Amplified fragment length polymorphism analysis of the population structure and genetic diversity of Phoebe zhennan (Lauraceae), a native species to China

Karst fissures mitigate the negative effects of drought on plant growth and photosynthetic physiology

Hard limestone substrates, which are extensively distributed, are believed to exacerbate drought and increase the difficulty of restoration in vulnerable karst regions. Fissures in such substrates may alleviate the negative effect of drought on plants, but the underlying mechanisms remain poorly understood. In a two-way factorial block design, the growth and photosynthesis of 2-year-old Phoebe zhennan seedlings were investigated in two water availabilities (high versus low) and three stimulated fissure habitat groups (soil, soil-filled fissure and non-soil-filled fissure). Moreover, the fissure treatments included both small and big fissures. Compared to the soil group, the non-soil-filled fissure group had decreased the total biomass, root biomass, total root length, and the root length of fine roots in the soil layer at both water availabilities, but increased net photosynthetic rate (Pn) and retained stable water use efficiency (WUE) at low water availability. However, there were no significant differences between the soil-filled fissure group and soil group in the biomass accumulation and allocation as well as Pn. Nevertheless, the SF group decreased the root distribution in total and in the soil layer, and also increased WUE at low water availability. Across all treatments, fissure size had no effect on plant growth or photosynthesis. Karst fissures filled with soil can alleviate drought impacts on plant root growth, which involves adjusting root distribution strategies and increasing water use efficiency. These results suggest that rock fissures can be involved in long-term plant responses to drought stress and vegetation restoration in rocky mountain environments under global climate change.

Boosting cadmium tolerance in Phoebe zhennan: the synergistic effects of exogenous nitrogen and phosphorus treatments promoting antioxidant defense and root development

Plants possess intricate defense mechanisms to resist cadmium (Cd) stress, including strategies like metal exclusion, chelation, osmoprotection, and the regulation of photosynthesis, with antioxidants playing a pivotal role. The application of nitrogen (N) and phosphorus (P) fertilizers are reported to bolster these defenses against Cd stress. Several studies investigated the effects of N or P on Cd stress in non-woody plants and crops. However, the relationship between N, P application, and Cd stress resistance in valuable timber trees remains largely unexplored. This study delves into the Cd tolerance mechanisms of Phoebe zhennan, a forest tree species, under various treatments: Cd exposure alone, combined Cd stress with either N or P and Cd stress with both N and P application. Our results revealed that the P application enhanced root biomass and facilitated the translocation of essential nutrients like K, Mn, and Zn. Conversely, N application, especially under Cd stress, significantly inhibited plant growth, with marked reductions in leaf and stem biomass. Additionally, while the application of P resulted in reduced antioxidant enzyme levels, the combined application of N and P markedly amplified the activities of peroxidase by 266.36%, superoxide dismutase by 168.44%, and ascorbate peroxidase by 26.58% under Cd stress. This indicates an amplified capacity of the plant to neutralize reactive oxygen species. The combined treatment also led to effective regulation of nutrient and Cd distribution in roots, shoots, and leaves, illustrating a synergistic effect in mitigating toxic impact of N. The study also highlights a significant alteration in photosynthetic activities under different treatments. The N addition generally reduced chlorophyll content by over 50%, while P and NP treatments enhanced transpiration rates by up to 58.02%. Our findings suggest P and NP fertilization can manage Cd toxicity by facilitating antioxidant production, osmoprotectant, and root development, thus enhancing Cd tolerance processes, and providing novel strategies for managing Cd contamination in the environment.

Comparative Metabolomics and Transcriptome Analysis Reveal the Fragrance-Related Metabolite Formation in Phoebe zhennan Wood

Nanmu (Phoebe zhennan) has a unique fragrance and is a high-quality tree species for forest conservation. The types and contents of volatile compounds in different tissues of nanmu wood are different, and the study of its volatile metabolites can help us to understand the source of its fragrance and functions. In order to explore the metabolites related to the wood fragrance of nanmu and to find out the unique volatile substances in the heartwood, gas chromatography-mass spectrometry (GC-MS) was performed to analyze the non-targeted metabolomics in five radial tissues from the sapwood to the heartwood of nanmu. A total of 53 volatile metabolites belonging to 11 classes were detected in all tissues, including terpenes, aromatic hydrocarbons, organoheterocyclics, phenols, esters, organic acids, alcohols, alkaloids, alkane, indoles derivatives, and others. And most of the volatile metabolites were identified for the first time in nanmu wood. Among them, terpenes and aromatic hydrocarbons were the main volatile components. In addition, 22 differential metabolites were screened from HW and SW, HW, and TZ via metabolomic analysis. Among these DAMs, three volatile metabolites (cadinene, a sesquiterpenoid; p-cymene, a monoterpenoid; 1,3,5-triisopropylbenzene, an aromatic hydrocarbon) contributed heavily to the characteristic fragrance of the heartwood. Additionally, the expression of transcripts showed that the unigenes in the terpenoid biosynthesis pathway were especially up-regulated in the SW. Therefore, we speculated that fragrance-related metabolites were synthesized in SW and then deposited in heartwood during sapwood transformed to heartwood. The expression levels of transcription factors (e.g., WRKY, C2H2, NAC) acted as the major regulatory factors in the synthesis of terpenoid. The results lay the foundations for further studies on the formation mechanism of fragrance components in nanmu wood and also provide a reference for the further development and utilization of nanmu wood.

Comparative chloroplast genome analyses of diverse Phoebe (Lauraceae) species endemic to China provide insight into their phylogeographical origin

The genus Phoebe (Lauraceae) includes about 90 evergreen tree species that are an ideal source of timber. Habitat destruction and deforestation have resulted in most of them being endemic to China. The accurate identification of endangered Phoebe species in China is necessary for their conservation. Chloroplast genome sequences can play an important role in species identification. In this study, comparative chloroplast genome analyses were conducted on diverse Phoebe species that are primarily distributed in China. Despite the conserved nature of chloroplast genomes, we detected some highly divergent intergenic regions (petA-psbE, ndhF-rpl32, and psbM-trnD-GUC) as well as three highly divergent genes (rbcL, ycf1, and ycf2) that have potential applications in phylogenetics and evolutionary analysis. The phylogenetic analysis indicated that various Phoebe species in China were divided into three clades. The complete chloroplast genome was better suited for phylogenetic analysis of Phoebe species. In addition, based on the phylogeographical analysis of Phoebe species in China, we inferred that the Phoebe species in China first originated in Yunnan and then spread to other southern areas of the Yangtze River. The results of this research will add to existing case studies on the phylogenetic analysis of Phoebe species and have the potential to contribute to the conservation of Phoebe species that are in danger of extinction.

Genetic Diversity and Population Structure of an Arctic Tertiary Relict Tree Endemic to China (Sassafras tzumu) Revealed by Novel Nuclear Microsatellite (nSSR) Markers

Sassafras tzumu (Hemsl.) Hemsl., as an Arctic Tertiary relict woody species, is an ecologically and economically important deciduous tree endemic to southern China. Nonetheless, the genetic resources and backgrounds of S. tzumu are still lacking and remain largely unclear. Here, we predicted 16,215 candidate polymorphic nuclear microsatellite (nSSR) loci from the assembled nucleus databases of six geographic-distant individuals of S. tzumu via CandiSSR. Among these nSSRs, the di- (75.53%) and tri-nucleotide (19.75%) repeats were the most abundant, and 27 new polymorphic SSRs were developed and characterized in 136 individuals from six natural populations of S. tzumu. The majority of the above 27 SSRs (24 loci, 88.89%) presented moderate polymorphism (mean PIC = 0.356), and the transferability of these markers in other Sassafras species was high (85.19%). A moderately low level of genetic diversity and a high variation (FST = 0.286) of six wild populations of S. tzumu were illuminated by 16 selected polymorphic nSSRs, with the average expected heterozygosity (HE) of 0.430 at the species level and HE ranging from 0.195 to 0.387 at the population level. Meanwhile, a bottleneck effect was shown in two populations. Consistent with the results of the principal coordinate analysis (PCoA) and phylogenetic trees, structure analysis optimally divided these six S. tzumu populations into two clusters, and the further strong population subdivision appeared from K = 2 to K = 5, which corresponded to two evolutionarily significant units (ESUs). Moreover, the significant correlation between genetic and geographic distance was tested by the Mantel test (r = 0.742, p = 0.006), clarifying the effect about isolation by distance (IBD), which could be possibly explained by the low gene flow (Nm = 0.625), a relatively high degree of inbreeding (FIS = 0.166), a relatively large distribution, and mountainous barriers. Above all, our research not only enlarged the useful genetic resources for future studies of population genetics, molecular breeding, and germplasm management of S. tzumu and its siblings but also contributed to proposing scientific conservation strategies and schemes for the better preservation of S. tzumu and other Sassafras (Lauraceae) species.

Transcriptomic and proteomic analyses uncover the drought adaption landscape of Phoebe zhennan

BACKGROUND

Phoebe zhennan S.Lee (nanmu) is listed as a threatened tree species in China, whose growth and development, especially during the seedling stage, can be severely limited by drought. Previous studies on nanmu responses to drought stress involved physiological and biochemical analyses, while the molecular mechanisms remained unclear. Therefore, it is of great significance to carry out molecular biology research on the drought resistance of nanmu and reveal the genetic background and molecular regulation mechanism of nanmu drought resistance.

RESULTS

Drought stress enhanced the soluble sugar (SS), free proline(PRO), superoxide anion (O2·-), and hydrogen peroxide (H₂O₂) contents as well as the peroxidase (POD) and monodehydroascorbate reductase (MDHAR) activities of nanmu. However, glutathione S-transferase (GST) activity was sensitive to drought stress. Further transcriptomic and proteomic analyses revealed the abundant members of the differentially expressed genes(DEGs) and differentially expressed proteins(DEPs) that were related to phenylpropanoid and flavonoid biosynthesis, hormone biosynthesis and signal transduction, chlorophyll metabolism, photosynthesis, and oxidation-reduction reaction, which suggested their involvement in the drought response of nanmu. These enhanced the osmotic regulation, detoxification, and enzyme-induced and non-enzyme-induced antioxidant ability of nanmu. Moreover, 52% (447/867) of proteins that were up-regulated and 34% (307/892) down-regulated ones were attributed to the increase and decrease of transcription abundance. Transcript up (T^U) and protein up (P^U) groups had 447 overlaps, while transcript down (T^D) and protein down (P^D) groups had 307 overlaps, accounting for 54% of up and 35% of down-regulated proteins. The lack of overlap between DEGs and DEPs also suggested that post-transcriptional regulation has a critical role in nanmu response to drought.

CONCLUSIONS

Our research results provide significant insights into the regulatory mechanisms of drought stress in nanmu.

Miocene diversification of a golden-thread nanmu tree species (Phoebe zhennan, Lauraceae) around the Sichuan Basin shaped by the East Asian monsoon

Understanding the role of climate changes and geography as drivers of population divergence and speciation is a long‐standing goal of evolutionary biology and can inform conservation. In this study, we used restriction site‐associated DNA sequencing (RAD‐seq) to evaluate genetic diversity, population structure, and infer demographic history of the endangered tree, Phoebe zhennan which is distributed around the Sichuan Basin. Genomic patterns revealed two distinct clusters, each largely confined to the West and East. Despite sympatry of the two genomic clusters at some sites, individuals show little or no evidence of genomic introgression. Demographic modeling supported an initial divergence time between the West and East lineages at ~15.08 Ma with further diversification within the West lineage at ~7.12 Ma. These times largely coincide with the two independent intensifications of the East Asian monsoon that were initiated during the middle (Langhian) and late Miocene (Messinian), respectively. These results suggest that the Miocene intensification phases of the East Asian monsoon played a pivotal role in shaping the current landscape‐level patterns of genetic diversity within P. zhennan, as has been found for the interspecific divergence of other subtropical Chinese plants. Based on isolation‐by‐distance and species distribution modeling, we hypothesize that P. zhennan followed a ring diversification which was facilitated by the Sichuan Basin acting as barrier to gene flow. In situ and ex situ conservation management plans should consider the results obtained in this study to help secure the future of this beautiful and culturally significant endangered tree.

Characterization of Ethyl Acetate and Trichloromethane Extracts from Phoebe zhennan Wood Residues and Application on the Preparation of UV Shielding Films

In this work, ethyl acetate (EA) and trichloromethane (TR) extracts were extracted from Phoebezhennan wood residues and the extracts were then applied to the preparation of UV shielding films (UV-SF). The results revealed that substances including olefins, phenols and alcohols were found in both EA and TR extracts, accounting for about 45% of all the detected substances. The two extracts had similar thermal stability and both had strong UV shielding ability. When the relative percentage of the extract is 1 wt% in solution, the extract solution almost blocked 100% of the UV-B (280–315 nm), and UV-A (315–400 nm). Two kinds of UV-SF were successfully prepared by adding the two extracts into polylactic acid (PLA) matrix. The UV-SF with the addition of 24 wt% of the extractive blocked 100% of the UV-B (280–315 nm) and more than 80% of the UV-A (315–400 nm). Moreover, the UV shielding performance of the UV-SF was still stable even after strong UV irradiation. Though the addition of extracts could somewhat decrease the thermal stability of the film, its effect on the end-use of the film was ignorable. EA extracts had less effect on the tensile properties of the films than TR extracts as the content of the extract reached 18%. The results of this study could provide fundamental information on the potential utilization of the extracts from Phoebe zhennan wood residues on the preparation of biobased UV shielding materials.

Transcriptome sequencing and SNP detection in Phoebe chekiangensis

Background

Phoebe chekiangensis is a rare tree species that is only distributed in south-eastern China. Although this species is famous for its excellent wood properties, it has not been extensively studied at the molecular level.

Results

Here, the transcriptome of P. chekiangensis was sequenced using next-generation sequencing technology, and 75,647 transcripts with 48,011 unigenes were assembled and annotated. In addition, 162,938 putative single nucleotide polymorphisms (SNPs) were predicted and 25 were further validated using the Sanger method.

Conclusion

The currently available SNP prediction software packages showed low levels of correspondence when compared. The transcriptome and SNPs will contribute to the exploration of P. chekiangensis genetic resources and the understanding of its molecular mechanisms.

ISSR Marker Based Population Genetic Study of Melocanna baccifera (Roxb.) Kurz: A Commercially Important Bamboo of Manipur, North-East India

Melocanna baccifera (Roxb.) Kurz is an economically important bamboo of North-East India experiencing population depletion in its natural habitats. Genetic variation studies were conducted in 7 populations sampled from 5 districts of Manipur using ISSR molecular markers. The investigation was carried out as a primary step towards developing effective conservation strategies for the protection of bamboo germplasm. ISSR marker analysis showed significant level of genetic variation within the populations as revealed by moderately high average values of Nei's genetic diversity (H 0.1639), Shannon's diversity index (I 0.2563), percentage of polymorphic bands (PPB 59.18), total genetic variation (H_t 0.1961), and genetic diversity within population (H_s 0.1639). The study also divulged a high genetic variation at species level with Shannon's diversity index (I), Nei's genetic diversity (H), and percentage of polymorphic band (PPB%) recorded at 0.3218, 0.1939, and 88.37, respectively. Genetic differentiation among the populations (G_st) was merely 19.42% leaving 80.58% of genetic variation exhibited within the populations. The low genetic diversity between populations was consistent with AMOVA. The low genetic differentiation among populations coupled with existence of significantly high genetic diversity at species level indicated the urgent necessity of preserving and protecting all the existing natural bamboo populations in the region.

Phosphorous Application Improves Drought Tolerance of Phoebe zhennan

Phoebe zhennan (Gold Phoebe) is a threatened tree species in China and a valuable and important source of wood and bioactive compounds used in medicine. Apart from anthropogenic disturbances, several biotic constraints currently restrict its growth and development. However, little attention has been given to building adaptive strategies for its conservation by examining its morphological and physio-biochemical responses to drought stress, and the role of fertilizers on these responses. A randomized experimental design was used to investigate the effects of two levels of irrigation (well-watered and drought-stressed) and phosphorous (P) fertilization treatment (with and without P) to assess the morphological and physio-biochemical responses of P. zhennan seedlings to drought stress. In addition, we evaluated whether P application could mitigate the negative impacts of drought on plant growth and metabolism. Drought stress had a significant negative effect on the growth and metabolic processes of P. zhennan. Despite this, reduced leaf area, limited stomatal conductance, reduced transpiration rate, increased water use efficiency, enhanced antioxidant enzymes activities, and osmolytes accumulation suggested that the species has good adaptive strategies for tolerating drought stress. Application of P had a significant positive effect on root biomass, signifying its improved water extracting capacity from the soil. Moreover, P fertilization significantly increased leaf relative water content, net photosynthetic rate, and maximal quantum efficiency of PSII under drought stress conditions. This may be attributable to several factors, such as enhanced root biomass, decreased malondialdehyde content, and the up-regulation of chloroplast pigments, osmolytes, and nitrogenous compounds. However, P application had only a slight or negligible effect on the growth and metabolism of well-watered plants. In conclusion, P. zhennan has a strong capability for drought resistance, while P application facilitates and improves drought tolerance mostly through physio-biochemical adjustments, regardless of water availability. It is imperative to explore the underlying metabolic mechanisms and effects of different levels of P fertilization on P. zhennan under drought conditions in order to design appropriate conservation and management strategies for this species, which is at risk of extinction.