Transcriptome analyses provide insights into the expression pattern and sequence similarity of several taxol biosynthesis-related genes in three Taxus species.

BACKGROUND: Taxol is an efficient anticancer drug; however, the accumulation of taxoids can vary hugely among Taxus species. The mechanism underlying differential accumulation of taxoids is largely unknown. Thus, comparative analysis of the transcriptomes in three Taxus species, including T. media, T. mairei and T. cuspidata, was performed. RESULTS: KEGG enrichment analysis revealed that the diterpenoid biosynthesis and cytochrome P450 pathways were significantly enriched in different comparisons. Differential expressions of these taxol biosynthesis related genes might be a potential explanation for the interspecific differential accumulation of taxol and its derivatives. Besides, the sequences of several MEP pathway-associated genes, such as DXS, DXR, MCT, CMK, MDS, HDS, HDR, IPPI, and GGPPS, were re-assembled based on independent transcriptomes from the three Taxus species. Phylogenetic analysis of these MEP pathway-associated enzymes also showed a high sequence similarity between T. media and T. cuspidata. Moreover, 48 JA-related transcription factor (TF) genes, including 10 MYBs, 5 ERFs, 4 RAPs, 3 VTCs, and 26 other TFs, were analyzed. Differential expression of these JA-related TF genes suggested distinct responses to exogenous JA applications in the three Taxus species. CONCLUSIONS: Our results provide insights into the expression pattern and sequence similarity of several taxol biosynthesis-related genes in three Taxus species. The data give us an opportunity to reveal the mechanism underlying the variations in the taxoid contents and to select the highest-yielding Taxus species.

Comparative metabolomics reveals the metabolic variations between two endangered Taxus species (T. fuana and T. yunnanensis) in the Himalayas.

BACKGROUND: Plants of the genus Taxus have attracted much attention owing to the natural product taxol, a successful anti-cancer drug. T. fuana and T. yunnanensis are two endangered Taxus species mainly distributed in the Himalayas. In our study, an untargeted metabolomics approach integrated with a targeted UPLC-MS/MS method was applied to examine the metabolic variations between these two Taxus species growing in different environments. RESULTS: The level of taxol in T. yunnanensis is much higher than that in T. fuana, indicating a higher economic value of T. yunnanensis for taxol production. A series of specific metabolites, including precursors, intermediates, competitors of taxol, were identified. All the identified intermediates are predominantly accumulated in T. yunnanensis than T. fuana, giving a reasonable explanation for the higher accumulation of taxol in T. yunnanensis. Taxusin and its analogues are highly accumulated in T. fuana, which may consume limited intermediates and block the metabolic flow towards taxol. The contents of total flavonoids and a majority of tested individual flavonoids are significantly accumulated in T. fuana than T. yunnanensis, indicating a stronger environmental adaptiveness of T. fuana. CONCLUSIONS: Systemic metabolic profiling may provide valuable information for the comprehensive industrial utilization of the germplasm resources of these two endangered Taxus species growing in different environments.

Development of SCoT-Based SCAR Marker for Rapid Authentication of Taxus Media.

Taxus media is an important species in the family Taxaceae with high medicinal and commercial value. Overexploitation and illegal trade have led T. media to a severe threat of extinction. In addition, T. media and other Taxus species have similar morphological traits and are easily misidentified, particularly during the seedling stage. The purpose of this study is to develop a species-specific marker for T. media. Through a screening of 36 start codon targeted (SCoT) polymorphism primers, among 15 individuals of 4 Taxus species (T. media, T. chinensis, T. cuspidate and T. fuana), a clear species-specific DNA fragment (amplified by primer SCoT3) for T. media was identified. After isolation and sequencing, a DNA sequence with 530 bp was obtained. Based on this DNA fragment, a primer pair for the sequence-characterized amplified region marker was designed and named MHSF/MHSR. PCR analysis with primer pair MHSF/MHSR revealed a clear amplified band for all individuals of T. media but not for T. chinensis, T. cuspidate and T. fuana. Therefore, this marker can be used as a quick, efficient and reliable tool to identify T. media among other related Taxus species. The results of this study will lay an important foundation for the protection and management of T. media as a natural resource.

Comparative proteomic analyses of two Taxus species (Taxus × media and Taxus mairei) reveals variations in the metabolisms associated with paclitaxel and other metabolites.

Taxus species are well-known for paclitaxel, which exhibits antitumor activities and is used for treating various cancers. Although most Taxus species are widespread in many areas, few studies have characterized the variation in metabolism among different Taxus species. Using an integrated approach involving 'tandem mass tag' labeling and liquid chromatography-tandem mass spectrometry (HPLC-MS), proteomes of T. media and T. mairei were investigated and 4078 proteins were quantified. Screening and classification of differentially expressed proteins revealed many metabolism-associated proteins. In detail, four enzymes involved in the flavonoid biosynthesis pathway were predominantly expressed in T. mairei. Four enzymes associated with supplying precursors for paclitaxel biosynthesis and three cytochrome P450 taxoid oxygenases were preferentially expressed in T. media compared with T. mairei. Furthermore, variations in taxoid contents between T. media and T. mairei were determined using HPLC-MS analysis. Variations in flavonoid contents between T. media and T. mairei were determined by HPLC analysis. A number of differentially expressed proteins may provide an explanation for the variation in metabolisms of different Taxus species.

Plant traits and ecosystem effects of clonality: a new research agenda.

BACKGROUND: Clonal plants spread laterally by spacers between their ramets (shoot-root units); these spacers can transport and store resources. While much is known about how clonality promotes plant fitness, we know little about how different clonal plants influence ecosystem functions related to carbon, nutrient and water cycling. APPROACH: The response-effect trait framework is used to formulate hypotheses about the impact of clonality on ecosystems. Central to this framework is the degree of correspondence between interspecific variation in clonal 'response traits' that promote plant fitness and interspecific variation in 'effect traits', which define a plant's potential effect on ecosystem functions. The main example presented to illustrate this concept concerns clonal traits of vascular plant species that determine their lateral extension patterns. In combination with the different degrees of decomposability of litter derived from their spacers, leaves, roots and stems, these clonal traits should determine associated spatial and temporal patterns in soil organic matter accumulation, nutrient availability and water retention. CONCLUSIONS: This review gives some concrete pointers as to how to implement this new research agenda through a combination of (1) standardized screening of predominant species in ecosystems for clonal response traits and for effect traits related to carbon, nutrient and water cycling; (2) analysing the overlap between variation in these response traits and effect traits across species; (3) linking spatial and temporal patterns of clonal species in the field to those for soil properties related to carbon, nutrient and water stocks and dynamics; and (4) studying the effects of biotic interactions and feedbacks between resource heterogeneity and clonality. Linking these to environmental changes may help us to better understand and predict the role of clonal plants in modulating impacts of climate change and human activities on ecosystem functions.

Invasive clonal plant species have a greater root-foraging plasticity than non-invasive ones.

Clonality is frequently positively correlated with plant invasiveness, but which aspects of clonality make some clonal species more invasive than others is not known. Due to their spreading growth form, clonal plants are likely to experience spatial heterogeneity in nutrient availability. Plasticity in allocation of biomass to clonal growth organs and roots may allow these plants to forage for high-nutrient patches. We investigated whether this foraging response is stronger in species that have become invasive than in species that have not. We used six confamilial pairs of native European clonal plant species differing in invasion success in the USA. We grew all species in large pots under homogeneous or heterogeneous nutrient conditions in a greenhouse, and compared their nutrient-foraging response and performance. Neither invasive nor non-invasive species showed significant foraging responses to heterogeneity in clonal growth organ biomass or in aboveground biomass of clonal offspring. Invasive species had, however, a greater positive foraging response in terms of root and belowground biomass than non-invasive species. Invasive species also produced more total biomass. Our results suggest that the ability for strong root foraging is among the characteristics promoting invasiveness in clonal plants.

United we stand, divided we fall: a meta-analysis of experiments on clonal integration and its relationship to invasiveness.

Many ecosystems are dominated by clonal plants. Among the most distinctive characteristics of clonal plants is their potential for clonal integration (i.e. the translocation of resources between interconnected ramets), suggesting that integration may play a role in their success. However, a general synthesis of effects of clonal integration on plant performance is lacking. We conducted a meta-analysis on the effects of clonal integration on biomass production and asexual reproduction of the whole clone, the recipient part (i.e. the part of a clone that imports resources) and the donor part (i.e. the part of a clone that exports resources). The final dataset contained 389 effect sizes from 84 studies covering 57 taxa. Overall, clonal integration increased performance of recipient parts without decreasing that of donor parts, and thus increased performance of whole clones. Among the studies and taxa considered, the benefits of clonal integration did not differ between two types of experimental approaches, between stoloniferous and rhizomatous growth forms, between directions of resource translocation (from younger to older ramet or vice versa), or among types of translocated resources (water, nutrients and carbohydrates). Clonal taxa with larger benefits of integration on whole-clone performance were not more invasive globally, but taxa in which recipient parts in unfavorable patches benefited more from integration were. Our results demonstrate general performance benefits of clonal integration, at least in the short term, and suggest that clonal integration contributes to the success of clonal plants.

Potential distribution of the extremely endangered species Ostrya rehderiana (Betulaceae) in China under future climate change.

Global climate change is a major threat to biodiversity, which may increase the extinction risk of rare species, particularly those like Ostrya rehderiana Chun (Betulaceae) with very few remaining extant wild individuals. We aimed to estimate the potential distribution of O. rehderiana under climate change and to analyze possible relevant climatic factors. Maximum entropy (Maxent) was employed to model the potential distribution of O. rehderiana under present and future climate scenarios. Suitable habitat areas in different periods and the main contributing climate factors were identified using species distribution models. The minimum temperature in winter and precipitation seasonality were the principal climatic factors influencing the establishment of O. rehderiana. The proportion of high potential distribution area in China was 3.91% and would further shrink significantly under changing climate, especially reduce by 97% under high radiative forcing. The extinction risk of O. rehderiana would still be extraordinarily high under future climate scenarios. The Tianmu and Luoxiao Mountains would be the only potential refugia for O. rehderiana in the future. Special conservation efforts are urgently required to rescue extremely endangered species as O. rehderiana. We propose priorities for the conservation region and suggestions for conservation management strategies.

Intraspecific and sex-dependent variation of leaf traits along altitude gradient in the endangered dioecious tree Taxus fuana Nan Li & R.R. Mill.

Plant intraspecific trait variation (ITV) including sex-dependent differences are matters of many ecological consequences, from individual to ecosystem, especially in endangered and rare species. Taxus fuana is an endangered dioecious species with small and isolated populations endemic to the Himalayas region. Little is known about its trait variation between sexes, and among populations. In this study, 18 leaf traits from 179 reproductive trees (males and females) along the altitude (2600-3200m a.s.l.) of the T. fuana populations distributed in Gyirong County, Tibet, China, were measured. ITV and sources of variation in leaf traits were assessed. The relationship between leaf traits of males and females and altitude was analyzed separately. Variations in leaf traits of T. fuana ranged from 3.1% to 24.2%, with the smallest in leaf carbon content and the largest in leaf thickness to area ratio. On average 78.13% of the variation in leaf traits was from within populations and 21.87% among populations. The trends in leaf width, leaf nitrogen to phosphorus ratio, leaf carbon to nitrogen ratio, leaf carbon isotope ratio, and leaf nitrogen isotope ratio in relation to altitude were the same for males and females. Leaf length to width ratio varied significantly with altitude only in males, while leaf phosphorus content, leaf nitrogen content, and leaf carbon to phosphorus ratio varied significantly with altitude only in females. The correlation coefficients of most leaf traits of females with altitude were larger than that of males. In the relationship between leaf traits, there was a high similarity among males and females, but the altitude accounted for more explanation in females than in males. Our results suggested that the variation in leaf traits of T. fuana was small and did not dominate the interspecific competition in the local communities. Adaptation to the altitude gradient of T. fuana might be through altering nutrient storage processes and water use efficiency. Adaptation of male and female T. fuana to environmental changes showed differences, where the males were more tolerant and the females responded greatly to altitude. The differences in adaptation strategies between male and female T. fuana may be detrimental to the maintenance of their populations.

Abundance-weighted plant functional trait variation differs between terrestrial and wetland habitats along wide climatic gradients.

Patterns of plant trait variation across spatial scales are important for understanding ecosystem functioning and services. However, habitat-related drivers of these patterns are poorly understood. In a conceptual model, we ask whether and how the patterns of within- and among-site plant trait variation are driven by habitat type (terrestrial vs. wetland) across large climatic gradients. We tested these through spatial-hierarchical-sampling of leaves in herbaceous-dominated terrestrial and wetland communities within each of 26 sites across China. For all 13 plant traits, within-site variation was larger than among-site variation in both terrestrial and wetland habitats. Within-site variation was similar in most leaf traits related to carbon and nutrient economics but larger in specific leaf area and size-related traits (plant height, leaf area and thickness) in wetland compared to terrestrial habitats. Among-site variation was larger in terrestrial than wetland habitats for 10 leaf traits but smaller for plant height, leaf area and leaf nitrogen. Our results indicate the important role of local ecological processes in driving plant trait variation among coexisting species and the dependence of functional variation across habitats on traits considered. These findings will help to understand and predict the effects of climatic or land-use changes on ecosystem functioning and services.

Intraspecific Variation of Samara Dispersal Traits in the Endangered Tropical Tree Hopea hainanensis (Dipterocarpaceae).

Propagule dispersal is a crucial life history stage, which affects population recruitment and regeneration as well as community structure and functions. The windborne process of samara dispersal is affected not only by samara traits and other plant traits, but also by environmental factors. Therefore, studying samara traits related to its dispersal and intraspecific variation in relation to other plant traits and environmental factors could help to understand population distribution and dynamics. Hopea hainanensis, a Dipterocarpaceae tree species dominant in lowland rainforests in Hainan (China) but endangered due to anthropogenic disturbances, is dispersed mainly by wind because of its sepal-winged samara. Here, we measured dispersal-related intraspecific samara traits of H. hainanensis, and analyzed their variation and correlation in relation to plant height, DBH (diameter at breast height), and elevation plant location. Great variations in the samara traits existed, and the variations were larger within than among individuals, which indicated a "bet-hedging" strategy of this species. Plant height, DBH, and elevation explained slight variation in the samara traits. Samara dispersal potential is mainly affected by the samara mass and morphological traits. Samara settling velocity was significantly positively correlated with fruit mass, seed mass, length and width, as well as samara wing loading, and negatively correlated with wing mass ratio, wing area, and wing aspect ratio. Substantial proportions of intraspecific variation in samara dispersal are explained by the samara mass and morphological traits. Natural regeneration with human-aided dispersal is necessary for recovering the H. hainanensis population. This finding contributes to the generalization of trait-based plant ecology, modeling of seed dispersal in tropical forests, and conservation and recovery of rare and endangered species such as H. hainanensis.

Species traits and decomposability predict water quality changes during litter submergence.

Plant litter plays an important role in affecting the water quality of wetland ecosystems. However, it is unknown whether litter decomposability and species traits might predict water quality changes during litter submergence. Here, we conducted a greenhouse experiment to examine the effects of four submerged plant species, together with two water sources (sampled from tourism and protected areas), and oxygen injection treatments on the changes of eight water quality parameters during litter submergence. Our results showed that litter submergence significantly affected water quality changes, and the observed effects changed through time and differed between two water sources, between oxygen injection and the control treatments, and among different litter species. Moreover, water electric conductivity (EC), total dissolved solids (TDS), water total nitrogen (TN), ammonium and nitrite nitrogen increased with increasing initial litter total carbon (TC), TN and total phosphorus (TP), but water dissolved oxygen (DO) decreased with increasing litter TC, TN and TP. Moreover, water EC, TDS and TN increased with the final mass losses after 10-week submergence. These results indicated that species traits (including decomposability) might be good predictors for the water quality changes during litter submergence, and such a trait-based approach might be a promising tool to link plant species diversity via plant functional traits to water quality or other wetland ecosystem services.

Nutrient enhancement of allelopathic effects of exotic invasive on native plant species.

Many ecosystems may suffer from both nutrient enrichment and exotic plant invasions simultaneously. Much has been known that nutrient inputs can promote growth and expansion of exotic invasive plants in wetlands, and that allelopathic effects of the exotic invasive plants can inhibit the growth of coexisting native plants, contributing to their invasion success. Thus, we hypothesized that allelopathic effects of exotics on natives in invaded ecosystems can be enhanced by nutrient enrichment. To test this hypothesis, we conducted two greenhouse hydroponic experiments. One is the monoculture experiment in which a widespread exotic invasive perennial Alternanthera philoxeroides and a native perennial Ludwigia peploides subsp. stipulacea in monoculture were subjected to five levels of nutrient supply. The other is the mixture experiment in which the two species in mixture were subjected to five levels of nutrient supply, each with and without activated carbon addition. Both A. philoxeroides and L. peploides grew better under higher level of nutrient availability in monoculture experiment. In the mixture experiment, A. philoxeroides formed less total and root biomass while L. peploides formed more in response to activated carbon addition and all of the responses had larger degree at higher level of nutrient availability, indicating A. philoxeroides had significant allelopathic effects on L. peploides and the effects was significantly enhanced by nutrient enrichment. Such results support our hypothesis and reveal a novel mechanism for exotic plant invasion in eutrophicated and invaded wetlands, i.e. nutrient enhancement of allelopathic effects of exotics on natives.

Phragmites australis meets Suaeda salsa on the "red beach": Effects of an ecosystem engineer on salt-marsh litter decomposition.

Suaeda salsa is a pioneer species in coastal wetlands of East Asia and recently an ecosystem engineer species, Phragmites australis, has started to enter into S. salsa communities owing to either autogenic or external drivers. The consequences of this phenomenon on the ecosystem functions of coastal wetlands are still unclear, especially for decomposition processes. Here we compared the decomposition rate of S. salsa litter, and associated litter chemistry dynamics, between sites with and without P. australis encroachment. We conducted a litter transplantation experiment to tease apart the effects of litter quality and decomposing environment or decomposer community composition. Our results showed that P. australis encroachment led to higher carbon and phosphorus losses of S. salsa litter, but equal losses of total mass, lignin, hemicellulose and nitrogen. Phragmites australis encroachment might affect decomposition rate indirectly by making S. salsa produce litter with higher lignin concentrations or via increasing the fungal diversity for decomposition. Moreover, P. australis as an ecosystem engineer might also alter the allocation of total phosphorus between the plants and the soils in coastal wetlands. Our findings indicate that P. australis could impact aboveground and belowground carbon and nutrient dynamics in coastal wetlands, and highlight the important consequences that encroaching plant species, especially ecosystem engineers, can have on ecosystem functions and services of coastal wetlands, not only in East Asia but probably also elsewhere in the world.

Is there coordination of leaf and fine root traits at local scales? A test in temperate forest swamps.

Examining the coordination of leaf and fine root traits not only aids a better understanding of plant ecological strategies from a whole-plant perspective, but also helps improve the prediction of belowground properties from aboveground traits. The relationships between leaf and fine root traits have been extensively explored at global and regional scales, but remain unclear at local scales. Here, we measured six pairs of analogous leaf and fine root traits related to resource economy and organ size for coexisting dominant and subordinate vascular plants at three successional stages of temperate forest swamps in Lingfeng National Nature Reserve in the Greater Hinggan Mountains, NE China. Leaf and fine root traits related to resource acquisition (e.g., specific leaf area [SLA], leaf N, leaf P, root water content, and root P) decreased with succession. Overall, we found strong linear relationships between leaf dry matter content (LDMC) and root water content, and between leaf and root C, N, and P concentrations, but only weak correlations were observed between leaf area and root diameter, and between SLA and specific root length (SRL). The strong relationships between LDMC and root water content and between leaf and root C, N, and P held at the early and late stages, but disappeared at the middle stage. Besides, C and P of leaves were significantly correlated with those of roots for woody plants, while strong linkages existed between LDMC and root water content and between leaf N and root N for herbaceous species. These results provided evidence for the existence of strong coordination between leaf and root traits at the local scale. Meanwhile, the leaf-root trait relationships could be modulated by successional stage and growth form, indicating the complexity of coordination of aboveground and belowground traits at the local scale.

Pond-bottom decomposition of leaf litters canopied by free-floating vegetation.

In wetland ecosystems, vegetation can float freely on water surface, forming dense canopy which may play important ecological roles. This is especially true in many urban wetlands in which fluidity is low and nutrient level is high. So far, effects of free-floating vegetation on abiotic and biotic factors of wetlands have been known, while little on wetland ecosystem functions such as litter decomposition. To examine whether the canopy of free-floating vegetation on water surface will influence litter decomposition in wetlands or not, we conducted a 50-day in situ decomposition experiment in a subtropical urban pond wetland, in which litter bags of nine combinations of three mesh sizes and three litter species were put on the bottoms of total 22 ponds which were half with and half without free-floating vegetation canopy on the water surface. The ponds with and without the canopy had different water physicochemical properties. Overall, the canopy, the species identity, and the mesh size significantly decelerated mass loss and carbon loss of leaf litters while slightly on nitrogen loss. Effects of the canopy on leaf litter decomposition also showed species- and mesh size-dependent. Our results suggest that free-floating vegetation on water surface can alter water environmental factors and consequently change ecosystem functioning in wetlands.

Riparian leaf litter decomposition on pond bottom after a retention on floating vegetation.

Allochthonous (e.g., riparian) plant litter is among the organic matter resources that are important for wetland ecosystems. A compact canopy of free-floating vegetation on the water surface may allow for riparian litter to remain on it for a period of time before sinking to the bottom. Thus, we hypothesized that canopy of free-floating vegetation may slow decomposition processes in wetlands. To test the hypothesis that the retention of riparian leaf litter on the free-floating vegetation in wetlands affects their subsequent decomposition on the bottom of wetlands, a 50-day in situ decomposition experiment was performed in a wetland pond in subtropical China, in which litter bags of single species with fine (0.5 mm) or coarse (2.0 mm) mesh sizes were placed on free-floating vegetation (dominated by Eichhornia crassipes, Lemna minor, and Salvinia molesta) for 25 days and then moved to the pond bottom for another 25 days or remained on the pond bottom for 50 days. The leaf litter was collected from three riparian species, that is, Cinnamomum camphora, Diospyros kaki, and Phyllostachys propinqua. The retention of riparian leaf litter on free-floating vegetation had significant negative effect on the carbon loss, marginal negative effects on the mass loss, and no effect on the nitrogen loss from leaf litter, partially supporting the hypothesis. Similarly, the mass and carbon losses from leaf litter decomposing on the pond bottom for the first 25 days of the experiment were greater than those from the litter decomposing on free-floating vegetation. Our results highlight that in wetlands, free-floating vegetation could play a vital role in litter decomposition, which is linked to the regulation of nutrient cycling in ecosystems.

Variations in Soil Bacterial Composition and Diversity in Newly Formed Coastal Wetlands.

Coastal ecosystems experience some of the most active land-ocean interactions in the world, and they are characterized by high primary productivity and biological diversity in the sediment. Given the roles of microorganisms in soil biogeochemical cycling and their multifaceted influence on soil ecosystems, it is critical to understand the variations and drivers of soil microbial communities across coastal ecosystems. Here, we studied soil bacterial community dynamics at different sites (from seawater to freshwater) in the Yellow River Delta, China. Bacterial community composition and diversity over four seasons were analyzed through 16S rRNA genes. Notably, the bacterial community near the ocean had the lowest alpha-diversity when compared with the other sites. No significant differences in bacterial communities among seasons were found, indicating that seasonal variation in temperature had little influence on bacterial community in the newly formed wetlands in the Yellow River Delta. Bacterial community structure changed substantially along the salinity gradient, revealing a clear ecological replacement along the gradual transformation gradient from freshwater to seawater environment. Redundancy analysis revealed that salinity was the main driver of variations in bacterial community structure and explained 17.5% of the variability. Our study provides a better understanding of spatiotemporally determined bacterial community dynamics in coastal ecosystems.

Effects of ploidy level and haplotype on variation of photosynthetic traits: Novel evidence from two Fragaria species.

To reveal the effects of ploidy level and haplotype on photosynthetic traits, we chose 175 genotypes of wild strawberries belonging to two haplotypes at two types of ploidy levels (diploidy and tetraploidy) and measured photosynthetic traits. Our results revealed that ploidy significantly affected the characteristics of light-response curves, CO2-response curves, and leaf gas exchange parameters, except intercellular CO2 concentration (Ci). Tetraploid species had a lower light saturation point (LSP) and CO2 saturation point (CSP), higher light compensation point (LCP), dark respiration (Rd), and CO2 compensation point (CCP) than diploid species. Furthermore, tetraploid species have lower photosynthetic capacity than diploid species, including net photosynthetic rate (Pn), stomatal conductivity (Gs), and transpiration rate (Tr). In addition, haplotype had a significant effect on LSP, CSP, Tr, and Ci as well as a significant interactive effect between ploidy and haplotype on the maximal photosynethic rate of the light-response curve and Rd. Most of the variance existed within haplotypes among individuals. These results suggest that polyploidization was the main driver for the evolution of photosynthesis with increasing ploidy level (i.e. from diploidy to tetraploidy in Fragaria species), while the origin of a chromosome could also affect the photosynthetic traits and the polyploidization effect on photosynthetic traits.

Identification of potential genes that contributed to the variation in the taxoid contents between two Taxus species (Taxus media and Taxus mairei).

Taxol is currently a valuable anticancer drug; however, the accumulated mixture of taxoids can vary greatly among Taxus species. So far, there is very little genomic information for the genus Taxus, except for Taxus baccata. Transcriptome analysis is a powerful approach to explore the different regulatory mechanisms underlying the taxoid biosynthesis pathway in Taxus species. First, we quantified the variation in the taxoid contents between Taxus media and Taxus mairei. The contents of paclitaxel and 10-deacetylpaclitaxel in T. media are higher than that in T. mairei. Then, the transcriptome profiles of T. media and T. mairei were analyzed to investigate the altered expressions. A total of 20,704 significantly differentially expressed genes (DEGs), including 9865 unigenes predominantly expressed in T. media and 10,839 unigenes predominantly expressed in T. mairei, were identified. In total, 120 jasmonic acid-related DEGs were analyzed, suggesting variations in 'response to JA stimulus' and 'JA biosynthetic process' pathways between T. media and T. mairei. Furthermore, a number of genes related to the precursor supply, taxane skeleton formation and hydroxylation, and C13-side chain assembly were also identified. The differential expression of the candidate genes involved in taxoid biosynthetic pathways may explain the variation in the taxoid contents between T. media and T. mairei.