The SMXL8-AGL9 module mediates crosstalk between strigolactone and gibberellin to regulate strigolactone-induced anthocyanin biosynthesis in apple.

Although the strigolactone (SL) signaling pathway and SL-mediated anthocyanin biosynthesis have been reported, the molecular association between SL signaling and anthocyanin biosynthesis remains unclear. In this study, we identified the SL signal transduction pathway associated with anthocyanin biosynthesis and the crosstalk between gibberellin (GA) and SL signaling in apple (Malus × domestica). ELONGATED HYPOCOTYL5 (HY5) acts as a key node integrating SL signaling and anthocyanin biosynthesis, and the SL response factor AGAMOUS-LIKE MADS-BOX9 (AGL9) promotes anthocyanin biosynthesis by activating HY5 transcription. The SL signaling repressor SUPPRESSOR OF MAX2 1-LIKE8 (SMXL8) interacts with AGL9 to form a complex that inhibits anthocyanin biosynthesis by downregulating HY5 expression. Moreover, the E3 ubiquitin ligase PROTEOLYSIS1 (PRT1) mediates the ubiquitination-mediated degradation of SMXL8, which is a key part of the SL signal transduction pathway associated with anthocyanin biosynthesis. In addition, the GA signaling repressor REPRESSOR-of-ga1-3-LIKE2a (RGL2a) mediates the crosstalk between GA and SL by disrupting the SMXL8-AGL9 interaction that represses HY5 transcription. Taken together, our study reveals the regulatory mechanism of SL-mediated anthocyanin biosynthesis and uncovers the role of SL-GA crosstalk in regulating anthocyanin biosynthesis in apple.

Functional characterization of NBS-LRR genes reveals an NBS-LRR gene that mediates resistance against Fusarium wilt.

BACKGROUND: Most disease resistance (R) genes in plants encode proteins that contain leucine-rich-repeat (LRR) and nucleotide-binding site (NBS) domains, which belong to the NBS-LRR family. The sequenced genomes of Fusarium wilt-susceptible Vernicia fordii and its resistant counterpart, Vernicia montana, offer significant resources for the functional characterization and discovery of novel NBS-LRR genes in tung tree. RESULTS: Here, we identified 239 NBS-LRR genes across two tung tree genomes: 90 in V. fordii and 149 in V. montana. Five VmNBS-LRR paralogous were predicted in V. montana, and 43 orthologous were detected between V. fordii and V. montana. The orthologous gene pair Vf11G0978-Vm019719 exhibited distinct expression patterns in V. fordii and V. montana: Vf11G0978 showed downregulated expression in V. fordii, while its orthologous gene Vm019719 demonstrated upregulated expression in V. montana, indicating that this pair may be responsible for the resistance to Fusarium wilt in V. montana. Vm019719 from V. montana, activated by VmWRKY64, was shown to confer resistance to Fusarium wilt in V. montana by a virus-induced gene silencing (VIGS) experiment. However, in the susceptible V. fordii, its allelic counterpart, Vf11G0978, exhibited an ineffective defense response, attributed to a deletion in the promoter's W-box element. CONCLUSIONS: This study provides the first systematic analysis of NBS-LRR genes in the tung tree and identifies a candidate gene that can be utilized for marker-assisted breeding to control Fusarium wilt in V. fordii.

Haplotype-resolved genome assembly of Bletilla striata (Thunb.) Reichb.f. to elucidate medicinal value.

Bletilla striata, commonly known as baiji, is a species used in traditional Chinese medicine; it is highly regarded for its medicinal applications and therefore has high economic value. Here, we report a high-quality haplotype-resolved genome of B. striata, haplotype A (2.37 Gb, with a scaffold N50 of 146.39 Mb and a contig N50 of 1.65 Mb) and haplotype B (2.43 Gb, with a scaffold N50 of 150.22 Mb and a contig N50 of 1.66 Mb), assembled from high-fidelity (HiFi) reads and chromosome conformation capture (Hi-C) reads. We find evidence that B. striata has undergone two whole-genome duplication (WGD) events: an ancient WGD event shared by most monocots and a recent WGD event unique to all orchids. We also reconstructed the ancestral orchid karyotype (AOK) of 18 ancient chromosomes and the evolutionary trajectories of 16 modern B. striata chromosomes. Comparative genomic analysis suggests that the expanded gene families of B. striata might play important roles in secondary metabolite biosynthesis and environmental adaptation. By combining genomic and transcriptomic data, we identified the 10 core members from nine gene families that were probably involved in B. striata polysaccharide (BSP) biosynthesis. Based on virus-induced gene silencing (VIGS) and yeast two-hybrid experiments, we present an MYB transcription factor (TF), BsMYB2, that can regulate BSP biosynthesis by directly interacting with eight key BSP-related genes: sacA1, HK1, scrK1, scrK2, GPI1, manA1, GMPP1 and UGP2_1. Our study will enhance the understanding of orchid evolution and accelerate the molecular-assisted breeding of B. striata for improving traits of medicinal value.

Flavonoids: a review on biosynthesis and transportation mechanism in plants.

In recent years, significant progress has been made in understanding the biosynthetic pathway and regulation of flavonoids through forward genetic approaches. However, there remains a notable gap in knowledge regarding the functional characterization and underlying processes of the transport framework responsible for flavonoid transport. This aspect requires further investigation and clarification to achieve a comprehensive understanding. Presently, there are a total of four proposed transport models associated with flavonoids, namely glutathione S-transferase (GST), multidrug and toxic compound extrusion (MATE), multidrug resistance-associated protein (MRPs), and bilitranslocase-homolog (BTL). Extensive research has been conducted on the proteins and genes related to these transport models. However, despite these efforts, numerous challenges still exist, leaving much to be explored in the future. Gaining a deeper understanding of the mechanisms underlying these transport models holds immense potential for various fields such as metabolic engineering, biotechnological approaches, plant protection, and human health. Therefore, this review aims to provide a comprehensive overview of recent advancements in the understanding of flavonoid transport mechanisms. By doing so, we aim to paint a clear and coherent picture of the dynamic trafficking of flavonoids.

Large-scale analysis of putative Euphorbiaceae R2R3-MYB transcription factors identifies a MYB involved in seed oil biosynthesis.

BACKGROUND: MYB transcription factors are widely distributed in the plant kingdom and play key roles in regulatory networks governing plant metabolism and biochemical and physiological processes. RESULTS: Here, we first determined the R2R3-MYB genes in five Euphorbiaceae genomes. The three Trp (W) residues from the first MYB domain (R2) were absolutely conserved, whereas the first W residue from the second MYB domain (R3) was preferentially mutated. The R2R3-MYBs were clustered into 48 functional subfamilies, of which 34 had both R2R3-MYBs of Euphorbiaceae species and AtMYBs, and four contained only Euphorbiaceae R2R3-MYBs. The whole-genome duplication (WGD) and/or segmental duplication (SD) played key roles in the expansion of the R2R3-MYB family. Unlike paralogous R2R3-MYB family members, orthologous R2R3-MYB members contained a higher selective pressure and were subject to a constrained evolutionary rate. VfMYB36 was specifically expressed in fruit, and its trend was consistent with the change in oil content, indicating that it might be involved in oil biosynthesis. Overexpression experiments showed that VfMYB36 could significantly provide linolenic acid (C18:3) content, which eventually led to a significant increase in oil content. CONCLUSION: Our study first provides insight into understanding the evolution and expression of R2R3-MYBs in Euphorbiaceae species, and also provides a target for the production of biomass diesel and a convenient way for breeding germplasm resources with high linolenic acid content in the future.

Functional and kinetics of two efficient phenylalanine ammonia lyase from Pyrus bretschneideri.

BACKGROUND: The enzyme phenylalanine ammonia lyase (PAL) controls the transition from primary to secondary metabolism by converting L-phenylalanine (L-Phe) to cinnamic acid. However, the function of PAL in pear plants (Pyrus bretschneideri) has not yet been fully elucidated. RESULTS: We identified three PAL genes (PbPAL1, PbPAL2 and PbPAL3) from the pear genome by exploring pear genome databases. The evolutionary tree revealed that three PbPALs were classified into one group. We expressed PbPAL1 and PbPAL2 recombinant proteins, and the purified PbPAL1 and PbPAL2 proteins showed strict substrate specificity for L-Phe, no activity toward L-Tyr in vitro, and modest changes in kinetics and enzyme characteristics. Furthermore, overexpression of PbAL1 and PbPAL1-RNAi, respectively, and resulted in significant changes in stone cell and lignin contents in pear fruits. The results of yeast one-hybrid (Y1H) assays that PbWLIM1 could bind to the conserved PAL box in the PbPAL promoter and regulate the transcription level of PbPAL2. CONCLUSIONS: Our findings not only showed PbPAL's potential role in lignin biosynthesis but also laid the foundation for future studies on the regulation of lignin synthesis and stone cell development in pear fruit utilizing molecular biology approaches.

Efficacy and Safety of Neoadjuvant Chemoimmunotherapy in Resectable Esophageal Squamous Cell Carcinoma: A Meta-analysis.

PURPOSE: This study aimed to summarize the efficacy and safety of neoadjuvant chemoimmunotherapy in resectable esophageal squamous cell carcinoma (ESCC). METHODS: Literature focusing on the efficacy and safety of neoadjuvant immunotherapy or chemoimmunotherapy in resectable ESCC published before June 2022 was retrieved from PubMed, Embase, Cochrane Library, and Web of Science. The risk of bias was assessed using the Cochrane risk-of-bias assessment tool. Subgroup and sensitivity analyses were further performed. RESULTS: A total of 452 patients from 15 studies were included in this meta-analysis. All of the studies explored the efficacy and safety of neoadjuvant chemoimmunotherapy. The pooled major pathological response (MPR) rate and pathological complete response (PCR) rate were 58.3% and 32.9%, respectively. The pooled incidence of treatment-related adverse events (TRAEs) and serious adverse events (SAEs) were 91.6% and 19.4%, respectively. The pooled R0 resection rate was 92.8%, and the resection rate was 81.1%. Incidence of anastomotic leakage, pulmonary infection, and postoperative hoarseness were 10.7%, 21.3%, and 13.0%, respectively. Compared with 2 cycles of neoadjuvant therapy, patients who received > 2 cycles of neoadjuvant therapy showed higher MPR rate (57.3% vs. 61.1%) and PCR rate (30.6% vs. 37.9%), and the incidence of TRAEs (89.2% vs. 98.9%) tended to be higher. However, no significant difference was found (P > 0.05). Two cycles of neoadjuvant therapy showed higher R0 resection rate and resection rate (R0 resection rate: 96.0% vs. 87.8%, P = 0.02; resection rate: 85.6% vs. 74.7%, P = 0.01). Pembrolizumab- and tislelizumab-based neoadjuvant therapy showed higher MPR rate (72.4% and 72.2%) and PCR rate (41.5 % and 50.0%). Compared with other ICIs, tislelizumab-based neoadjuvant therapy showed lower R0 resection rate (80.5%). The pooled incidence of SAEs for pembrolizumab-based neoadjuvant therapy (2.0%) was lower. Camrelizumab-based neoadjuvant therapy showed lower incidence of pulmonary infection (11.5%). CONCLUSIONS: Neoadjuvant chemoimmunotherapy is effective and safe for resectable ESCC.

Two monolignoid biosynthetic genes 4-coumarate:coenzyme A ligase (4CL) and p-coumaric acid 3-hdroxylase (C3H) involved in lignin accumulation in pear fruits.

One of the most important factors impacting the quality of pear fruit is the presence of stone cells and lignin. Lignin is the main component of stone cells in pear fruits. Two monolignoid biosynthetic genes 4-coumarate:coenzyme A ligase (4CL) and p-coumaric acid 3-hdroxylase (C3H) are involved in lignin accumulation in pear fruits. However, the functions of these genes in lignin biosynthesis were excluded in pear. In our study, we isolated and cloned Pb4CL11 (GenBank: KM455955.1) and PbC3H1 (GenBank: KM373790.1) from pear, which contained 1644 bp encoded 54 amino acids (AA), and 1539 bp encoded 513 AA, respectively. The expression of Pb4CL11 and PbC3H1 in Arabidopsis thaliana led to an increase in cell wall thickness for intervascular fibers and xylem cells and lignin content. Overexpression of Pb4CL11 and PbC3H1 in A. thaliana can significantly increase the expression of AtPAL, AtC4H, AtHCT, AtC3H, AtCCOMT, AtCCR, AtF5H, AtCOMT, AtCAD4 and AtCAD5 with promotion of lignin biosynthesis. Taken together, our study's findings not only demonstrated the probable function of Pb4CL11 and PbC3H1 in lignin biosynthesis but also laid the groundwork for future studies using molecular biological methods to control lignin production and the formation of stone cells in pear fruits.

The red flower wintersweet genome provides insights into the evolution of magnoliids and the molecular mechanism for tepal color development.

Wintersweet (Chimonanthus praecox) is one of the most important ornamental plants. Its color is mainly determined by the middle tepals. However, the molecular mechanisms underlying the intriguing flower color development among different wintersweet groups are still largely unknown. In addition, wintersweet belongs to magnoliids, and the phylogenetic position of magnoliids remains to be determined conclusively. Here, the whole genome of red flower wintersweet, a new wintersweet type, was sequenced and assembled with high quality. The genome comprised 11 super-scaffolds (chromosomes) with a total size of 737.03 Mb. Based on the analyses of the long branch attraction, incomplete lineage sorting, sparse taxon sampling, and other factors, we suggest that a bifurcating tree may not fully represent the complex early diversification of the angiosperms and that magnoliids are most likely sister to the eudicots. The wintersweet genome appears to have undergone two whole-genome duplication (WGD) events: a recent WGD event representing an independent event specific to the Calycanthaceae and an ancient WGD event shared by Laurales. By integrating genomic, transcriptomic, and metabolomic data, CpANS1 and the transcription factor CpMYB1 were found to play key roles in regulating tepal color development, whereas CpMYB1 needs to form a complex with bHLH and WD40 to fully perform its regulatory function. The present study not only provides novel insights into the evolution of magnoliids and the molecular mechanism for flower color development, but also lays the foundation for subsequent functional genomics study and molecular breeding of wintersweet.

Machine learning for the micropeptide encoded by LINC02381 regulates ferroptosis through the glucose transporter SLC2A10 in glioblastoma.

Glioblastoma (GBM) is the most common primary intracranial tumor in the central nervous system, and resistance to temozolomide is an important reason for the failure of GBM treatment. We screened out that Solute Carrier Family 2 Member 10 (SLC2A10) is significantly highly expressed in GBM with a poor prognosis, which is also enriched in the NF-E2 p45-related factor 2 (NRF2) signalling pathway. The NRF2 signalling pathway is an important defence mechanism against ferroptosis. SLC2A10 related LINC02381 is highly expressed in GBM, which is localized in the cytoplasm/exosomes, and LINC02381 encoded micropeptides are localized in the exosomes. The micropeptide encoded by LINC02381 may be a potential treatment strategy for GBM, but the underlying mechanism of its function is not precise yet. We put forward the hypothesis: "The micropeptide encoded by LINC02381 regulates ferroptosis through the glucose transporter SLC2A10 in GBM." This study innovatively used machine learning for micropeptide to provide personalized diagnosis and treatment plans for precise treatment of GBM, thereby promoting the development of translational medicine. The study aimed to help find new disease diagnoses and prognostic biomarkers and provide a new strategy for experimental scientists to design the downstream validation experiments.

Identification of exosomal circRNA CD226 as a potent driver of nonsmall cell lung cancer through miR-1224-3p/high mobility group AT-hook 2 axis.

Circular RNAs (circRNAs) are crucial for the pathogenesis of nonsmall lung cancer (NSCLC). Here, we set out to unravel the precise function of circRNA CD226 (circCD226) in NSCLC pathogenesis. The exosomes from serum specimens were observed by transmission electron microscopy. CircCD226, miR-1224-3p and high mobility group AT-hook 2 (HMGA2) were quantified by qRT-PCR, western blot and immunohistochemistry. Actinomycin D and Ribonuclease (RNase) R treatments and subcellular localization assay were used for circCD226 characterization. Cell viability, proliferation, migration, invasion and sphere formation abilities were gauged by CCK-8, EDU, wound-healing, transwell and sphere formation assays, respectively. Directed relationships among circCD226, miR-1224-3p and HMGA2 were examined by RNA pull-down, dual-luciferase reporter and RNA immunoprecipitation (RIP) assays. The abundance of circCD226 was elevated in serum exosomes, tissues and cells of NSCLC. NSCLC serum exosomes enhanced NSCLC cell proliferation, migration, invasion and stemness. Loss of circCD226 impeded cell proliferation, migration, invasion and stemness in vitro , as well as tumor growth in vivo . Mechanistically, circCD226 sponged miR-1224-3p, and miR-1224-3p targeted HMGA2. CircCD226 involved the posttranscriptional regulation of HMGA2 through miR-1224-3p. Moreover, the miR-1224-3p/HMGA2 axis was identified as a functionally downstream effector of circCD226 in regulating NSCLC cell behaviors. Our study identifies circCD226 as a potential driver in NSCLC development depending on the regulation of miR-1224-3p/HMGA2 axis.

Efficient fish-scale CeO2/NiFeCo composite material as electrocatalyst for oxygen evolution reaction.

An electrochemical catalyst with efficient, stable, inexpensive energy storage for oxygen evolution and hydrogen evolution has raised global concerns on energy, calling for high-performance materials for effective treatments. In this paper, novel amorphous polymetallic doped CeO2particles were prepared for an electrochemical catalyst via homogeneous phase precipitation at room temperature. Metal ions can be easily embedded into the oxygen vacancies formed by CeO2, and the the electron transport capacity of the CeO2/NiFeCo electrocatalyst is improved owing to the increase in active sites. In addition, the amorphous CeO2/NiFeCo composite material is in a metastable state and will transform into different active states in a reducing or oxidizing environment. Furthermore, the amorphous material drives oxygen evolution reaction (OER) through the lattice oxygen oxidation mechanism (LOM), while LOM can effectively bypass the adsorption of strongly related intermediates in the adsorbate release mechanism, thus promoting OER procedure in a timely manner. As a result, CeO2/NiFeCo exhibits a lower oxygen evolution overpotential of 260 mV at 10 mA cm-2current density, which shows a predatorily competitive advantage compared with commercially available RuO2and the reported catalysts.

Functional analysis of four Class III peroxidases from Chinese pear fruit: a critical role in lignin polymerization.

Pear fruit could be used as good medicine to relieve coughs, promote salivation, nourish lungs, and reduce the risk of many diseases for its phytochemical action. Lignin is a major secondary metabolite in Chinese pear fruit. Class III peroxidase (Class III PRX) is an important enzyme in the biosynthesis of lignin in plants. However, we poorly understand the role of PRXs in lignin biosynthesis in Chinese pear fruit. In our study, we cloned five PRXs from Chinese pear (Pyrus bretschneideri), namely PbPRX2, PbPRX22, PbPRX34, PbPRX64, and PbPRX75, which contained 978 bp encoded 326 amino acids (AA), 2607 bp encoded 869 AA, 972 bp encoded 324 AA, 687 bp encoded 229 AA, and 1020 bp encoded 340 AA, respectively. Enzyme activity analysis showed that four recombinant PbPRX proteins had catalytic activities for pyrogallol, guaiacol, ferulic acid, coniferyl alcohol, and sinapyl alcohol. Subcellular localization experiments showed that these genes were located in the cell wall or cell membrane. Enzyme activity and kinetics of PbPRX2 revealed its role in polymerization of lignin in Chinese pear fruit. The present study suggested that PbPRXs played critical roles in lignin biosynthesis in Chinese pear fruit. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-00949-9.

Method for fast staining and obtaining high-magnification and high-resolution cell images of Nicotiana benthamiana.

As tools of plant molecular biology, fluorescence microscopy and Nicotiana benthamiana have been used frequently to study the structure and function of plant cells. However, it is difficult to obtain ideal micrographs; for example, the images are typically unclear, the inner cell structure cannot be observed under a high-power lens by fluorescence microscopy, etc. Here, we describe a method for observing the cell structure of N. benthamiana. This method significantly improves imaging by fluorescence microscopy and allows clear images to be obtained under a high-power lens. This method is easy to perform with good stability, and the stomatal structure, nucleus, nucleolus, chloroplast and other organelles in N. benthamiana cells as well as protein localizations and the locations of protein-protein interactions have been observed clearly. Furthermore, compared with traditional methods, fluorescent dye more efficiently dyes cells with this method. The applicability of this method was verified by performing confocal scanning laser microscopy (CSLM), and CSLM imaging was greatly improved. Thus, our results provided a method to visualize the subcellular structures of live cells in the leaves of N. benthamiana by greatly improving imaging under a fluorescence microscope and provided new insights and references for the study of cell structures and functions in other plants. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-00931-5.

Comparative analysis of B-BOX genes and their expression pattern analysis under various treatments in Dendrobium officinale.

BACKGROUND: Studies have demonstrated that BBX (B-BOX) genes play crucial roles in regulatory networks controlling plant growth, developmental processes and stress response. Nevertheless, comprehensive study of BBX genes in orchids (Orchidaceae) is not well studied. The newly released genome sequences of Dendrobium officinale and Phalaenopsis equestris have allowed a systematic analysis of these important BBX genes in orchids. RESULTS: Here we identified 19 (DoBBX01-19) and 16 (PeBBX01-16) BBX genes from D. officinale and P. equestris, respectively, and clustered into five clades (I-V) according to phylogenetic analysis. Thirteen orthologous, two DoBBXs paralogous and two PeBBXs paralogous gene pairs were validated. This gene family mainly underwent purifying selection, but five domains experienced positive selection during evolution. Noteworthy, the expression patterns of root, root_tips, stem, leaf, speal, column, lip, and flower_buds revealed that they might contribution to the formation of these tissues. According to the cis-regulatory elements analysis of BBX genes, qRT-PCR experiments were carried out using D. officinale PLBs (protocorm-like bodies) and displayed that these BBX genes were differentially regulated under AgNO3, MeJA (Methyl Jasmonate), ABA (abscisic acid) and SA (salicylic acid) treatments. CONCLUSIONS: Our analysis exposed that DoBBX genes play significant roles in plant growth and development, and response to different environmental stress conditions of D. officinale, which provide aid in the selection of appropriate candidate genes for further functional characterization of BBX genes in plants.

Phylogenetically conserved TAK1 participates in Branchiostoma belcheri innate immune response to LPS stimulus.

Transforming growth factor-ß activated kinase-1 (TAK1) is an important member of the mitogen-activated protein kinase kinase kinase (MAP3K) family, which plays an important role in animal innate immune response. However, the TAK1 gene has yet not been reported in amphioxus to date. Here, we have identified and characterized a TAK1 gene from amphioxus (Branchiostoma belcheri) (named as AmphiTAK1) with the full-length cDNA of 3479 bp, including an ORF sequence of 1905 bp, a 5' UTR of 394 bp and a 3' UTR of 1180 bp. Moreover, the predicted AmphiTAK1 protein contains STKc_TAK1 domain, TAB1 and TAB2/3 binding domain which are conserved among chordate, and phylogenetic analysis also shows that the AmphiTAK1 is located at the bottom of the chordate, revealing AmphiTAK1 as a new member of the TAK1 gene family. The further qRT-PCR analysis has shown that AmphiTAK1 is widely expressed in six investigated tissues (gonad, gill, hepatic cecum, intestine, muscle and notochord) of Branchiostoma belcheri, with high expression in notochord and gonad, moderate in gill and hepatic cecum. Notably, the expression level of AmphiTAK1 is significantly up-regulated after LPS stimulation. Specially, we also find that AmphiTAK1 protein can interact with AmphiTAB1 by immunoprecipitation assay. These findings reveal that AmphiTAK1 might interact with AmphiTAB1 to involve in innate immune response of Branchiostoma belcheri. Taken together, our present works provide a new insight into evolution and innate immune response mechanism of AmphiTAK1 gene in Branchiostoma belcheri.

Comparative Analysis and Expression Patterns of the PLP_deC Genes in Dendrobium officinale.

Studies have shown that the type II pyridoxal phosphate-dependent decarboxylase (PLP_deC) genes produce secondary metabolites and flavor volatiles in plants, and TDC (tryptophan decarboxylase), a member of the PLP_deC family, plays an important role in the biosynthesis of terpenoid indole alkaloids (TIAs). In this study, we identified eight PLP_deC genes in Dendrobium officinale (D. officinale) and six in Phalaenopsis equestris (P. equestris), and their structures, physicochemical properties, response elements, evolutionary relationships, and expression patterns were preliminarily predicted and analyzed. The results showed that PLP_deC genes play important roles in D. officinale and respond to different exogenous hormone treatments; additionally, the results support the selection of appropriate candidates for further functional characterization of PLP_deC genes in D. officinale.

Expansion and evolutionary patterns of GDSL-type esterases/lipases in Rosaceae genomes.

GDSL-type esterase/lipase (GELP) is mainly characterized by a conserved GDSL domain at N terminus, and is widely found in all living species, both prokaryotes and eukaryotes. GELP gene family consists of a wide range of members playing important roles in plant physiological processes, such as development, stress responses, and functional divergences. In our study, 597 GELP genes were identified from six Rosaceae genomes (i.e., Fragaria vesca, Prunus persica, Prunus avium, Prunus mume, Pyrus bretschneideri, and Malus domestica) by a comprehensive analysis. All GELP genes were further divided into ten subfamilies based on phylogenetic tree analysis. Subfamily D and subfamily E are the two largest subfamilies. Microcollinearity analysis suggested that WGD/segmental events contribute to the expansion of the GELP gene family in M. domestica and P. bretschneideri compared to F. vesca, P. persica, P. avium, and P. mume. Some PbGELPs were expressed during the fruit development of P. bretschneideri and pollen tubes, indicating their activity in these tissues. The expression divergence of PbGELP duplication gene pairs suggests that many mutations were allowed during evolution, although the structure of GELP genes was highly conserved. The current study results provided the feasibility to understand the expansion and evolution patterns of GELP in Rosaceae genomes, and highlight the function during P. bretschneideri fruits and pollen tubes development.

Systematic analysis and comparison of the PHD-Finger gene family in Chinese pear (Pyrus bretschneideri) and its role in fruit development.

PHD-finger proteins, which belongs to the type of zinc finger family, and that play an important role in the regulation of both transcription and the chromatin state in eukaryotes. Currently, PHD-finger proteins have been well studied in animals, while few studies have been carried out on their function in plants. In the present study, 129 non-redundant PHD-finger genes were identified from 5 Rosaceae species (pear, apple, strawberry, mei, and peach); among them, 31 genes were identified in pear. Subsequently, we carried out a bioinformatics analysis of the PHD-finger genes. Thirty-one PbPHD genes were divided into 7 subfamilies based on the phylogenetic analysis, which are consistent with the intron-exon and conserved motif analyses. In addition, we identified five segmental duplication events, implying that the segmental duplications might be a crucial role in the expansion of the PHD-finger gene family in pear. The microsynteny analysis of five Rosaceae species showed that there were independent duplication events in addition to the genome-wide duplication of the pear genome. Subsequently, ten expressed PHD-finger genes of pear fruit were identified using qRT-PCR, and one of these genes, PbPHD10, was identified as an important candidate gene for the regulation of lignin synthesis. Our research provides useful information for the further analysis of the function of PHD-finger gene family in pear.