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Background: Phenylalanine ammonia-lyase (PAL) serves as a key gateway enzyme, bridging primary metabolism and the phenylpropanoid pathway, and thus playing an indispensable role in flavonoid, anthocyanin and lignin biosynthesis. PAL gene families have been extensively studied across species using public genomes. However, a comprehensive exploration of PAL genes in Epimedium species, especially those involved in prenylated flavonol glycoside, anthocyanin, or lignin biosynthesis, is still lacking. Moreover, an in-depth investigation into PAL gene family evolution is warranted., Results: Seven PAL genes (EpPAL1-EpPAL7) were identified. EpPAL2 and EpPAL3 exhibit low sequence identity to other EpPALs (ranging from 61.09 to 64.38%) and contain two unique introns, indicating distinct evolutionary origins. They evolve at a rate ~ 10 to ~ 54 times slower compared to EpPAL1 and EpPAL4-7, suggesting strong purifying selection. EpPAL1 evolved independently and is another ancestral gene. EpPAL1 formed EpPAL4 through segmental duplication, which lead to EpPAL5 and EpPAL6 through tandem duplications, and EpPAL7 through transposed duplication, shaping modern EpPALs. Correlation analysis suggests EpPAL1, EpPAL2 and EpPAL3 play important roles in prenylated flavonol glycosides biosynthesis, with EpPAL2 and EpPAL3 strongly correlated with both Epimedin C and total prenylated flavonol glycosides. EpPAL1, EpPAL2 and EpPAL3 may play a role in anthocyanin biosynthesis in leaves. EpPAL2, EpPAL3, EpPAL6, and EpPAL7 might be engaged in anthocyanin production in petals, and EpPAL2 and EpPAL3 might also contribute to anthocyanin synthesis in sepals. Further experiments are needed to confirm these hypotheses. Novel insights into the evolution of PAL gene family suggest that it might have evolved from a monophyletic group in bryophytes to large-scale sequence differentiation in gymnosperms, basal angiosperms, and Magnoliidae. Ancestral gene duplications and vertical inheritance from gymnosperms to angiosperms likely occurred during PAL evolution. Most early-diverging eudicotyledons and monocotyledons have distinct histories, while modern angiosperm PAL gene families share similar patterns and lack distant gene types., Conclusions: EpPAL2 and EpPAL3 may play crucial roles in biosynthesis of prenylated flavonol glycosides and anthocyanins in leaves and flowers. This study provides novel insights into PAL gene family evolution. The findings on PAL genes in E. pubescens will aid in synthetic biology research on prenylated flavonol glycosides production., (© 2024. The Author(s).)

Phosphorus, a crucial macronutrient essential for plant growth and development. Due to widespread phosphorus deficiency in soils, phosphorus deficiency stress has become one of the major abiotic stresses that plants encounter. Despite the evolution of adaptive mechanisms in plants to address phosphorus deficiency, the specific strategies employed by species such as Epimedium pubescens remain elusive. Therefore, this study observed the changes in the growth, physiological reponses, and active components accumulation in E. pubescensunder phosphorus deficiency treatment, and integrated transcriptome and miRNA analysis, so as to offer comprehensive insights into the adaptive mechanisms employed by E. pubescens in response to phosphorus deficiency across various stages of phosphorus treatment. Remarkably, our findings indicate that phosphorus deficiency induces root growth stimulation in E. pubescens, while concurrently inhibiting the growth of leaves, which are of medicinal value. Surprisingly, this stressful condition results in an augmented accumulation of active components in the leaves. During the early stages (30 days), leaves respond by upregulating genes associated with carbon metabolism, flavonoid biosynthesis, and hormone signaling. This adaptive response facilitates energy production, ROS scavenging, and morphological adjustments to cope with short-term phosphorus deficiency and sustain its growth. As time progresses (90 days), the expression of genes related to phosphorus cycling and recycling in leaves is upregulated, and transcriptional and post-transcriptional regulation (miRNA regulation and protein modification) is enhanced. Simultaneously, plant growth is further suppressed, and it gradually begins to discard and decompose leaves to resist the challenges of long-term phosphorus deficiency stress and sustain survival. In conclusion, our study deeply and comprehensively reveals adaptive strategies utilized by E. pubescens in response to phosphorus deficiency, demonstrating its resilience and thriving potential under stressful conditions. Furthermore, it provides valuable information on potential target genes for the cultivation of E. pubescens genotypes tolerant to low phosphorus., (© 2024. The Author(s).)

Prenylated flavonol glycosides in Epimedium plants, as key medicinal components, are known to have great pharmaceutical activities for human health. Among the main prenylated flavonol glycosides, the modification mechanism of different sugar moieties is still not well understood. In the current study, a novel prenylated flavonol rhamnoside xylosyltransferase gene ( EpF3R2″XylT ) was cloned from E. pubescens , and the enzymatic activity of its decoding proteins was examined in vitro with different prenylated flavonol rhamnoside substrates and different 3- O -monosaccharide moieties. Furthermore, the functional and structural domains of EpF3R2″XylT were analyzed by bioinformatic approaches and 3-D protein structure remodeling. In summary, EpF3R2″XylT was shown to cluster with GGT (glycosyltransferase that glycosylates sugar moieties of glycosides) through phylogenetic analysis. In enzymatic analysis, EpF3R2″XylT was proven to transfer xylose moiety from UDP-xylose to prenylated flavonol rhamnoside at the 2″-OH position of rhamnose. The analysis of enzymatic kinetics showed that EpF3R2″XylT had the highest substrate affinity toward icariin with the lowest K m value of 75.96 ± 11.91 mM. Transient expression of EpF3R2″XylT in tobacco leaf showed functional production of EpF3R2″XylT proteins in planta. EpF3R2″XylT was preferably expressed in the leaves of E. pubescens , which is consistent with the accumulation levels of major prenylflavonol 3- O -triglycoside. The discovery of EpF3R2″XylT will provide an economical and efficient alternative way to produce prenylated flavonol trisaccharides through the biosynthetic approach.

Epimedium L. is an important genus in the family Berberidaceae. Epimedium trifoliolatobinatum (Koidz.) Koidz. 1939 is inhabited on the west side of the Shikoku, Japan. In this study, the first complete chloroplast genome of E. trifoliolatobinatum was assembled with Illumina paired-end sequencing data, which was 157,272 bp in length with a total GC content of 38.70%. A total of 112 unique genes were annotated, comprising 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis suggested that E. trifoliolatobinatum was sister to E. koreanum. The current results provided fundamental information for further conducting molecular systematics and phylogenetic research of Epimedium genus. [ABSTRACT FROM AUTHOR]

Epimedium L. is an important medicinal herbaceous genus that belongs to the family Berberidaceae. Epimedium campanulatum Ogisu is a plant species only inhabited in the northwestern part of Sichuan province, China. Here, we reported the complete chloroplast genome sequence, assembly, and characterization of E. campanulatum. The chloroplast genome of E. campanulatum was 157,343 bp in length, and a total of 112 unique genes were identified. Phylogenetic results revealed that E. campanulatum formed a sister relationship with the cluster of Epimedium ecalcaratum, Epimedium davidii, and Epimedium chlorandrum. Our findings provided valuable data for future taxonomic and phylogenetic research within the genus Epimedium. [ABSTRACT FROM AUTHOR]

Epimedium L. is an important medicinal herbaceous genus in the family Berberidaceae. Epimedium platypetalum K. Mey. is a plant species only narrowly distributed in the western part of China. Here, the complete chloroplast genome of Epimedium platypetalum was assembled. The chloroplast genome of E. platypetalum was 159,088 bp in length, with a total GC content of 38.79%. A total of 112 unique genes were identified, among which 78 are protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic results revealed that E. platypetalum formed a sister relationship with E. membranaceum K. Mey. Our findings provided valuable data for future research on phylogenetic relationship and germplasm exploration within the genus Epimedium. [ABSTRACT FROM AUTHOR]

Epimedium L. is the largest herbaceous genus in the family Berberidaceae which comprises more than 60 species. Epimedium sutchuenense Franch. is narrowly inhabited in the Daba Mountains of China. In the current study, we assembled the first complete chloroplast genome of E. sutchuenense through Illumina paired-end sequencing. The complete chloroplast genome of E. sutchuenense was 157,218 bp in length and the total GC content was 38.78%. A total of 112 unique genes were identified, including 78 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The phylogenetic analysis demonstrated that E. sutchuenense was sister to Epimedium wushanense T. S. Ying. Our results provided valuable information for further phylogenetic research and germplasm exploration of Epimedium genus. [ABSTRACT FROM AUTHOR]

Epimedium L. is a medicinally important herbaceous genus in the family Berberidaceae. Epimedium fargesii Franch. is only narrowly inhabited in the Daba Mountains in China. Here, we sequenced and assembled the first complete chloroplast genome of Epimedium fargesii Franch. The chloroplast genome of E. fargesii was 157,208 bp in length, with a total GC content of 38.77%. A total of 112 unique genes were identified, including 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis indicated that E. fargesii formed a sister relationship with E. wushanense T. S. Ying. Our results provided fundamental data for further taxonomic and phylogenetic research of the genus Epimedium. [ABSTRACT FROM AUTHOR]

Epimedium L. is the largest herbaceous genus of Berberidaceae which comprises more than 60 species. Epimedium pudingense is a rare plant species only narrowly inhabited in the Puding County in the Guizhou Province of China. Here, we first report the complete chloroplast genome of E. pudingense assembled from Illumina short-read sequencing data. The chloroplast genome of E. pudingense was 157,325 bp in length, with a total GC content of 36.11%. A total of 112 unique genes were identified, among which are 78 protein-coding genes, 30 tRNA genes and four rRNA genes. The phylogenetic analysis revealed that E. pudingense closely related to E. elachyphyllum. Our study will provide useful fundamental data for further phylogenetic and evolutionary studies of the Epimedium genus. [ABSTRACT FROM AUTHOR]

Epimedium xichangense, a critically endangered herb with limited population, mainly distributes in Sichuan province, China. In our study, we obtained the complete chloroplast genome of E. xichangense with a length of 158,955 bp, including a large single copy region of 86,478 bp, small single copy region of 17,027 bp, and a pair of inverted repeat regions of 27,725 bp. The GC content in the whole chloroplast genome of E. xichangense is 38.81%. Among the 112 unique genes in the circular genome, 30 tRNA, four rRNA and 78 protein-coding genes were successfully annotated. We constructed the Maximum likelihood (ML) tree with 26 species, and came to the conclusion that E. xichangense was phylogenetically closely related to E. acuminatum and E. chlorandrum. [ABSTRACT FROM AUTHOR]

Epimedium rhizomatosum is a rare endemic plant species inhabited in some high-elevation mountain area in the Sichuan province of China. In this study, we assembled the complete chloroplast genome of E. rhizomatosum from Illumina short-read sequencing data. The chloroplast genome of E. rhizomatosum was 159,151 bp in length, which comprises of a large single copy (LSC) region of 86,604 bp, a small single copy (SSC) region of 17,071 bp and two inverted repeat regions (IRa and IRb) of 27,737 bp for each. The total GC content of E. rhizomatosum chloroplast genome was 38.8%, while the corresponding values of LSC, SSC, and IR regions were 37.3%, 32.8%, and 43.0%, respectively. A total of 112 unique genes was identified from the chloroplast genome of E. rhizomatosum, including 78 protein-coding genes, four ribosomal RNA genes, and 30 tRNA genes. The phylogenetic analysis showed that E. rhizomatosum closely related to E. acuminatum. Our study will provide useful information on further clarifying the phylogenetic and evolutionary relationship in the genus Epimedium. [ABSTRACT FROM AUTHOR]

Epimedium elachyphyllum, which belongs to Berberidaceae, is only distributed in Guizhou province of China. In this study, the complete chloroplast (cp)genome of E. elachyphyllum was sequenced and assembled. The circular genome is 157,201 bp in length, which comprises of a large single-copy region (LSC, 88,519 bp), a small single-copy region (SSC, 17,042 bp), and a pair of inverted repeat regions (IRa and IRb, 25,820 bp). The genome of E. elachyphyllum contains 112 unique genes, of which 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis based on 18 complete cp genome sequences indicated that E. elachyphyllum was closely related to E. dolichostemon. [ABSTRACT FROM AUTHOR]

In this study, the complete chloroplast (cp) genome of Epimedium tianmenshanense was sequenced and assembled. The circular genome is 157,066 bp in size. The whole chloroplast genome of E. tianmenshanense contains 112 unique genes, of which 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis based on 17 complete chloroplast genomes demonstrated a closer relationship between E. tianmenshanense and E. lishihchenii. [ABSTRACT FROM AUTHOR]

Epimedii Folium has been used as a common traditional Chinese medicine for more than 2000 years in China. In this study, we assembled the complete chloroplast (cp) genome of Epimedium brevicornu. The whole cp genome of E. brevicornu is 158,658 bp in length, comprising a pair of inverted repeat (IR) regions (27,699 bp) separated by a large single copy (LSC) region (86,558 bp) and a small single copy (SSC) region (16,702bp). The E. brevicornu cp genome contains 129 genes, of which 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis shows that E. brevicornu is closely clustered with E. wushanense, E. lishihchenii, and E. sagittatum. The published E. brevicornu chloroplast genome will provide useful information for the phylogenetic and evolutionary study on Epimedium family of Berberidaceae. [ABSTRACT FROM AUTHOR]

Epimedium mikinorii is a vulnerable species in the Epimedium genus of Berberaceae. Here, we sequenced the complete chloroplast genome of E. mikinorii, which is 157,136 bp in length, and is a typical quadripartite circular molecule composed of two inverted repeats (IRs) of 25,896 bp for each, a large single-copy region (LSC) of 88,395 bp, and a small single-copy region (SSC) of 16,949 bp. The complete chloroplast genome of E. mikinorii contains 134 genes, including 83 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and 5 pseudogenes. Phylogenetic analysis showed that E. mikinorii was closely related to E. dolichostemon. [ABSTRACT FROM AUTHOR]

Epimedium qingchengshanense G. Y. Zhong & B. L. Guo is an endangered species with high ornamental value and medicinal value in China. In this study, we reported the first complete chloroplast (cp) genome of E. qingchengshanense. The whole cp genome of E. qingchengshanense is 159,087 bp in length, comprising a pair of inverted repeat regions (IRs) (27,709 bp) that are separated by a large single-copy (LSC) region (86,607 bp) and a small single-copy (SSC) region (17,062 bp). The circular genome contains 112 unique genes, of which 78 are protein-coding genes, 30 tRNA, and 4 rRNA genes. Phylogenetic analysis shows that E. qingchengshanense has a closer relationship with other Epimedium species. [ABSTRACT FROM AUTHOR]