Evolution and Expression Patterns of the Fructose 1,6-Bisphosptase Gene Family in a Miracle Tree (Neolamarckia cadamba).

Neolamarckia cadamba (N. cadamba) is a fast-growing tree species with tremendous economic and ecological value; the study of the key genes regulating photosynthesis and sugar accumulation is very important for the breeding of N. cadamba. Fructose 1,6-bisphosptase (FBP) gene has been found to play a key role in plant photosynthesis, sugar accumulation and other growth processes. However, no systemic analysis of FBPs has been reported in N. cadamba. A total of six FBP genes were identifed and cloned based on the N. cadamba genome, and these FBP genes were sorted into four groups. The characteristics of the NcFBP gene family were analyzed such as phylogenetic relationships, gene structures, conserved motifs, and expression patterns. A cis-acting element related to circadian control was first found in the promoter region of FBP gene. Phylogenetic and quantitative real-time PCR analyses showed that NcFBP5 and NcFBP6 may be chloroplast type 1 FBP and cytoplasmic FBP, respectively. FBP proteins from N. cadamba and 22 other plant species were used for phylogenetic analyses, indicating that FBP family may have expanded during the evolution of algae to mosses and differentiated cpFBPase1 proteins in mosses. This work analyzes the internal relationship between the evolution and expression of the six NcFBPs, providing a scientific basis for the evolutionary pattern of plant FBPs, and promoting the functional studies of FBP genes.

How Do Landscape Heterogeneity, Community Structure, and Topographical Factors Contribute to the Plant Diversity of Urban Remnant Vegetation at Different Scales?

In highly fragmented urban areas, plant diversity of remnant vegetation may depend not only on community structure and topographical factors, but also on landscape heterogeneity. Different buffer radius settings can affect the relative importance of these factors to plant diversity. The aim of this study was to examine the relative importance of landscape heterogeneity, community structure, and topographical factors on plant diversity under different buffer radii in biodiversity hotspots. We established 48 plots of remnant vegetation in Guangzhou city, one of the biodiversity hotspots. A buffer radius of 500 m, 1000 m, and 2000 m was established around the center of each sample plot, and 17 landscape heterogeneity indices in each buffer were calculated by FRAGSTATS 4.2 software. Combined with the community structure and topographical factors, the impact factors of plant diversity under different buffer radii were analyzed by multiple regression analysis. We found the following: (1) The combined explanatory power of the three factors accounted for 43% of the species diversity indices and 62% of the richness index at its peak. The three impact factors rarely act independently and usually create comprehensive cumulative effects. (2) Scale does matter in urban landscape studies. At a 500 m buffer radius, community structure combined with road disturbance indices was strongly related to diversity indices in herb and shrub layers. The stand age was negatively correlated with the tree-layer richness index. As the scale increased, the diversity indices and richness index in the three layers decreased or increased under the influence of comprehensive factors. (3) The richness index in the herb layer was more responsive to impact factors than other biodiversity indices. Except for the herb layer, the interpretation of landscape heterogeneity for each plant diversity index was more stable than that for the other two factors. Road disturbance indices, combined with the other six landscape pattern metrics, can well indicate species diversity and richness. We suggest that the vegetation area of remnant patches within a radius of 500-2000 m should be appropriately increased to protect plant diversity, and the negative effects of road disturbance should also be considered.

Climate-Driven Adaptive Differentiation in Melia azedarach: Evidence from a Common Garden Experiment.

Studies of local adaptation in populations of chinaberry (Melia azedarach L.) are important for clarifying patterns in the population differentiation of this species across its natural range. M. azedarach is an economically important timber species, and its phenotype is highly variable across its range in China. Here, we collected M. azedarach seeds from 31 populations across its range and conducted a common garden experiment. We studied patterns of genetic differentiation among populations using molecular markers (simple sequence repeats) and data on phenotypic variation in six traits collected over five years. Our sampled populations could be subdivided into two groups based on genetic analyses, as well as patterns of isolation by distance and isolation by environment. Significant differentiation in growth traits was observed among provenances and families within provenances. Geographic distance was significantly correlated with the quantitative genetic differentiation (QST) in height (HEIT) and crown breadth. Climate factors were significantly correlated with the QST for each trait. A total of 23 climatic factors were examined. There was a significant effect of temperature on all traits, and minimum relative humidity had a significant effect on the survival rate over four years. By comparing the neutral genetic differentiation (FST) with the QST, the mode of selection acting on survival rate varied, whereas HEIT and the straightness of the main trunk were subject to the same mode of selection. The variation in survival rate was consistent with the variation in genetic differentiation among populations, which was indicative of local adaptation. Overall, our findings provide new insights into the responses of the phenological traits of M. azedarach to changes in the climate conditions of China.

Transcriptome profiling of Toona ciliata young stems in response to Hypsipyla robusta Moore.

Toona ciliata is a traditional woody plant that can be used as a medicinal material in China. The extracts of its roots, stems, leaves, and flowers all have a wide range of bioactive compounds. However, T. ciliata has been facing an unresolved pest problem caused by Hypsipyla robusta Moore (HRM), which seriously affects its growth and development. In this study, the expression level of TcMYB3 gene reached the maximum (28-fold) at 12 h and transcriptome sequencing of young stems eaten by HRM for 0, 3, 12, and 21 h were performed. A large number of differentially expressed genes (DEGs) were identified including jointly up-regulated genes (263) and down-regulated genes (378). JA synthesis and signaling transduction, terpene biosynthesis, and MAPKs signaling pathway were analyzed in depth and found that TcOPR3, TcJAR1, TcJAZs, and TcTPS9 genes possessed anti-insect potential. Moreover, MYB and ERF transcription factor (TF) families were significantly strengthened to the point that they may participate in induced defense mechanisms in T. ciliata. These data not only provide insights into the molecular mechanisms in resistance of T. ciliata to HRM but also helps to explore the new biocontrol strategies against insects in eco-friendly woody plants.

Efficient In Vitro Sterilization and Propagation from Stem Segment Explants of Cnidoscolus aconitifolius (Mill.) I.M. Johnst, a Multipurpose Woody Plant.

Cnidoscolus aconitifolius (Mill.) I.M. Johnst is a multipurpose woody plant. In this study, an in vitro efficient propagation system of stem segment explants derived from field-grown C. aconitifolius plants was established for the first time. The sterilization effect, axillary bud initiation, and proliferation efficiency of stem segments were evaluated. The results showed that the sterilization time of 0.1% mercuric chloride, the concentration of Plant Preservative Mixture (PPM), the pretreatment method, and the sampling season had significant effects on the sterilization of stem segments (p < 0.05). The type of medium and plant growth regulators (PGRs) affected the initiation of axillary buds, and the proliferation efficiency was significantly affected by PGRs. The results showed that the best sterilization method for stem segment explants was as follows: a pretreatment by rinsing with running water for 120 min, soaking in 75% ethanol for 50 s, soaking in 0.1% mercuric chloride for 10 min, and medium supplemented with 3 mL/L PPM. When inoculated on the medium in spring, the contamination rate was as low as 25.56%. The optimal initiation medium for axillary buds in stem segments was half-strength Murashige and Skoog (1/2 MS) medium supplemented with 0.5 mg/L 6-benzyladenine (6-BA). The induction rate was as high as 93.33%, and the mean length of axillary buds was 2.47 cm. The optimal proliferation medium was 1/2 MS medium supplemented with 4.0 mg/L 6-BA and 0.2 mg/L indole-3-butyric acid (IBA). The induction rate was up to 80.00%, the total proliferation coefficient was 4.56, and the net proliferation coefficient was 5.69. The 1/2 MS medium supplemented with 0.1 mg/L 6-BA and 1.5 mg/L indole-3-acetic acid (IAA) was most conducive to the elongation of the adventitious shoot, and the adventitious shoot of approximately 1 cm reached 1.93 cm after culturing for 14 days. The best medium for adventitious shoot rooting was 1/2 MS medium supplemented with 0.1 mg/L α-naphthalene acetic acid (NAA), the highest rooting rate was 82.00%, and the survival rate of transplanting was over 90%.

An Efficient Propagation System through Root Cuttings of an Ecological and Economic Value Plant-Broussonetia papyrifera (L.) L'Hér. ex Vent.

Broussonetia papyrifera (L.) L'Hér. ex Vent. has considerable economic and ecological value and a long history of use in China. In this paper, root cuttings were used as the material to establish an efficient vegetative propagation of B. papyrifera. The results revealed that root segments with a diameter of 1.5~2.0 cm and a length of 20~30 cm were most suitable for shoot regeneration, as these segments had the highest adventitious shoot induction rates (93.3%), strongest adventitious shoots, and highest multiplication coefficients (7.07). With regard to the methods used for root burial, a horizontal burial at a depth of 1~3 cm yielded the best results, in this case, the adventitious shoot induction rate can reach 86.7%. The best substrate combination was perlite: peat: coconut chaff = 1:1:1 (v/v/v), wherein the adventitious shoot induction rate can reach 75.6%. The best sterilization method was mixing soil with carbendazim and soaking the root sections in carbendazim for 30 min, wherein the adventitious shoot induction rate can reach 77.8%. Adding 0.2 mg/L naphthaleneacetic acid (NAA) to 1/4 Hoagland nutrient solution significantly improved the rooting rate of adventitious shoots to 82.2%, and the survival rate of the acclimatized plants was more than 90.0%.

Chromosome-level assembly of the Neolamarckia cadamba genome provides insights into the evolution of cadambine biosynthesis.

Neolamarckia cadamba (Roxb.), a close relative of Coffea canephora and Ophiorrhiza pumila, is an important traditional medicine in Southeast Asia. Three major glycosidic monoterpenoid indole alkaloids (MIAs), cadambine and its derivatives 3ß-isodihydrocadambine and 3ß-dihydrocadambine, accumulate in the bark and leaves, and exhibit antimalarial, antiproliferative, antioxidant, anticancer and anti-inflammatory activities. Here, we report a chromosome-scale N. cadamba genome, with 744.5 Mb assembled into 22 pseudochromosomes with contig N50 and scaffold N50 of 824.14 Kb and 29.20 Mb, respectively. Comparative genomic analysis of N. cadamba with Co. canephora revealed that N. cadamba underwent a relatively recent whole-genome duplication (WGD) event after diverging from Co. canephora, which contributed to the evolution of the MIA biosynthetic pathway. We determined the key intermediates of the cadambine biosynthetic pathway and further showed that NcSTR1 catalyzed the synthesis of strictosidine in N. cadamba. A new component, epoxystrictosidine (C27H34N2O10, m/z 547.2285), was identified in the cadambine biosynthetic pathway. Combining genome-wide association study (GWAS), population analysis, multi-omics analysis and metabolic gene cluster prediction, this study will shed light on the evolution of MIA biosynthetic pathway genes. This N. cadamba reference sequence will accelerate the understanding of the evolutionary history of specific metabolic pathways and facilitate the development of tools for enhancing bioactive productivity by metabolic engineering in microbes or by molecular breeding in plants.

In the Subtropical Monsoon Climate High-Density City, What Features of the Neighborhood Environment Matter Most for Public Health?

Urbanization and climate change have been rapidly occurring globally. Evidence-based healthy city development is required to improve living quality and mitigate the adverse impact of the outdoor neighborhood environment on public health. Taking Guangzhou as an example to explore the association of neighborhood environment and public health and preferably to offer some implications for better future city development, we measured ten environmental factors (temperature (T), wind-chill index (WCI), thermal stress index (HSI), relative humidity (RH), average wind speed (AWS), negative oxygen ions (NOI), PM2.5, luminous flux (LF), and illuminance (I)) in four seasons in four typical neighborhoods, and the SF-36 health scale was employed to assess the physical and mental health of neighborhood residents in nine subscales (health transition(HT), physiological functions (PF), general health status (GH), physical pain (BP), physiological functions (RP), energy vitality (VT), mental health (MH), social function (SF), and emotional functions (RE)). The linear mixed model was used in an analysis of variance. We ranked the different environmental factors in relation to aspects of health and weighted them accordingly. Generally, the thermal environment had the greatest impact on both physical and mental health and the atmospheric environment and wind environment had the least impact on physical health and mental health, respectively. In addition, the physical health of the resident was more greatly affected by the environment than mental health. According to the results, we make a number of strategic suggestions for the renewal of the outdoor neighborhood environment in subtropical monsoon climate high-density cities and provide a theoretical basis for improving public health through landscape architecture at the neighborhood scale.

Selection and validation of reference genes for measuring gene expression in Toona ciliata under different experimental conditions by quantitative real-time PCR analysis.

BACKGROUND: Before studying gene expression of different organisms, it is important to determine the best reference gene. At present, the most accurate method of detecting gene expression is quantitative real-time PCR (RT-qPCR). With this method, reference genes that are stable in different biological systems and under different conditions can be obtained. Toona ciliata Roem (T. ciliata). is a valuable and fast-growing timber specie. In this study, 20 reference genes were identified using RT-qPCR, as a primary prerequisite for future gene expression analysis. Four different methods, geNorm, NormFinder, BestKeeper, and RankAggreg were used to evaluate the expression stability of the 20 candidate reference genes in various tissues under different conditions. RESULTS: The experimental results showed that TUB-α was the most stably expressed reference gene across all samples and UBC17 was the most stable in leaves and young stems under Hypsipyla robusta (H. robusta) and methyl jasmonate (MeJA) treatments. In addition, PP2C59 and UBC5B were the best-performing genes in leaves under H. robusta treatment, while HIS1 and ACT7 were the best reference genes in young stems. The two best reference genes were 60S-18 and TUB-α after treatment at 4 °C. The expression of HIS6 and MUB1 was the most stable under PEG6000 treatment. The accuracy of the selected reference genes was verified using the transcription factor MYB3 (TcMYB3) gene. CONCLUSIONS: This is the first report to verify the best reference genes for normalizing gene expression in T. ciliata under different conditions, which will facilitate future elucidation of gene regulations in this species.

De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism.

BACKGROUND: Zanthoxylum armatum (Z. armatum) is a highly economically important tree that presents a special numbing taste. However, the underlying regulatory mechanism of the numbing taste remains poorly understood. Thus, the elucidation of the key genes associated with numbing taste biosynthesis pathways is critical for providing genetic information on Z. armatumand the breeding of high-quality germplasms of this species. RESULTS: Here, de novo transcriptome assembly was performed for the five major organs of Z. armatum, including the roots, stems, leaf buds, mature leaves and fruits. A total of 111,318 unigenes were generated with an average length of 1014 bp. Additionally, a large number of SSRs were obtained to improve our understanding of the phylogeny and genetics of Z. armatum. The organ-specific unigenes of the five major samples were screened and annotated via GO and KEGG enrichment analysis. A total of 53 and 34 unigenes that were exclusively upregulated in fruit samples were identified as candidate unigenes for terpenoid biosynthesis or fatty acid biosynthesis, elongation and degradation pathways, respectively. Moreover, 40 days after fertilization (Fr4 stage) could be an important period for the accumulation of terpenoid compounds during the fruit development and maturation of Z. armatum. The Fr4 stage could be a key point at which the first few steps of the fatty acid biosynthesis process are promoted, and the catalysis of subsequent reactions could be significantly induced at 62 days after fertilization (Fr6 stage). CONCLUSIONS: The present study realized de novo transcriptome assembly for the five major organs of Z. armatum. To the best of our knowledge, this study provides the first comprehensive analysis revealing the genes underlying the special numbing taste of Z. armatum. The assembled transcriptome profiles expand the available genetic information on this species and will contribute to gene functional studies, which will aid in the engineering of high-quality cultivars of Z. armatum.

Transcriptomic Analysis of Multipurpose Timber Yielding Tree Neolamarckia cadamba during Xylogenesis Using RNA-Seq.

Neolamarckia cadamba is a fast-growing tropical hardwood tree that is used extensively for plywood and pulp production, light furniture fabrication, building materials, and as a raw material for the preparation of certain indigenous medicines. Lack of genomic resources hampers progress in the molecular breeding and genetic improvement of this multipurpose tree species. In this study, transcriptome profiling of differentiating stems was performed to understand N. cadamba xylogenesis. The N. cadamba transcriptome was sequenced using Illumina paired-end sequencing technology. This generated 42.49 G of raw data that was then de novo assembled into 55,432 UniGenes with a mean length of 803.2bp. Approximately 47.8% of the UniGenes (26,487) were annotated against publically available protein databases, among which 21,699 and 7,754 UniGenes were assigned to Gene Ontology categories (GO) and Clusters of Orthologous Groups (COG), respectively. 5,589 UniGenes could be mapped onto 116 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Among 6,202 UniGenes exhibiting differential expression during xylogenesis, 1,634 showed significantly higher levels of expression in the basal and middle stem segments compared to the apical stem segment. These genes included NAC and MYB transcription factors related to secondary cell wall biosynthesis, genes related to most metabolic steps of lignin biosynthesis, and CesA genes involved in cellulose biosynthesis. This study lays the foundation for further screening of key genes associated with xylogenesis in N. cadamba as well as enhancing our understanding of the mechanism of xylogenesis in fast-growing trees.

A simple method for RNA isolation from various tissues of the tree Neolamarckia cadamba.

Plant tissues contain abundant polysaccharides, phenolic compounds and other metabolites, which makes it difficult to isolate high-quality RNA from them. In addition, Neolamarckia cadamba contains large quantities of other components, particularly RNA-binding alkaloids, which makes the isolation even more challenging. Here, we describe a concise and efficient RNA isolation method that combines the cetyltrimethyl ammonium bromide (CTAB) and Plant RNA Kit (Omega) protocols. Gel electrophoresis showed that RNA extracted from all tissues, using this protocol, was of good integrity and without DNA contamination. Furthermore, the isolated RNA was of high purity, with an A260/A280 ratio of 2.1 and an A260/A230 ratio of >2.0. The isolated RNA was also suitable for downstream applications, such as reverse transcription-polymerase chain reaction (RT-PCR) and quantitative RT-PCR (RT-qPCR). The RNA isolation method was also efficient for recalcitrant plant tissues.

[Study of the recognition between alpinetin and calf thymus DNA].

The recognition between alpinetin and DNA under physiological condition (pH 7.4) was investigated by fluorescence and UV-visible spectrometry. The experiment demonstrated that the fluorescence of alpinetin could be quenched by DNA. A quenching mechanism was proved to be the single static quenching procedure according to the deescalating quenching constants Ksv (3.288 X 10(3) , 2.923 X 10(3) and 2.467 X 10(3) L x mol(-1), respectively) along with the escalating temperatures (25, 32 and 39 degrees C) and the quenching rate constant Kq was greater than the maximum scatter collision quenching rate constant of various quenchers with the biomolecule. From the UV-visible spectra of alpinetin and DNA, the result showed that the UV-visible spectra of alpinetin did not changed in the presence of DNA, i. e. neither the decrease in the maximum absorbance intensity nor the red shift of the maximum absorption wavelength changed. Both the fluorescence intensity and the maximum emission wavelength of ethidium bromide-DNA system remained unchanged in the presence of alpinetin, indicating that there is no direct competition for binding DNA between alpinetin and ethidium bromide. Furthermore, DNA thermal denaturation test indicated that the fluorescence quenching effect of alpinetin with unlinking DNA was stronger than that of alpinetin with natural DNA. It was concluded that there was not intercalation binding mode between alpinetin and DNA. At the same time, fluorescence quenching effect and salt effect on the binding of alpinetin with DNA were investigated. It was shown that the major mode of recognition was groove binding between alpinetin and DNA.

[Studies on the interaction between puerarin and bovine serum albumin].

The interaction of puerarin and bovine serum albumin (BSA) under physiological condition was studied by fluorospectrophotometry. The experiment demonstrated that the quenching mechanism of puerarin a BSA was static quenching process. The quenching constant is 7.29 x 10(12) L x mol(-1) x s(-1), and the binding constant is 5.04 x 10(4) L x mol(-1). According to the Forster nonradiative energy transfer theory, the binding distance between donor (BSA) and acceptor (puerarin) was calculated to be 3.35 nm. The influence of the presence of puerarin on structure of BSA was studied by synochronous fluorescence method, the binding distance between BSA and puerarin was also measured, and the binding mechanism was discussed. In addition, the effect of some ions on the binding constant of puerarin with BSA was also studied.