Hui Guo Li

Platycodon grandiflorum (P. grandiflorum) is a commonly used medicinal plant in China. Transcriptome sequencing studies of different tissues of P. grandiflorum have been widely conducted. However, studies on transcriptome sequencing and expression patterns of key genes in the saponin synthesis pathway of Tongcheng P. grandiflorum, a high-quality medicinal resource of different years, are relatively limited. This study involved transcriptome sequencing and bioinformatics analysis of the roots from annual, biennial, and triennial P. grandiflorum in the Tongcheng area. After data filtering and assembly, we obtained 111.44 Gb of clean base data, including 742,880616 clean reads. We identified 5,156 differential expression unigenes between at least two sample groups, with differences noted among annual, biennial, and triennial P. grandiflorum plants. GO enrichment analysis annotated 3509, 1819, and 1393 DEGs in comparison TC1vsTC2, TC1vsTC3, and TC2vsTC3, respectively. Furthermore, KEGG enrichment analysis identified 16 genes encoding key enzymes in the terpene skeleton biosynthesis, sesquiterpene and triterpene biosynthesis pathways, including SE, AACT, FPPS, DXR, HMGR, HMGS, and DXS. The results of qRT-PCR experiments showed that most of the genes were most highly expressed in annual P. grandiflorum. The present study provided transcriptomic data from the roots of Tongcheng P. grandiflorum of different years, which provides critical bioinformatics data on the growth and development of P. grandiflorum, laying a foundation for further research on saponins and identifying key enzymes involved in this process across different growth stages.

The TIFY family consists of plant-specific genes that regulates multiple plant functions, including developmental and defense responses. Here, we performed a comprehensive genomic analysis of TIFY genes in Dendrobium huoshanense. Our analysis encompassed their phylogenetic relationships, gene structures, chromosomal distributions, promoter regions, and patterns of collinearity. A total of 16 DhTIFY genes were identified, and classified into distinct clusters named JAZ, PPD, ZIM, and TIFY based on their phylogenetic relationship. These DhTIFYs exhibited an uneven distribution across 7 chromosomes. The expansion of the DhTIFY gene family appears to have been significantly influenced by whole-genome and segmental duplication events. The ratio of non-synonymous to synonymous substitutions (Ka/Ks) implies that the purifying selection has been predominant, maintaining a constrained functional diversification after duplication events. Gene structure analysis indicated that DhTIFYs exhibited significant structural variation, particularly in terms of gene organization and intron numbers. Moreover, numerous cis-acting elements related to hormone signaling, developmental processes, and stress responses were identified within the promoter regions. Subsequently, qRT-PCR experiments demonstrated that the expression of DhTIFYs is modulated in response to MeJA (Methyl jasmonate), cold, and drought treatment. Collectively, these results enhance our understanding of the functional dynamics of TIFY genes in D. huoshanense and may pinpoint potential candidates for detailed examination of the biological roles of TIFY genes.

Jasmonate (JA) signaling plays a pivotal role in plant stress responses and secondary metabolism. Many studies have demonstrated that JA effectively induce the expressions of alkaloid biosynthetic genes in various plants, which rendered to the accumulation of alkaloid to counteract stresses. Despite the multiple roles of JA in the regulation of plant growth and different stresses, less studied involved in the regulatory role of JA in Dendrobium officinale alkaloids. A strategy for the rapid identification of alkaloid and the intermediates of D. officinale was established based on a solid-phase extraction coupled with high-performance liquid chromatography tandem mass spectrometry method. By using SPE-LC-MS/MS method, the potential compounds were tentatively identified by aligning the accurate molecular weight with the METLIN and Dictionary of Natural Products databases. The chemical structures and main characteristic fragments of the potential compounds were further confirmed by retrieving the multistage mass spectra from the MassBank and METLIN databases. The Mass Frontier software was used to speculate the fragmentation pathway of the identified compounds. Seven alkaloids were separated and identified from D. officinale, which were mainly classified into five types (tropane alkaloids, tetrahydroisoquinoline alkaloids, quinolizidine alkaloids, piperidine alkaloids, and spermidine alkaloids). Besides the alkaloids, forty-nine chemical substances, including guanidines, nucleotides, dipeptides, sphingolipids and nitrogen-containing glucosides, were concurrently identified. These findings gives the composition of chemicals currently found in D. officinale, which could provide the scientific method for the identification of alkaloids in other Dendrobium plants.

JA signaling plays a pivotal role in plant stress responses and secondary metabolism. Many studies have demonstrated that jasmonates effectively induce the expressions of alkaloid biosynthesis genes in various plants, which rendered to the accumulation of alkaloid to counteract stresses. Despite the multiple roles of jasmonate (JA) in the regulation of plant growth and different stresses, less studied involved in the regulatory role of JA in D. officinale alkaloids. A strategy for the rapid identification of alkaloid and the intermediates of D. officinale was established based on a solid-phase extraction coupled with high-performance liquid chromatography tandem mass spectrometry method. By using SPE-HPLC-LTQ-Orbitrap method, the potential compounds were tentatively identified by aligning the accurate molecular weight with the METLIN and Dictionary of Natural Products databases. The chemical structures and main characteristic fragments of the potential compounds were further confirmed by retrieving the multistage mass spectra from the MassBank and METLIN databases.The Mass Frontier software was used to speculate the fragmentation pathway of the identified compounds. Seven alkaloids were separated and identified from D. officinale , which were mainly classified into five types (tropane alkaloids, tetrahydroisoquinoline alkaloids, quinolizidine alkaloids, piperidine alkaloids and spermidine alkaloids). Besides the alkaloids, forty-nine chemical substances, including guanidines, nucleotides, dipeptides, sphingolipids and nitrogen-containing glucosides, were concurrently identified. These findings gives the composition of chemicals currently found in D. officinale , which could provide the scientific method for the identification of alkaloids in other Dendrobium plants.

Superoxide dismutases (SODs) are antioxidant enzymes that play a critical role in the polymerization of lignin monomers. Although current research has indicated that SODs are involved in plant growth and development, information on SODs in pear (Pyrus bretschneideri) and their function in lignin formation is scarce. In this study, 25 SODs, containing three kinds of plant SODs (Cu/Zn-SODs, Mn-SODs, and Fe-SODs), were identified from three Rosaceae species, and 11 of these genes were found in pear. According to the evolutionary analysis, the genes were divided into four subgroups, the division of which is consistent with the intron–exon and conserved motif analyses. These PbSODs were randomly scattered across 7 chromosomes. We have analysed the conserved domains and gene family evolution and predicted the cis-elements of the promoter. Ka/Ks analysis pointed that SOD genes mainly underwent purifying selection. Subsequently, the expression patterns of 11 PbSODs were examined in different tissues, at different developmental periods, in different pear varieties and under different hormone treatments. Gene expression analysis showed that PbCSD3 exhibited transcript levels consistent with the typical changes in lignin content. The changes in SOD activity and hydrogen peroxide (H₂O₂) content combined with the results of a spatio-temporal expression analysis showed that PbCSD3 was a candidate gene in reactive oxygen species (ROS) metabolism during the lignification of pear stone cells. Thus, our research reveals the evolutionary features of the SOD family in Rosaceae species and provide useful information for analysis of functional genome of the SOD family in pear.

Members of the cellulose synthase (CesA) and cellulose synthase–like (Csl) families from the cellulose synthase gene superfamily participate in cellulose and hemicellulose synthesis in the plasma membrane. The members of this superfamily are vital for cell wall construction during plant growth and development. However, little is known about their function in pear fruit, a model for Rosaceae species and for fleshy fruit development. In our research, a total of 36 CesA/Csl family members were identified from the pear and were grouped into six subfamilies (CesA, CslB, CslC, CslD, CslE, and CslG) according to phylogenetic relationships. We performed a protein sequence physicochemical analysis, phylogenetic tree construction, a gene structure, a conserved domain, and chromosomal localization analysis. The results indicated that most of the CesA/Csl genes from pear are closely related to genes in Arabidopsis, but these families have unique characteristics in terms of their gene structure, chromosomal localization, phylogeny, and deduced protein sequences, suggesting that they have evolved through different processes. Tissue expression analysis results showed that most of the CesA/Csl genes were constitutively expressed at different levels in different organs. Furthermore, the expression levels of four genes (Pbr032894.2, Pbr016107.1, Pbr00518.1, and Pbr034218.1) tended to first increase and then decrease during fruit development, implying that these four genes may be involved in the development of stone cells of pear fruit. Our results may help elucidate the evolutionary history and functional differences of the CesA/Csl genes in pear and lay a foundation for further investigation of the CesA/Csl genes in pear and other Rosaceae species.

Phenylalanine ammonia lyase (PAL) plays an important role in the biosynthesis of secondary metabolites regulating plant growth response. To date, the evolutionary history of the PAL family in Rosaceae plants remains unclear. In this study, we identified 16 PAL homologous genes in five Rosaceae plants (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Prunus persica, and Malus × domestica). We classified these PAL genes into three categories based on phylogenetic analysis，and all PAL genes were distributed on 13 chromosomes. Subsequently, we track gene replication events and perform sliding window analysis. These results revealed the evolution of PAL genes in five Rosaceae plants. We predicted the promoter of the PbPAL genes by PLANTR CARE online software, and found that the 5'regulatory region of both PbPAL1 and PbPAL3 has at least one AC element motif. The results of qRT-PCR analysis found that PbPAL1 and PbPAL2 were highly expressed in the stem and root , while expression level of PbPAL3 was relatively low in different tissues. The expression of PbPAL1 and PbPAL2 genes increased firstly and then decreased at different developmental periods of pear fruit. Among them, the expression of PbPAL1 reached the highest level 55 days after flower. Three PbPAL genes were induced by abiotic stress to varying degrees. We transfected PbPAL1 and PbPAL2 genes into Arabidopsis thaliana, resulting in lignin content increased significantly and thick cell wall of intervascular fibers and xylem cells. In summary, This study laid a foundation for better understanding the molecular evolution of PAL genes in five Rosaceae plants. Furthermore, the present study revealed the role of PbPAL genes in lignin synthesis, and provided basic data for regulating lignin synthesis and stone cell development of pear.

Phenylalanine ammonia lyase (PAL) plays an important role in the biosynthesis of secondary metabolites regulating plant growth response. To date, the evolutionary history of the PAL family in Rosaceae plants remains unclear. In this study, we identified 16 PAL homologous genes in five Rosaceae plants (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Prunus persica, and Malus × domestica). We classified these PAL genes into three categories based on phylogenetic analysis，and all PAL genes were distributed on 13 chromosomes. Subsequently, we track gene replication events and perform sliding window analysis. These results revealed the evolution of PAL genes in five Rosaceae plants. We predicted the promoter of the PbPAL genes by PLANTR CARE online software, and found that the 5'regulatory region of both PbPAL1 and PbPAL3 has at least one AC element motif. The results of qRT-PCR analysis found that PbPAL1 and PbPAL2 were highly expressed in the stem and root , while expression level of PbPAL3 was relatively low in different tissues. The expression of PbPAL1 and PbPAL2 genes increased firstly and then decreased at different developmental periods of pear fruit. Among them, the expression of PbPAL1 reached the highest level 55 days after flower. Three PbPAL genes were induced by abiotic stress to varying degrees. We transfected PbPAL1 and PbPAL2 genes into Arabidopsis thaliana, resulting in lignin content increased significantly and thick cell wall of intervascular fibers and xylem cells. In summary, This study laid a foundation for better understanding the molecular evolution of PAL genes in five Rosaceae plants. Furthermore, the present study revealed the role of PbPAL genes in lignin synthesis, and provided basic data for regulating lignin synthesis and stone cell development of pear.

Phenylalanine ammonia lyase (PAL) plays an important role in the biosynthesis of secondary metabolites regulating plant growth response. To date, the evolutionary history of the PAL family in Rosaceae plants remains unclear. In this study, we identified 16 PAL homologous genes in five Rosaceae plants (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Prunus persica, and Malus × domestica). We classified these PAL genes into three categories based on phylogenetic analysis，and all PAL genes were distributed on 13 chromosomes. Subsequently, we track gene replication events and perform sliding window analysis. These results revealed the evolution of PAL genes in five Rosaceae plants. We predicted the promoter of the PbPAL genes by PLANTR CARE online software, and found that the 5'regulatory region of both PbPAL1 and PbPAL3 has at least one AC element motif. The results of qRT-PCR analysis found that PbPAL1 and PbPAL2 were highly expressed in the stem and root , while expression level of PbPAL3 was relatively low in different tissues. The expression of PbPAL1 and PbPAL2 genes increased firstly and then decreased at different developmental periods of pear fruit. Among them, the expression of PbPAL1 reached the highest level 55 days after flower. Three PbPAL genes were induced by abiotic stress to varying degrees. We transfected PbPAL1 and PbPAL2 genes into Arabidopsis thaliana, resulting in lignin content increased significantly and thick cell wall of intervascular fibers and xylem cells. In summary, This study laid a foundation for better understanding the molecular evolution of PAL genes in five Rosaceae plants. Furthermore, the present study revealed the role of PbPAL genes in lignin synthesis, and provided basic data for regulating lignin synthesis and stone cell development of pear.

Phenylalanine ammonia lyase (PAL) plays an important role in the biosynthesis of secondary metabolites regulating plant growth response. To date, the evolutionary history of the PAL family in Rosaceae plants remains unclear. In this study, we identified 16 PAL homologous genes in five Rosaceae plants (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Prunus persica, and Malus × domestica). We classified these PAL genes into three categories based on phylogenetic analysis，and all PAL genes were distributed on 13 chromosomes. Subsequently, we track gene replication events and perform sliding window analysis. These results revealed the evolution of PAL genes in five Rosaceae plants. We predicted the promoter of the PbPAL genes by PLANTR CARE online software, and found that the 5'regulatory region of both PbPAL1 and PbPAL3 has at least one AC element motif. The results of qRT-PCR analysis found that PbPAL1 and PbPAL2 were highly expressed in the stem and root , while expression level of PbPAL3 was relatively low in different tissues. The expression of PbPAL1 and PbPAL2 genes increased firstly and then decreased at different developmental periods of pear fruit. Among them, the expression of PbPAL1 reached the highest level 55 days after flower. Three PbPAL genes were induced by abiotic stress to varying degrees. We transfected PbPAL1 and PbPAL2 genes into Arabidopsis thaliana, resulting in lignin content increased significantly and thick cell wall of intervascular fibers and xylem cells. In summary, This study laid a foundation for better understanding the molecular evolution of PAL genes in five Rosaceae plants. Furthermore, the present study revealed the role of PbPAL genes in lignin synthesis, and provided basic data for regulating lignin synthesis and stone cell development of pear.