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Lycoris is a perennial bulbous flower belonging to the Amaryllidaceae family, which is commonly known as surprise lily, hurricane lily, or spider lily due to its distinctive flowering characteristics. They bloom from summer to early fall when the flower stalks emerge from the ground without foliage, giving rise to name like “surprise lilies” (Knox 2006). Among the species, Lycoris radiata stands as a representative with its spider-like appearance, featuring six tepals arranged radially around a central reproductive structure. The petals display a diverse array of colors, including red, yellow, white, pink, and multicolor variations across different species and cultivars (Ji and Meerow 2000). In addition, the strap-like or linear-shaped leaves of Lycoris also add ornamental value, emerging before or after flowering and providing visual interest during winter and spring when the plants are not in bloom. Therefore, its surprising blooms, abundant colors, and unique growth habits make it valuable for gardens and cut flowers. According to the latest published data, there are more than 30 species in the genus, predominantly native to East Asia (Zhang et al. 2022b), with ∼80% of them naturally distributed in China. So, Lycoris boasts a rich cultivation history in Chinese gardens. Furthermore, ongoing research focuses on breeding new Lycoris cultivars, with unique traits. For instance, L. longituba cultivar Yi Xian Chun Tao exhibits pink-purple flowers, distinguishing from white L. longituba (Zhang et al. 2022a), and L. straminea cultivar E Huang Xiao Ran stands out with a larger plant and flower size with vivid red stripes on the petals, surpassing the color intensity of L. straminea (Wang et al. 2023). These new cultivars contribute to horticultural diversity and hold higher economic value for landscape and cut flower application.

AbstractThe color of the leaves is one of the most important factors for horticultural crops that are considered by breeders, and is also attracting more and more attention from economists and academics. 'Quanhong poplar’ (QHP), a rare, bright reddish-purple color-leaf cultivar that has been widely cultivated in China as a landscape tree, is a very precious color-leaf cultivar. In the present study, a reference-based assembly was performed using whole-genome sequencing data to characterize the chloroplast genome of 'QHP'. The total chloroplast genome size of ‘QHP’ is 156,950 bp, which is divided into two inverted repeat structures of 27,649 bp each, a small single-copy region of 16,563 bp, and a large single-copy region (LSC) of 85,089 bp. From the chloroplast genome, 130 genes have been predicted, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. A chloroplast genome containing 36.68% GC content was detected in 'QHP'. Three SNP sites have been developed between 'QHP' and Populus deltoides Zhonglin 2025. Based on the phylogenetic analysis of chloroplast genomes reported for Populus, the chloroplast of 'QHP' is closest to several strains of Populus deltoides.

Environmental stresses, including abiotic and biotic stresses, have complex and diverse effects on the growth and development of woody plants, which have become a matter of contention due to concerns about the outcomes of climate change on plant resources, genetic diversity, and world food safety. Plant basic helix–loop–helix (bHLH) transcription factors (TFs) are involved in a variety of physiological processes and play an important role in biotic and abiotic stress responses of woody plants. In recent years, an increasing body of studies have been conducted on the bHLH TFs in woody plants, and the roles of bHLH TFs in response to various stresses are increasingly clear and precise. Therefore, it is necessary to conduct a systematic and comprehensive review of the progress of the research of woody plants. In this review, the structural characteristics, research history and roles in the plant growth process of bHLH TFs are summarized, the gene families of bHLH TFs in woody plants are summarized, and the roles of bHLH TFs in biotic and abiotic stresses in woody plants are highlighted. Numerous studies mentioned in this review have shown that bHLH transcription factors play a crucial role in the response of woody plants to biotic and abiotic stresses. This review serves as a reference for further studies about enhancing the stress resistance and breeding of woody plants. Also, the future possible research directions of bHLH TFs in response to various stresses in woody plants will be discussed.

Heat shock transcription factors (HSFs) are an essential plant-specific transcription factor family that regulates the developmental and growth stages of plants, their signal transduction, and their response to different abiotic and biotic stresses. The HSF gene family has been characterized and systematically observed in various species; however, research on its association with Lycoris radiata is limited. This study identified 22 HSF genes (LrHSFs) in the transcriptome-sequencing data of L. radiata and categorized them into three classes including HSFA, HSFB, and HSFC, comprising 10, 8, and 4 genes, respectively. This research comprises basic bioinformatics analyses, such as protein sequence length, molecular weight, and the identification of its conserved motifs. According to the subcellular localization assessment, most LrHSFs were present in the nucleus. Furthermore, the LrHSF gene expression in various tissues, flower developmental stages, two hormones stress, and under four different abiotic stresses were characterized. The data indicated that LrHSF genes, especially LrHSF5, were essentially involved in L. radiata development and its response to different abiotic and hormone stresses. The gene–gene interaction network analysis revealed the presence of synergistic effects between various LrHSF genes’ responses against abiotic stresses. In conclusion, these results provided crucial data for further functional analyses of LrHSF genes, which could help successful molecular breeding in L. radiata.

The APETALA2/ethylene-responsive transcription factor (AP2/ERF) family has been extensively investigated because of its significant involvement in plant development, growth, fruit ripening, metabolism, and plant stress responses. To date, there has been little investigation into how the AP2/ERF genes influence flower formation and anthocyanin biosynthesis in Lycoris. Herein, 80 putative LrAP2/ERF transcription factors (TFs) with complete open reading frames (ORFs) were retrieved from the Lycoris transcriptome sequence data, which could be divided into five subfamilies dependent on their complete protein sequences. Furthermore, our findings demonstrated that genes belonging to the same subfamily had structural similarities and conserved motifs. LrAP2/ERF genes were analyzed for playing an important role in plant growth, water deprivation, and flower formation by means of gene ontology (GO) enrichment analysis. The expression pattern of the LrAP2/ERF genes differed across tissues and might be important for Lycoris growth and flower development. In response to methyl jasmonate (MeJA) exposure and drought stress, the expression of each LrAP2/ERF gene varied across tissues and time. Moreover, a total of 20 anthocyanin components were characterized using ultra-performance liquid chromatography-electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS) analysis, and pelargonidin-3-O-glucoside-5-O-arabinoside was identified as the major anthocyanin aglycone responsible for the coloration of the red petals in Lycoris. In addition, we mapped the relationships between genes and metabolites and found that LrAP2/ERF16 is strongly linked to pelargonidin accumulation in Lycoris petals. These findings provide the basic conceptual groundwork for future research into the molecular underpinnings and regulation mechanisms of AP2/ERF TFs in anthocyanin accumulation and Lycoris floral development.

As one of the biggest plant specific transcription factor (TF) families, basic helix–loop–helix (bHLH) protein, plays significant roles in plant growth, development, and abiotic stress responses. However, there has been minimal research about the effects of methyl jasmonate (MeJA) treatment on the bHLH gene family in Lycoris radiata (L’Her.) Herb. In this study, based on transcriptome sequencing data, 50 putative L. radiata bHLH (LrbHLH) genes with complete open reading frames (ORFs), which were divided into 20 bHLH subfamilies, were identified. The protein motif analyses showed that a total of 10 conserved motifs were found in LrbHLH proteins and motif 1 and motif 2 were the most highly conserved motifs. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of LrbHLH genes revealed their involvement in regulation of plant growth, jasmonic acid (JA) mediated signaling pathway, photoperiodism, and flowering. Furthermore, subcellular localization revealed that most LrbHLHs were located in the nucleus. Expression pattern analysis of LrbHLH genes in different tissues and at flower developmental stages suggested that their expression differed across lineages and might be important for plant growth and organ development in Lycoris. In addition, all LrbHLH genes exhibited specific spatial and temporal expression patterns under MeJA treatment. Moreover, protein-protein interaction (PPI) network analysis and yeast two-hybrid assay showed that numerous LrbHLHs could interact with jasmonate ZIM (zinc-finger inflorescence meristem) domain (JAZ) proteins. This research provides a theoretical basis for further investigation of LrbHLHs to find their functions and insights for their regulatory mechanisms involved in JA signaling pathway.

Abstract Background MYB transcription factors, comprising one of the largest transcription factor families in plants, play many roles in secondary metabolism, especially in anthocyanin biosynthesis. However, the functions of the PdeMYB transcription factor in colored-leaf poplar remain elusive. Results In the present study, genome-wide characterization of the PdeMYB genes in colored-leaf poplar (Populus deltoids) was conducted. A total of 302 PdeMYB transcription factors were identified, including 183 R2R3-MYB, five R1R2R3-MYB, one 4R-MYB, and 113 1R-MYB transcription factor genes. Genomic localization and paralogs of PdeMYB genes mapped 289 genes on 19 chromosomes, with collinearity relationships among genes. The conserved domain, gene structure, and evolutionary relationships of the PdeMYB genes were also established and analyzed. The expression levels of PdeMYB genes were obtained from previous data in green leaf poplar (L2025) and colored leaf poplar (QHP) as well as our own qRT-PCR analysis data in green leaf poplar (L2025) and colored leaf poplar (CHP), which provide valuable clues for further functional characterization of PdeMYB genes. Conclusions The above results provide not only comprehensive insights into the structure and functions of PdeMYB genes but also provide candidate genes for the future improvement of leaf colorization in Populus deltoids.

Taxus is a rare and endangered woody plant worldwide with important economic and ecological values. However, the weak environmental adaptability of Taxus species, in particular the unstable photosynthetic activity in different seasons, always affects its normal growth and development and limits its conservation and exploitation. To improve the survival of Taxus trees in cultivated areas, the seasonal dynamics of chlorophyll fluorescence (CF) and key physiological parameters were comprehensively investigated in T. media and T. mairei. The results demonstrated that the photosynthetic activity of both Taxus species was sensitive to local summer and winter environmental conditions, with the heterogeneity of fluorescence signatures intuitively presented on the needle surface by CF-Imaging detection, while images of maximum quantum efficiency of PSII photochemistry (Fv/Fm) demonstrated values below 0.7 in the blue–green sectors in winter. The distribution of light energy was regulated by the photosynthetic apparatus in both Taxus species to maintain a stable actual quantum yield of PSII photochemistry (φPSII), which was around 0.4–0.5. Based on a redundancy discriminant analysis, the interpretation rate of light intensity and air temperature ranked as the top two in both Taxus species, which were considered the main environmental factors affecting the photosynthetic performance of Taxus by disturbing the electron transport chain. In the winter, T. mairei exhibited weaker electron transport activity than T. media, thus caused lower photochemistry and more severe photosynthetic damages. Interestingly, both Taxus species demonstrated consistent response patterns, including diverse energy dissipation strategies and enhancement of osmoregulatory substances and antioxidative activities, thus maintaining stable photosynthetic functions in response to environmental changes.

Lycoris is an important plant with both medicinal and ornamental values. However, it does not have an efficient genetic transformation system, which makes it difficult to study gene function of the genus. Virus-induced gene silencing (VIGS) is an effective technique for studying gene functions in plants. In this study, we develop an efficient virus-induced gene-silencing (VIGS) system using the leaf tip needle injection method. The widely used TRV vector is constructed, and the Cloroplastos Alterados 1 (CLA1) and Phytoene Desaturase (PDS) genes are selected as visual indicators in the VIGS system. As a result, it is observed that leaves infected with TRV-LcCLA1 and TRV-LcPDS both show a yellowing phenotype (loss of green), and the chlorosis range of TRV-LcCLA1 was larger and deeper than that of TRV-LcPDS. qRT-PCR results show that the expression levels of LcCLA1 and LcPDS are significantly reduced, and the silencing efficiency of LcCLA1 is higher than that of LcPDS. These results indicate that the VIGS system of L. chinensis was preliminarily established, and LcCLA1 is more suitable as a gene-silencing indicator. For the monocotyledonous plant leaves with a waxy surface, the leaf tip injection method greatly improves the infiltration efficiency. The newly established VIGS system will contribute to gene functional research in Lycoris species.

Lycoris radiata, belonging to the Amaryllidaceae family, is a well-known Chinese traditional medicinal plant and susceptible to many stresses. WRKY proteins are one of the largest families of transcription factors (TFs) in plants and play significant functions in regulating physiological metabolisms and abiotic stress responses. The WRKY TF family has been identified and investigated in many medicinal plants, but its members and functions are not identified in L. radiata. In this study, a total of 31 L. radiata WRKY (LrWRKY) genes were identified based on the transcriptome-sequencing data. Next, the LrWRKYs were divided into three major clades (Group I–III) based on the WRKY domains. A motif analysis showed the members within same group shared a similar motif component, indicating a conservational function. Furthermore, subcellular localization analysis exhibited that most LrWRKYs were localized in the nucleus. The expression pattern of the LrWRKY genes differed across tissues and might be important for Lycoris growth and flower development. There were large differences among the LrWRKYs based on the transcriptional levels under drought stress and MeJA treatments. Moreover, a total of 18 anthocyanin components were characterized using an ultra-performance liquid chromatography-electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS) analysis and pelargonidin-3-O-glucoside-5-O-arabinoside as well as cyanidin-3-O-sambubioside were identified as the major anthocyanin aglycones responsible for the coloration of the red petals in L. radiata. We further established a gene-to-metabolite correlation network and identified LrWRKY3 and LrWRKY27 significant association with the accumulation of pelargonidin-3-O-glucoside-5-O-arabinoside in the Lycoris red petals. These results provide an important theoretical basis for further exploring the molecular basis and regulatory mechanism of WRKY TFs in anthocyanin biosynthesis and in response to drought stress and MeJA treatment.

Lycoris is used as a garden flower due to the colorful and its special flowers. Floral coloration of Lycoris is a vital trait that is mainly regulated via the anthocyanin biosynthetic pathway. In this study, we performed a comparative transcriptome analysis of Lycoris radiata petals at four different flower development stages. A total of 38,798 differentially expressed genes (DEGs) were identified by RNA sequencing, and the correlation between the expression level of the DEGs and the anthocyanin content was explored. The identified DEGs are significantly categorized into ‘flavonoid biosynthesis,’ ‘phenylpropanoid biosynthesis,’ ‘Tropane, piperidine and pyridine alkaloid biosynthesis,’ ‘terpenoid backbone biosynthesis’ and ‘plant hormone signal transduction’ by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The candidate genes involved in anthocyanin accumulation in L. radiata petals during flower development stages were also identified, which included 56 structural genes (especially LrDFR1 and LrFLS) as well as 27 key transcription factor DEGs (such as C3H, GATA, MYB, and NAC). In addition, a key structural gene namely LrDFR1 of anthocyanin biosynthesis pathway was identified as a hub gene in anthocyanin metabolism network. During flower development stages, the expression level of LrDFR1 was positively correlated with the anthocyanin content. Subcellular localization revealed that LrDFR1 is majorly localized in the nucleus, cytoplasm and cell membrane. Overexpression of LrDFR1 increased the anthocyanin accumulation in tobacco leaves and Lycoris petals, suggesting that LrDFR1 acts as a positively regulator of anthocyanin biosynthesis. Our results provide new insights for elucidating the function of anthocyanins in L. radiata petal coloring during flower development.

The transition from vegetative to reproductive growth is important for controlling the flowering of Lycoris radiata. However, the genetic control of this complex developmental process remains unclear. In this study, 18 shoot apical meristem (SAM) samples were collected from early-, mid- and late-flowering populations during floral bud differentiation. The histological analysis of paraffin sections showed that the floral bud differentiation could be divided into six stages; the differentiation time of the early group was earlier than that of the middle and late groups, and the late group was the latest. In different populations, some important differential genes affecting the flowering time were identified by transcriptome profiles of floral bud differentiation samples. Weighted gene co-expression network analysis (WGCNA) was performed to enrich the gene co-expression modules of diverse flowering time populations (FT) and floral bud differentiation stages (ST). In the MEyellow module, five core hub genes were identified, including CO14, GI, SPL8, SPL9, and SPL15. The correlation network of hub genes showed that they interact with SPLs, AP2, hormone response factors (auxin, gibberellin, ethylene, and abscisic acid), and several transcription factors (MADS-box transcription factor, bHLH, MYB, and NAC3). It suggests the important role of these genes and the complex molecular mechanism of floral bud differentiation and flowering time in L. radiata. These results can preliminarily explain the molecular mechanism of floral bud differentiation and provide new candidate genes for the flowering regulation of Lycoris.

Lycoris is a summer bulbous flower that commonly needs to go through a long period of vegetative growth for 3 to 5 years before flowering. Plant flowering is regulated by a complex genetic network. Compared with most perennial flowers, knowledge on the molecular mechanism responsible for floral transition in bulbous flowers is lacking, and only a few genes that regulate flowering have been identified with few reports on the floral transition in Lycoris. In this study, we identified many differentially expressed genes (DEGs) and transcription factors (TFs) by RNA-Seq in L. chinensis bulbs of different ages, including one- to four-year-old nonflowering bulbs and four-year-old flowering bulbs. Some DEGs were enriched in Gene Ontology (GO) terms between the three- and four-year-old bulbs, and there most genes were enriched in terms of metabolic process and catalytic activity. In the four-year old bulbs, most of the DEGs that may be involved in flowering were classified under the GO term biological process, which was a totally different result from the vegetative bulbs. Some DEGs between flowering and nonflowering bulbs were enriched in plant hormone signal transduction, including the hormones auxin, cytokinin, abscisic acid, and ethylene, but no DEGs were enriched in the gibberellin pathway. Auxin is the main endogenous phytohormone involved in bulb growth and development, but cytokinin, abscisic acid, and ethylene were shown to increase in flowering bulbs. In addition, energy-metabolism-related genes maintain a high expression level in large bulbs, and some positive regulators (SPL, COL, and AP1) and early flowering genes were also shown to be highly expressed in the meristems of flowering bulbs. It suggested that sugar molecules may be the energy source that regulates the signal transduction of flowering by connecting with phytohormone signaling in Lycoris. A total of 1911 TFs were identified and classified into 89 categories, where the top six families with the largest gene numbers were C2H2, NAC, AP2/ERF-ERF, C3H, MYB-related, and WRKY. Most DEGs were in the AP2/ERF-ERF family, and most of them were downregulated in 4-year-old flowering bulbs. A number of families were reported to be involved in plant flowering, including NAC, AP2/ERF, MYB, WRKY, bZIP, MADS, and NF-Y. These results can act as a genetic resource to aid in the explanation of the genetic mechanism responsible for the flowering of Lycoris and other bulbous flowers.

Objectives To develop a model of in-hospital mortality using medical record front page (MRFP) data and assess its validity in case-mix standardisation by comparison with a model developed using the complete medical record data.Design A nationally representative retrospective study.Setting Representative hospitals in China, covering 161 hospitals in modelling cohort and 156 hospitals in validation cohort.Participants Representative patients admitted for acute myocardial infarction. 8370 patients in modelling cohort and 9704 patients in validation cohort.Primary outcome measures In-hospital mortality, which was defined explicitly as death that occurred during hospitalisation, and the hospital-level risk standardised mortality rate (RSMR).Results A total of 14 variables were included in the model predicting in-hospital mortality based on MRFP data, with the area under receiver operating characteristic curve of 0.78 among modelling cohort and 0.79 among validation cohort. The median of absolute difference between the hospital RSMR predicted by hierarchical generalised linear models established based on MRFP data and complete medical record data, which was built as ‘reference model’, was 0.08% (10th and 90th percentiles: −1.8% and 1.6%). In the regression model comparing the RSMR between two models, the slope and intercept of the regression equation is 0.90 and 0.007 in modelling cohort, while 0.85 and 0.010 in validation cohort, which indicated that the evaluation capability from two models were very similar.Conclusions The models based on MRFP data showed good discrimination and calibration capability, as well as similar risk prediction effect in comparison with the model based on complete medical record data, which proved that MRFP data could be suitable for risk adjustment in hospital performance measurement.

Melatonin, widely found in various plants as a new antioxidant, could protect plants from various biotic and/or abiotic stresses, including salt stress. MzASMT 1 (KJ123721), a gene from Malus zumi Mats, is a key enzyme required for melatonin synthesis. However, whether the overexpression of MzASMT 1 could regulate the synthesis of melatonin and improve the salt tolerance in tobacco remains unknown. In this study, the overexpression of MzASMT 1 in tobacco increased the melatonin content, and the transgenic lines owned higher salt tolerance capacity. The transgenic lines overexpressing MzASMT 1 exhibited lower degree of leaf wilting; much more fresh weight; higher plant height; longer root; higher relative water content (RWC) of leaves, stem, and root; and higher chlorophyll content and Fv/Fm, which makes transgenic lines better adapt to salt stress. The transgenic lines also had higher accumulation of proline, lower accumulation of malondialdehyde (MDA), and improved antioxidant systems, which protected plants from cell damage and oxidative stress due to excess reactive oxygen species (ROS) accumulation under salt treatment. The transcription of salt response genes was much more highly activated in transgenic lines than in wild type under salt stress. The above results contributed to the understanding of functions for MzASMT 1 in tobacco under salt stress and provided a new choice for the application of MzASMT 1 in improving plant salt tolerance.

Colored-leaf plants are increasingly popular, which has higher ecological, economic and social benefits. Caihong poplar, one of colored-leaf plants from Populus deltoides, has been widely used in courtyard embellishment, road greening, garden set King and so on. In this study, the complete chloroplast genome of Caihong poplar was evaluated, and the total chloroplast genome size of which is 156,957 bp in length with 36.69% GC content, including large single-copy region (LSC) of 85,096 bp, a pair of inverted repeat regions (IRs) of 27,649 bp each, and a small single-copy region (SSC) of 16,563 bp. There were 22 tRNA genes, 83 protein-coding genes, and four rRNA genes. The phylogenetic analysis with 22 species indicated that Caihong poplar was closely clustered with Populus deltoides Zhonglin 2025. In conclusion, the complete chloroplast genomes of Caihong poplar in this study provided valuable genomic resources for further phylogeny and species identification in the Populus family.

Leaf coloration changes evoke different photosynthetic responses among different poplar cultivars. The aim of this study is to investigate the photosynthetic difference between a red leaf cultivar (ZHP) and a green leaf (L2025) cultivar of Populus deltoides. In this study, ‘ZHP’ exhibited wide ranges and huge potential for absorption and utilization of light energy and CO2 concentration which were similar to those in ‘L2025’ and even showed a stronger absorption for weak light. However, with the increasing light intensity and CO2 concentration, the photosynthetic capacity in both ‘L2025’ and ‘ZHP’ was gradually restricted, and the net photosynthetic rate (Pn) in ‘ZHP’ was significantly lower than that in ‘L2025’under high light or high CO2 conditions, which was mainly attributed to stomatal regulation and different photosynthetic efficiency (including the light energy utilization efficiency and photosynthetic CO2 assimilation efficiency) in these two poplars. Moreover, the higher anthocyanin content in ‘ZHP’ than that in ‘L2025’ was considered to be closely related to the decreased photosynthetic efficiency in ‘ZHP’. According to the results from the JIP-test, the capture efficiency of the reaction center for light energy in ‘L2025’ was significantly higher than that in ‘ZHP’. Interestingly, the higher levels of light quantum caused relatively higher accumulation of QA- in ‘L2025’, which blocked the electron transport and weakened the photosystem II (PSII) performance as compared with ‘ZHP’; however, the decreased capture of light quantum also could not promote the utilization of light energy, which was the key to the low photosynthetic efficiency in ‘ZHP’. The differential expressions of a series of photosynthesis-related genes further promoted these specific photosynthetic processes between ‘L2025’ and ‘ZHP’.

The genus Lycoris (Amaryllidaceae) consists of about 20 species, which is endemic to East Asia. Although the Lycoris species is of great horticultural and medical importance, challenges in accurate species identification persist due to frequent natural hybridization and large-scale intraspecific variation. In this study, we sequenced chloroplast genomes of four Lycoris species and retrieved seven published chloroplast (cp) genome sequences in this genus for comparative genomic and phylogenetic analyses. The cp genomes of these four newly sequenced species were found to be 158,405–158,498 bp with the same GC content of 37.8%. The structure of the genomes exhibited the typical quadripartite structure with conserved gene order and content. A total of 113 genes (20 duplicated) were identified, including 79 protein-coding genes (PCGs), 30 tRNAs, and 4 rRNAs. Phylogenetic analysis showed that the 11 species were clustered into three main groups, and L. sprengeri locate at the base of Lycoriss. The L. radiata was suggested to be the female donor of the L. incarnata, L. shaanxiensis, and L. squamigera. The L. straminea and L. houdyshelii may be derived from L. anhuiensis, L. chinensis, or L. longituba. These results could not only offer a genome-scale platform for identification and utilization of Lycoris but also provide a phylogenomic framework for future studies in this genus.

The complete chloroplast genome of Populus deltoides was characterized by reference-based assembly using whole-genome sequencing data. The total chloroplast genome size of Populus deltoides included a pair of inverted repeat regions (IRs) of 27,649 bp each, a small single-copy region (SSC) of 16,563 bp, and large single-copy region (LSC) of 85,096 bp, which was 156,957 bp in length. A total of 109 genes were predicted from the chloroplast genome, including 83 protein-coding genes, 22 tRNA genes, and four rRNA genes. The GC content of chloroplast genome for Populus deltoides was 36.68%. The phylogenetic analysis based on the reported chloroplast genomes of Populus showed that the chloroplast of the Populus deltoides is most closely related to the Populus fremontii. The complete chloroplast genome of Populus deltoides provides new insights into Populus evolutionary and genomic studies.

Taxol is one of the most potent and effective anticancer drugs and is originally isolated from Taxus species. To investigate the specific regulatory mechanisms of taxol synthesis in Taxus wallichiana var. mairei, RNA-seq was conducted to reveal the differences in transcriptional levels between wild type (WT) and “Jinxishan” (JXS), a cultivar selected from a population of Taxus mairei that shows about 3-fold higher taxol content in the needles than WT. Our results indicated that high expressions of the genes taxadienol acetyltransferase (TAT), taxadiene 5-alpha hydroxylase (T5H), 5-alpha-taxadienol-10-beta-hydroxylase (T10OH), and 2-debenzoyl-7,13-diacetylbaccatin III-2-O-benzoyl-transferase (DBBT), which catalyze a series of key acetylation and hydroxylation steps, are the main cause of high taxol content in JXS. Moreover, in the present study, the activation of jasmonic acid (JA) signal transduction and its crosstalk with gibberellin (GA), auxin, and ethylene (ET) explained the elevation of differentially expressed genes (DEGs) from the taxol biosynthesis pathway. This also indicates that taxol biosynthesis in T. mairei is associated with the balance of cell development and defense. TF-encoding (transcriptional factor) genes, represented by the ethylene-responsive transcription factor (ERF), basic/helix-loop-helix (bHLH), MYB, and WRKY families, were detected as differentially expressed between JXS and WT, further indicating that the regulation of hormone signaling on taxol biosynthesis genes was mediated by transcription factors (TFs). To our knowledge, this is the first study to illustrate the regulatory mechanisms of taxol synthesis in a new cultivar of T. mairei with a high taxol content in its needles. These transcriptome data provide reasonable explanations for the variation of taxol content between WT and JXS.

Taxol is one of the most effective anticancer drugs in the world that is widely used in the treatments of breast, lung and ovarian cancer. The elucidation of the taxol biosynthetic pathway is the key to solve the problem of taxol supply. So far, the taxol biosynthetic pathway has been reported to require an estimated 20 steps of enzymatic reactions, and sixteen enzymes involved in the taxol pathway have been well characterized, including a novel taxane-10β-hydroxylase (T10βOH) and a newly putative β-phenylalanyl-CoA ligase (PCL). Moreover, the source and formation of the taxane core and the details of the downstream synthetic pathway have been basically depicted, while the modification of the core taxane skeleton has not been fully reported, mainly concerning the developments from diol intermediates to 2-debenzoyltaxane. The acylation reaction mediated by specialized Taxus BAHD family acyltransferases (ACTs) is recognized as one of the most important steps in the modification of core taxane skeleton that contribute to the increase of taxol yield. Recently, the influence of acylation on the functional and structural diversity of taxanes has also been continuously revealed. This review summarizes the latest research advances of the taxol biosynthetic pathway and systematically discusses the acylation reactions supported by Taxus ACTs. The underlying mechanism could improve the understanding of taxol biosynthesis, and provide a theoretical basis for the mass production of taxol.

The genus Lycoris (about 20 species) includes important medicinal and ornamental plants. Due to the similar morphological features and insufficient genomic resources, germplasm identification and molecular phylogeny analysis are very limited. Here, we sequenced the complete chloroplast genomes of L. chinensis, L. anhuiensis, and L. aurea; they have very similar morphological traits that make it difficult to identify. The full length of their cp genomes was nearly 158k bp with the same guanine-cytosine content of 37.8%. A total of 137 genes were annotated, including 87 protein-coding genes, 42 tRNAs, and eight rRNAs. A comparative analysis revealed the conservation in sequence size, GC content, and gene content. Some variations were observed in repeat structures, gene expansion on the IR-SC (Inverted Repeat-Single-Copy) boundary regions. Together with the cpSSR (chloroplast simple sequence repeats), these genetic variations are useful to develop molecular markers for germplasm identification. Phylogenetic analysis showed that seven Lycoris species were clustered into a monophyletic group, and closed to Narcissus in Amaryllidaceae. L. chinensis, L. anhuiensis, and L. longituba were clustered together, suggesting that they were very likely to be derived from one species, and had the same ancestor with L. squamigera. Our results provided information on the study of genetic diversity, origins or relatedness of native species, and the identification of cultivars.

Lycoris radiata, widely known as red spider lily. It belongs to the Amaryllidaceae family and has highly ornamental and medical value. Here, we assembled the complete chloroplast genome sequence by high-throughput sequencing and bioinformatics, which will provide more genomic information to the analysis of genetic diversity and phylogenetic relationship. The full length of chloroplast genome is 158,335 bp, composed of a large single-copy region (LSC) of 86,612 bp, a small single-copy region (SSC) of 18,261 bp, and a pair of inverted repeats (IR) of 26,731 bp. A total of 137 genes were annotated, including 87 protein-coding genes, 42 tRNA, and 8 rRNA genes. Phylogenetic tree analysis revealed that the close relationship between L. radiata and L. squamigera in the Amaryllidaceae family.

Lycoris sprengeri is native to China and has various variations. It belongs to the Amaryllidaceae family, which contains abundant alkaloids for medical use and also was planted as garden bulbous flowers. In this study, we assembled the complete chloroplast (cp) genome of L. sprengeri by DNA sequencing, which will improve the complete cp genomic information for analysis of phylogenetic relationships and germplasm identification in Lycoris. The whole cp genome is 158,687 bp, which contained a large single-copy region (LSC) of 86,489 bp, a small single-copy region (SSC) of 18,540 bp, and a pair of inverted repeats (IRs) of 26,829 bp. A total of 137 genes were annotated, including 87 protein coding genes (PCGs), 42 tRNA, and 8 rRNA genes. Phylogenetic tree analysis revealed that the close relationship of three species of Lycoris (L. sprengeri, L. radiate, and L. squamigera) in the Amaryllidaceae family.

Lycoris longituba is a species in the Amaryllidaceae with high ornamental and medicinal value. It is also an endangered species in East China due to the narrow distribution. Here, we assembled and characterised the complete chloroplast (cp) genome of this species using high throughput sequencing and bioinformatics analysis. As a result, the whole cp genome size is 158,484 bp, including two inverted repeat (IR) regions of 26,765 bp, large single-copy region (LSC) of 86,458 bp and small single-copy region (SSC) of 18,496 bp. A total of 137 genes were identified, including 87 protein-coding genes, 42 tRNA genes, and eight rRNA genes. Phylogenomic analysis was carried out using complete cp genome of 18 species in five families, supporting the closer relationship between L. longituba and L. squamigera than L. radiata and L. sprengeri in Amaryllidaceae.

The needles of Taxus species contain a large number of bioactive compounds, such as flavonoids. In the present study, the total flavonoid content in leaves of Taxus media and Taxus mairei was 19.953 and 14.464 mg/g, respectively. A total of 197 flavonoid metabolites (70 flavones, 42 flavonols, 26 flavone C-glycosides, 20 flavanones, 15 anthocyanins, 13 isoflavones, 6 flavonolignans, and 5 proanthocyanidins) were identified for the first time by a widely targeted Ultra Performance Liquid Chromatography-Electrospray Ionization-Tandem Mass Spectrometry (UPLC-ESI-MS/MS) method within the two Taxus species, containing 160 common metabolites, with 37 unique metabolites merely determined in T. mairei or T. media. Moreover, 42 differential flavonoid metabolites were screened in the two Taxus species, which showed specific metabolic patterns in isoflavonoid biosynthesis, anthocyanin biosynthesis, and flavone and flavonol biosynthesis pathways. Compared to T. mairei, a more activated phenylpropanoid pathway was found in T. media, which could be responsible for the higher content of total flavonoids in T. media. Our results provide new insights into the diversity of flavonoid metabolites between T. mairei and T. media, and provide a theoretical basis for the sufficient utilization of Taxus species and the development of novel drugs.

Based on the SODA ocean analysis data, the interannual cycle features of the tropical Pacific-Indian Ocean associated mode (PIOAM) are studied by means of wavelet analysis and synthetic analysis. It is pointed out that PIOAM has a quasi-biennial cycle and a 3-4-year cycle. Furthermore, the dynamic and thermal mechanisms of the PIOAM interannual cycle are analyzed. The results show that the anomaly of Walker circulation over the two oceans is the key factor which forms the PIOAM. The propagation and reflection of ocean waves and the horizontal and vertical heat transfer of ocean circulation also play an important role in the cycle of PIOAM. [ABSTRACT FROM AUTHOR]