane helices. Conclusion: The phylogenetic tree showed that the putative SAG21 MS007 gene had a close relationship with the SAG21 protein of H. annuus, with a bootstrap value of more than 70%. [ABSTRACT FROM AUTHOR]

Litter decomposition is an important process in ecosystem and despite recent research elucidating the significant influence of plant phylogeny on plant-associated microbial communities, it remains uncertain whether a parallel correlation exists between plant phylogeny and the community of decomposers residing in forest litter. In this study, we conducted a controlled litterbag experiment using leaf litter from ten distinct tree species in a central subtropical forest ecosystem in a region characterized by subtropical humid monsoon climate in China. The litterbags were placed in situ using a random experimental design and were collected after 12 months of incubation. Then, the litter chemical properties, microbial community composition and activities of enzyme related to the decomposition of organic carbon (C) and nitrogen (N) were assessed. Across all ten tree species, Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria were identified as the predominant bacterial classes, while the primary fungal classes were Dothideomycetes, Sordariomycetes and Eurotiomycetes. Mantel test revealed significant correlations between litter chemical component and microbial communities, as well as enzyme activities linked to N and C metabolism. However, after controlling for plant phylogenetic distance in partial Mantel test, the relationships between litter chemical component and microbial community structure and enzyme activities were not significant. Random forest and structural equation modeling indicated that plant phylogenetic distance exerted a more substantial influence than litter chemical components on microbial communities and enzyme activities associated with the decomposition of leaf litter. In summary, plant phylogenic divergence was found to be a more influential predictor of enzyme activity variations than microbial communities and litter traits, which were commonly considered reliable indicators of litter decomposition and ecosystem function, thereby highlighting the previously underestimated significance of plant phylogeny in shaping litter microbial communities and enzyme activities associated with degradation processes in forest litter. [ABSTRACT FROM AUTHOR]

Background: Plant nitrogen use efficiency (NUE) is an important ecological indicator that reflects the capacity of a plant to transform nitrogen into production, which is essential for further elucidating plant growth and terrestrial ecosystem productivity. Although there are a growing number of studies that address NUE changes at local scales, the variations of NUE over large spatial scales remain unclear. In this study, we analyzed the geographic patterns of NUE and explored its phylogenic and environmental drivers across 1452 species at 1102 sites in China. Results: NUE tended to decrease with latitude (r = − 0.56), whereas it increased with longitude (r = 0.54), and varied widely in different ecosystems and plant life forms. Furthermore, NUE was negatively correlated with plant foliar phosphorus concentration (r = − 0.53), soil pH (r = − 0.10), soil total phosphorus (r = − 0.13) and available phosphorus (r = − 0.05), but positively with the mean annual temperature (r = 0.32), annual precipitation (r = 0.27), and aridity index (r = 0.26). NUE was significantly altered with phylogeny and evolved toward a lower value (r = − 0.28), which may have been due to increasing nitrogen deposition and fixation in biogeochemical evolution. Overall, the combination of foliar phosphorus concentration, phylogeny, climate, and soil properties accounted for 52.7% of the total variations of NUE. In particular, foliar phosphorus concentration was the most important factor, whereas plant evolutionary history was second in contributing to NUE variations. Conclusions: Our study emphasizes the pivotal role of plant stoichiometry and phylogeny in nitrogen cycling and suggests incorporating them into earth system models to better understanding plant growth and nitrogen cycling in the context of environmental changes. [ABSTRACT FROM AUTHOR]

In February 2020, stem cankers and necrotic lesions were observed on Fatsia japonica in the Khuzestan province, Iran. Four identical isolates were obtained from symptomatic tissue and identified as Botryosphaeria dothidea based on morphology and phylogenetic analysis of the ITS and tef1 gene regions. The pathogenicity of the isolates was confirmed by inoculating healthy shrubs of F. japonica. [ABSTRACT FROM AUTHOR]

Aim: There have been numerous studies of forest‐soil microbial biogeography, but an integrated view of edaphic factors, plant, climatic factors, and geographic distance in determining the variation of bacterial community and assembly processes remains unclear at large spatial scales. Here, we analysed the factors affecting the biogeographic pattern and assembly processes of soil bacterial communities under 58 tree species in five natural mountain forests. Location: Eastern China. Major taxa studied: Bacterial communities. Methods: Hierarchical partitioning analysis and distance decay models were performed to evaluate the relative contributions of plant phylogeny, environmental, and spatial variables to the composition of bacterial communities. We applied the nearest taxon index (NTI), β‐nearest taxon index (βNTI), and the modified Raup–Crick metric to reveal the mechanisms of bacterial assembly processes. Results: We found that plant phylogeny accounted for a significant, but minor, fraction (0.7%) of the variation in composition of bacterial communities. In contrast, soil pH was the primary determinant of bacterial diversity and community composition, independently explaining 68.6 and 69.9% of the variation, respectively. Based on the NTI analysis, bacterial community assembly was more phylogenetically clustered with increasing soil pH. Variable selection was the predominant process explaining bacterial community assembly when differences in soil pH were ≥ 0.83, whereas homogenizing dispersal dominated when differences in soil pH were <0.83. However, there was no significant relationship between plant phylogenetic distance and βNTI. Main conclusions: Our findings provide strong evidence that soil pH predominantly determines bacterial distribution and mediates the relative impact of stochasticity and determinism in soil bacterial community assembly. This suggests that climate‐change associated forest soil acidification could have a dramatic impact on soil bacterial diversity, composition, and function. [ABSTRACT FROM AUTHOR]

Societal Impact Statement: Humans rely on plants in their environment for food and medicine. Understanding how humans select plant species will help us anticipate what plant species will be valuable for society in the future. However, previous approaches to study the drivers of plant selection have been criticized. We explored medicinal plant selection using a refined methodology and corroborate that humans select plant species for medicine in a non‐random way. Furthermore, we found that selection of specific plant organs across similar species is also non‐random. Improved understanding of medicinal plant selection can help identify new medicinal plants and the particular organs of plant species that are most likely to contain bioactive compounds to help improve human health and well‐being. Summary: Ethnobotany, the science of human–plant interactions, has for long focused on documenting the traditional knowledge that humans have developed and accumulated over centuries toward plant uses. However, how such knowledge is constructed remains poorly understood and some of the methodological approaches developed for this purpose have been criticized.Here, we combine negative binomial models and phylogenetic comparative methods to test whether selection of medicinal plant species and organs by local people are non‐random using data from Benin, a country in West Africa with roughly 3,000 plant species.We found evidence for taxonomic and phylogenetic non‐random selection of medicinal plants: some taxa are preferentially used for medicine. Our analysis uncovers that plant organs are also non‐randomly selected for medicine. Beyond plant taxonomy, similar plant organs of closely related species tended to be used for similar treatments because these organs are likely to have similar secondary chemistry. Such non‐random organ selection was more apparent for certain plant organs such as roots, bark, and leaves, which are predicted to be more vital for population fitness and species persistence.Collectively, our study suggests that the emerging non‐random pattern of medicinal plant selection may be a consequence of heterogeneous within‐plant distribution of secondary chemistry across different organs proportionally to their importance to plant fitness as predicted by the optimal defense theory. [ABSTRACT FROM AUTHOR]

Members of the family Tylenchidae are highly abundant in soil habitats, including agricultural settings, where they play key ecological roles. In the present study, we identified three Tylenchidae species, namely Basiria bhabi, Coslenchus acceptus, and Filenchus vulgaris, using integrative taxonomy. The detailed morphological and morphometric characteristics, distribution, and host associations of each species were also discussed. Phylogenetic analyses of these populations with other Tylenchidae nematodes indicated the presence of divergent lineages in Filenchus and Basiria, whereas Coslenchus appeared to be a monophyletic genus. Herein, we aim to grow awareness about this common but least studied group of nematodes. The species reported in this study are new records for Canada, revealing that the identified nematode diversity in our cultivated areas is relatively underrepresented. Our analyses also provided greater taxonomic resolution and captured rare taxa that might have been missed or misidentified in prior nematode inventory surveys. These findings will add to our understanding of the nematofauna of southern Alberta, thereby providing a more complete picture of existing nematode diversity present in the fields of this highly cultivated region. [ABSTRACT FROM AUTHOR]

The tree tomato (Solanum betaceum Cav.) is an underutilized fruit crop native to the Andean region and phylogenetically related to the tomato and potato. Tree tomato fruits have a high amount of nutrients and bioactive compounds. However, so far there are no studies at the genome or transcriptome level for this species. We performed a de novo assembly and transcriptome annotation for purple-fruited (A21) and an orange-fruited (A23) accessions. A total of 174,252 (A21) and 194,417 (A23) transcripts were assembled with an average length of 851 and 849 bp. A total of 34,636 (A21) and 36,224 (A23) transcripts showed a significant similarity to known proteins. Among the annotated unigenes, 22,096 (A21) and 23,095 (A23) were assigned to the Gene Ontology (GO) term and 14,035 (A21) and 14,540 (A23) were found to have Clusters of Orthologous Group (COG) term classifications. Furthermore, 22,096 (A21) and 23,095 (A23) transcripts were assigned to 155 and 161 (A23) KEGG pathways. The carotenoid biosynthetic process GO terms were significantly enriched in the purple-fruited accession A21. Finally, 68,647 intraspecific single-nucleotide variations (SNVs) and almost 2 million interspecific SNVs were identified. The results of this study provide a wealth of genomic data for the genetic improvement of the tree tomato. [ABSTRACT FROM AUTHOR]

Auxin response factors (ARFs) are a transcription factor family that regulates the expression of auxin phase-responsive genes. Here, we performed a genome-wide investigation of the tetraploid blueberry (Vaccinium corymbosum cv. ‘Draper’) genome sequence. Physical and chemical properties, phylogenetic evolution, gene structure, conservative motifs, chromosome location, and cis-acting elements of blueberry ARF genes were comprehensively evaluated. A total of 70 blueberry ARF genes (VcARF) were found in its genome, which could be divided into six subfamilies. VcARF genes were unevenly distributed on 40 chromosomes and were observed to encode protein sequences ranging in length from 162 to 1117 amino acids. Their exon numbers range from 2 to 22. VcARF promoter regions contain multiple functional domains associated with light signaling, aerobic metabolism, plant hormones, stress, and cell cycle regulation. More family members of VcARF genes were discovered in blueberry than in previously studied plants, likely because of the occurrence of wholegenome duplication and/or tandem duplication. VcARF expression patterns were analyzed at different stages of fruit development, and VcARF3, VcARF4, VcARF14, VcARF37, and VcARF52 were observed to play important roles. VcARF3 and VcARF4 appeared to function as repressors, while VcARF14 acted as an essential factor in fruit firmness differences between firm and soft flesh cultivars. [ABSTRACT FROM AUTHOR]

The roles of natural and anthropogenic factors in contributing to the organization of biodiversity at large and small scales have long been challenging to disentangle, and doing so has never been attempted for the island province of Hainan in China based on patterns of taxonomic and phylogenetic diversity. Therefore, in this study, we evaluated the taxonomic and phylogenetic diversity of endemic plants on the island as a function of anthropogenic and natural variables based on non-metric multi-dimensional scaling (NMDS) ordination and generated generalized linear models (GLMs). We found that the highest phylogenetic diversity (1006) and the lowest mean phylogenetic distance (515.5) was in the provincial capital, Haikou. The NMDS analyses indicated that taxonomic diversity was significantly correlated with industrial revenue (p = 0.006) and population (p = 0.004). Furthermore, most phylogenetic diversity indices were strongly correlated with population and agricultural revenue, while the sampled natural environmental variables were not significantly correlated with plant diversity indices. These findings indicate that anthropogenic factors are the main present-day driving forces of plant diversity in Hainan, though we did detect a significant latitudinal diversity gradient of richness that likely reflects the historical roles of natural environmental factors in the organization of biodiversity on the island. Overall, our results are alarming for biodiversity of the island and indicate that conservation and sustainable use of endemic plant species must be made a critical priority. [ABSTRACT FROM AUTHOR]

In the tropics, antagonistic seed predation networks may have different properties than mutualistic pollination and seed dispersal networks, but the former have been considerably less studied. We tested whether the structure of antagonistic tripartite networks composed of host plants, insects developing within seeds and fruits, and their insect parasitoids could be predicted from plant phylogenetic distance and plant traits. We considered subsets of the networks ('subnetworks') at three rainforest locations (Panama, Thailand, Papua New Guinea), based on insect families, plant families or plant functional groups. We recorded 3197 interactions and observed a low percentage of realized interactions, especially in Panama, where insect host specificity was higher than in Thailand or New Guinea. Several factors may explain this, including insect faunal composition, incidence of dry fruits, high fruit production and high occurrence of Fabaceae at the Panamanian site. Host specificity was greater among seed‐eaters than pulp‐eaters and for insects feeding on dry fruits as opposed to insects feeding on fleshy fruits. Plant species richness within plant families did not influence insect host specificity, but site characteristics may be important in this regard. Most subnetworks were extremely specialized, such as those including Tortricidae and Bruchinae in Panama. Plant phylogenetic distance, plant basal area and plant traits (fruit length, number of seeds per fruit) had important effects on several network statistics in regressions weighted by sampling effort. A path analysis revealed a weak direct influence of plant phylogenetic distance on parasitoid richness, indicating limited support for the 'nasty host hypothesis'. Our study emphasizes the duality between seed dispersal and seed predation networks in the tropics, as key plant species differ and host specificity tends to be low in the former and higher in the latter. This underlines the need to study both types of networks for sound practices of forest regeneration and conservation. [ABSTRACT FROM AUTHOR]

Hawthorns (Crataegus L.) are one of the most important processing and table fruits in China, due to their medicinal properties and health benefits. However, the interspecific relationships and evolution history of cultivated Crataegus in China remain unclear. Our previously published data showed C. bretschneideri may be derived from the hybridization of C. pinnatifida with C. maximowiczii, and that introgression occurs between C. hupehensis, C. pinnatifida, and C. pinnatifida var. major. In the present study, chloroplast sequences were used to further elucidate the phylogenetic relationships of cultivated Crataegus native to China. The chloroplast genomes of three cultivated species and one related species of Crataegus were sequenced for comparative and phylogenetic analyses. The four chloroplast genomes of Crataegus exhibited typical quadripartite structures and ranged from 159,607 bp (C. bretschneideri) to 159,875 bp (C. maximowiczii) in length. The plastomes of the four species contained 113 genes consisting of 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Six hypervariable regions (ndhC-trnV(UAC)-trnM(CAU), ndhA, atpH-atpI, ndhF, trnR(UCU)-atpA, and ndhF-rpl32), 196 repeats, and a total of 386 simple sequence repeats were detected as potential variability makers for species identification and population genetic studies. In the phylogenomic analyses, we also compared the entire chloroplast genomes of three published Crataegus species: C. hupehensis (MW201730.1), C. pinnatifida (MN102356.1), and C. marshallii (MK920293.1). Our phylogenetic analyses grouped the seven Crataegus taxa into two main clusters. One cluster included C. bretschneideri, C. maximowiczii, and C. marshallii, whereas the other included C. hupehensis, C. pinnatifida, and C. pinnatifida var. major. Taken together, our findings indicate that C. maximowiczii is the maternal origin of C. bretschneideri. This work provides further evidence of introgression between C. hupehensis, C. pinnatifida, and C. pinnatifida var. major, and suggests that C. pinnatifida var. major might have been artificially selected and domesticated from hybrid populations, rather than evolved from C. pinnatifida. [ABSTRACT FROM AUTHOR]

As the number of non‐native invasive species in the world is increasing, there is a pressing need to understand the effects of invasive species on recipient biotic communities to improve our ability to migrate or relieve their potential negative effects on biodiversity and ecosystem functions. Plant invasions have been shown to impose great threats to aboveground biotic communities; however, invasive impacts on soil biota remain ambiguous, partially because of the paucity of studies with a large number of species across biogeographic gradients. Here, we characterized rhizosphere fungal communities of 53 native and invasive plants spanning approximately 1800 km in China, as well as eight pairs of phylogenetically related native versus invasive plants in a greenhouse experiment. The results of both field survey and greenhouse experiment showed that rhizosphere fungal composition was primarily predicted by plant phylogeny (e.g. family and species), and plant geographic origin (native vs. invasive) and abiotic factors had much smaller effects. We detected no differences in the number and relative abundance of total and family/species‐specific OTUs (i.e. overall, pathogens and mutualists) associated with these native and invasive plants on average, suggesting novel co‐evolution between native soil fungi and these invasive plants. These results suggest that non‐native plant invasions had only a weak impact on soil fungi, partially due to stronger controls of plant evolution on rhizosphere fungi and adaptation of native fungi to these invasive species. Interestingly, rhizosphere fungal composition was more variable between invasive plants than between native plants at middle latitudes, potentially creating spatial variations in plant–soil interactions and, in turn, invasion dynamics. These novel findings highlight the importance of integrating phylogenetic and biogeographical approaches to explore invasive effects on native biota. [ABSTRACT FROM AUTHOR]

The E3 ubiquitin ligases have been known to intrigue many researchers to date, due to their heterogenicity and substrate mediation for ubiquitin transfer to the protein. HECT (Homologous to the E6-AP Carboxyl Terminus) E3 ligases are spatially and temporally regulated for substrate specificity, E2 ubiquitin-conjugating enzyme interaction, and chain specificity during ubiquitylation. However, the role of the HECT E3 ubiquitin ligase in plant development and stress responses was rarely explored. We have conducted an in-silico genome-wide analysis to identify and predict the structural and functional aspects of HECT E3 ligase members in tomato. Fourteen members of HECT E3 ligases were identified and analyzed for the physicochemical parameters, phylogenetic relations, structural organizations, tissue-specific gene expression patterns, and protein interaction networks. Our comprehensive analysis revealed the HECT domain conservation throughout the gene family, close evolutionary relationship with different plant species, and active involvement of HECT E3 ubiquitin ligases in tomato plant development and stress responses. We speculate an indispensable biological significance of the HECT gene family through extensive participation in several plant cellular and molecular pathways. [ABSTRACT FROM AUTHOR]

During March 2016, leaf blight, followed by death, was observed on yard-long bean plants (Vigna unguiculata subsp. sesquipedalis) in Brazil. Based on morphological characteristics and phylogenetic analysis, the pathogen was identified as Rhizoctonia solani AG-1 IA. Koch's postulates were fulfilled. All accessions studied were classified as susceptible. This is the first report of Rhizoctonia solani AG1-IA infecting yard-long bean. [ABSTRACT FROM AUTHOR]

Gleditsia sinensis is an endemic species widely distributed in China with high economic and medicinal value. To explore the genomic evolution and phylogenetic relationships of G. sinensis, the complete mitochondrial (mt) genome of G. sinensis was sequenced and assembled, which was firstly reported in Gleditsia. The mt genome was circular and 594,121 bp in length, including 37 protein-coding genes (PCGs), 19 transfer RNA (tRNA) genes and 3 ribosomal RNA (rRNA) genes. The overall base composition of the G. sinensis mt genome was 27.4% for A, 27.4% for T, 22.6% for G, 22.7% for C. The comparative analysis of PCGs in Fabaceae species showed that most of the ribosomal protein genes and succinate dehydrogenase genes were lost. In addition, we found that the rps4 gene was only lost in G. sinensis, whereas it was retained in other Fabaceae species. The phylogenetic analysis based on shared PCGs of 24 species (22 Fabaceae and 2 Solanaceae) showed that G. sinensis is evolutionarily closer to Senna species. In general, this research will provide valuable information for the evolution of G. sinensis and provide insight into the phylogenetic relationships within the family Fabaceae. [ABSTRACT FROM AUTHOR]

Plants belonging to family Paeoniaceae are not only economically important ornamental plants but also medicinal plants used as an important source of traditional Chinese medicine. Owing to the complex network evolution and polyploidy evolution of this family, its systematics and taxonomy are controversial and require a detailed investigation. In this study, three complete chloroplast genomes of sect. Paeonia, one of the sections of Paeonia, were sequenced and then analysed together with 16 other published chloroplast genomes of Paeoniaceae species. The total lengths of the chloroplast genomes of these species were 152,153–154,405 bp. A total of 82–87 protein-coding genes, 31–40 tRNA genes and 8 rRNA genes were annotated. Bioinformatics analysis revealed 61–74 simple sequence repeats (SSRs) in the chloroplast genomes, most of which have A/T base preference. Codon usage analysis showed that A/U-ending codons were more positive than C/G-ending codons, and a slight bias in codon usage was observed in these species. A comparative analysis of these 19 species of Paeoniaceae was then conducted. Fourteen highly variable regions were selected for species relationship study. Phylogenetic analysis revealed that the species of sect. Paeonia gathered in one branch and then divided into different small branches. P. lactiflora, P. anomala, P. anomala subsp. veitchii and P. mairei clustered together. P. intermedia was related to P. obovata and P. obovata subsp. willmottiae. P. emodi was the sister to all other species in the sect. Paeonia. [ABSTRACT FROM AUTHOR]

The genus Hoya is highly diverse and many of its species are popular ornamental plants. However, the relationships between Hoya and related genera (the Hoya group) are not fully resolved. In this study, we report 20 newly sequenced plastomes of species in the Hoya group. The complete plastomes vary in length from 175,405 to 178,525 bp while the LSCs vary from 90,248 to 92,364 bp and the complete SSCs vary from 2,285 to 2,304 bp, making the SSC in the Hoya group one of the shortest known in the angiosperms. The plastome structure in the Hoya group is characterised by a massive increase in the size of the inverted repeats as compared to the outgroups. In all ingroup species, the IR/SSC boundary moved from ycf1 to ndhF while this was not observed in outgroup taxa, making it a synapomorphy for the Hoya group. We have also assembled the mitogenome of Hoya lithophytica, which, at 718,734 bp, is the longest reported in the family. The phylogenetic analysis using exons from 42 taxa in the Hoya group and three outgoups confirms that the earliest divergent genus in the Hoya group is Papuahoya, followed by Dischidia. The relationship between Dischidia and the clade which includes all Hoya and Oreosparte taxa, is not fully supported. Oreosparte is nested in Hoya making it paraphyletic unless Clemensiella is recognised as a separate genus. [ABSTRACT FROM AUTHOR]