Basic helix-loop-helix (bHLH) proteins, one of the most important and largest transcription factor family in plants, play important roles in regulating growth and development, stress response. In ...recent years, many bHLH family genes have been identified and characterized in woody plants. However, a systematic analysis of the bHLH gene family has not been reported in Ginkgo biloba, the oldest relic plant species. In this study, we identifed a total of 85 GbbHLH genes from the genomic and transcriptomic databases of G. biloba, which were classified into 17 subfamilies based on the phylogenetic analysis. Gene structures analysis indicated that the number of exon-intron range in GbbHLHs from 0 to 12. The MEME analysis showed that two conserved motifs, motif 1 and motif 2, distributed in most GbbHLH protein. Subcellular localization analysis exhibited that most GbbHLHs located in nucleus and a few GbbHLHs were distributed in chloroplast, plasma membrane and peroxisome. Promoter cis-element analysis revealed that most of the GbbHLH genes contained abundant cis-elements that involved in plant growth and development, secondary metabolism biosynthesis, various abiotic stresses response. In addition, correlation analysis between gene expression and flavonoid content screened seven candidate GbbHLH genes involved in flavonoid biosynthesis, providing the targeted gene encoding transcript factor for increase the flavonoid production through genetic engineering in G. biloba.
is an important medicinal plant widely used in traditional Chinese medicine. Luteoloside is a critical bioactive compound in
. To date, the molecular mechanisms underlying luteoloside biosynthesis ...are still largely unknown. In this work, high performance liquid chromatography (HPLC) was employed to determine the luteoloside contents in leaves, stems, and flowers at different developmental stages. Results showed that senescing leaves can accumulate large amounts of luteoloside, extremely higher than that in young and semi-lignified leaves and other tissues. RNA-Seq analysis identified that twenty-four differentially expressed unigenes (DEGs) associated with luteoloside biosynthesis were significantly up-regulated in senescing leaves, which are positively correlated with luteoloside accumulation. These DEGs include
,
, thirteen
,
, six
(
) and two
(
) genes. Further analysis demonstrated that two
(
and
) and two
(
and
) might play vital roles in luteoloside generation. Furthermore, several transcription factors (TFs) related to flavonoid biosynthesis including MYB, bHLH and WD40, were differentially expressed during leaf senescence. Among these TFs,
,
,
and
were considered to be key factors involved in the regulation of luteoloside biosynthesis. These findings provide insights for elucidating the molecular signatures of luteoloside accumulation in
.
Fraxinus hupehensis is an endangered tree species that is endemic to in China; the species has very high commercial value because of its intricate shape and potential to improve and protect the ...environment. Its seeds show very low germination rates in natural conditions. Preliminary experiments indicated that gibberellin (GA
) effectively stimulated the seed germination of F. hupehensis. However, little is known about the physiological and molecular mechanisms underlying the effect of GA
on F. hupehensis seed germination.
We compared dormant seeds (CK group) and germinated seeds after treatment with water (W group) and GA
(G group) in terms of seed vigor and several other physiological indicators related to germination, hormone content, and transcriptomics. Results showed that GA
treatment increases seed vigor, energy requirements, and trans-Zetain (ZT) and GA
contents but decreases sugar and abscisic acid (ABA) contents. A total of 116,932 unigenes were obtained from F. hupehensis transcriptome. RNA-seq analysis identified 31,856, 33,188 and 2056 differentially expressed genes (DEGs) between the W and CK groups, the G and CK groups, and the G and W groups, respectively. Up-regulation of eight selected DEGs of the glycolytic pathway accelerated the oxidative decomposition of sugar to release energy for germination. Up-regulated genes involved in ZT (two genes) and GA
(one gene) biosynthesis, ABA degradation pathway (one gene), and ABA signal transduction (two genes) may contribute to seed germination. Two down-regulated genes associated with GA
signal transduction were also observed in the G group. GA
-regulated genes may alter hormone levels to facilitate germination. Candidate transcription factors played important roles in GA
-promoted F. hupehensis seed germination, and Quantitative Real-time PCR (qRT-PCR) analysis verified the expression patterns of these genes.
Exogenous GA
increased the germination rate, vigor, and water absorption rate of F. hupehensis seeds. Our results provide novel insights into the transcriptional regulation mechanism of effect of exogenous GA
on F. hupehensis seed germination. The transcriptome data generated in this study may be used for further molecular research on this unique species.
The morphological, physiological, and biochemical characteristics of leaves result from the long-term adaptation of plants to their environment and are closely related to plant growth and ...development. In this study, 37 prickly ash germplasm resources from 18 production areas were utilized as the subjects of research. Logistic equations, principal component analysis, and cluster analysis were employed to comprehensively evaluate the leaf traits of prickly ash germplasm resources, with an analysis of their correlation with ecological and geographical factors in the production areas. The results showed that the leaf traits of prickly ash germplasms of different origins are substantially different and diverse. The coefficient of variation for the 14 leaf traits was greater than 10%. The coefficient of variation of the compound leaflet number was the highest among all the considered leaf traits, and the coefficient of variation of leaf thickness was the lowest, at 49.86% and 11.37%, respectively. The leaf traits of the prickly ash germplasm originating from Chongqing in Yongchuan, Chongqing in Rongchang, and Yunnan in Honghe ranked highest, whereas the leaf traits of the prickly ash germplasm from Henan in Jiaozuo, Gansu in Tianshui, and Shanxi in Yuncheng ranked lowest. The results of the correlation analysis showed that among the ecological and geographical factors of the origins, latitude had the strongest correlation with the leaf traits of the prickly ash germplasm. As latitude increased, the leaves of prickly ash gradually decreased in size, weight, and leaf shape index. The factor with the second strongest correlation was temperature. The leaves of the prickly ash germplasm originating from warmer climate areas were larger and heavier than those from areas with colder climates. Altitude and longitude did not significantly affect the leaf traits of the prickly ash germplasm, but at similar latitudes, the leaves of the prickly ash germplasm in high-altitude areas were smaller, and the leaves of the prickly ash germplasm in low-altitude areas were larger. These findings can provide valuable references for breeding and the sustainable utilization of new varieties of prickly ash resources.
In this study, we prepared high-nitrogen self-doped porous carbons (NPC1 and NPC2) derived from the pruned branches and seeds of
using a simple one-step method. NPC1 and NPC2 exhibited elevated ...nitrogen contents of 3.56% and 4.22%, respectively, along with rich porous structures, high specific surface areas of 1492.9 and 1712.7 m
g
and abundant surface groups. Notably, both NPC1 and NPC2 demonstrated remarkable adsorption abilities for the pollutant methylene blue (MB), with maximum monolayer adsorption capacities of 568.18 and 581.40 mg g
, respectively. The adsorption kinetics followed the pseudo-second-order kinetics and the adsorption isotherms conformed to the Langmuir isotherm model. The adsorption mechanism primarily relied on the hierarchical pore structures of NPC1 and NPC2 and their diverse strong interactions with MB molecules. This study offers a new approach for the cost-effective design of nitrogen self-doped porous carbons, facilitating the efficient removal of MB from wastewater.
Lonicera macranthoides Hand.-Mazz (L. macranthoides) is a medicinal herb that is widely distributed in southern China. The biosynthetic and metabolic pathways for a core secondary metabolite in L. ...macranthoides, chlorogenic acid (CGA), have been elucidated in many species. However, the mechanisms of CGA biosynthesis and the related gene regulatory network in L. macranthoides are still not well understood. In this study, CGA content was quantified by high performance liquid chromatography (HPLC), and CGA levels differed significantly among three tissues; specifically, the CGA content in young leaves (YL) was greater than that in young stems (YS), which was greater than that in mature flowers (MF). Transcriptome analysis of L. macranthoides yielded a total of 53,533,014 clean reads (average length 90 bp) and 76,453 unigenes (average length 703 bp). A total of 3,767 unigenes were involved in biosynthesis pathways of secondary metabolites. Of these unigenes, 80 were possibly related to CGA biosynthesis. Furthermore, differentially expressed genes (DEGs) were screened in different tissues including YL, MF and YS. In these tissues, 24 DEGs were found to be associated with CGA biosynthesis, including six phenylalanine ammonia lyase (PAL) genes, six 4-coumarate coenzyme A ligase (4CL) genes, four cinnamate 4-Hydroxylase (C4H) genes, seven hydroxycinnamoyl transferase/hydroxycinnamoyl-CoA quinate transferase HCT/HQT genes and one coumarate 3-hydroxylase (C3H) gene.These results further the understanding of CGA biosynthesis and the related regulatory network in L. macranthoides.
As a typical dioecious species,
establishes apomictic reproduction, hence only female trees are cultivated. However, male and hermaphrodite flowers have recently appeared in female plants, resulting ...in a dramatic yield reduction. To date, the genetic basis underlying sex determination and apomixis in
has been largely unknown. Here, we observed abortion of the stamen or carpel prior to primordium initiation, thus corroborating the potential regulation of MADS-box in sex determination. In
, a total of 105 MADS-box genes were identified, harboring 86 MIKC-type MADSs with lack of FLC orthologues. Transcriptome analysis revealed candidate
involved in floral organ identity, including ten male-biased
, represented by
(AP3/PI-like), and twenty-six female-specified, represented by
(STK/AGL11-like) and
(AG-like). Overexpressing
resulted in earlier flowering, while
overexpression triggered precocious fruit set and parthenocarpy as well as dramatic modifications in floral organs. To characterize their regulatory mechanisms, a comprehensive protein-protein interaction network of the represented MADSs was constructed based on yeast two-hybrid and bimolecular fluorescence complementation assays. Compared with model plants, the protein interaction patterns in
exhibited both conservation and divergence. ZaMADS70 (SEP3-like) interacted with ZaMADS42 and ZaMADS48 (AP3-like) but not ZaMADS40 (AP1-like), facilitating the loss of petals in
. The ZaMADS92/ZaMADS40 heterodimer could be responsible for accelerating flowering in
-OX lines. Moreover, the interactions between ZaMADS80 and ZaMADS67(AGL32-like) might contribute to apomixis. This work provides new insight into the molecular mechanisms of MADS-boxes in sex organ identity in
.
Introduction
Terpene trilactones (TTLs) are one of the main active ingredients of
Ginkgo biloba
. Owing to TTL’s unique chemical structure, it is difficult to increase TTL content through chemical ...and biological methods. Studying its regulatory mechanism is important in the
G. biloba
industry.
Results
The effect of exogenous methyl jasmonate (MeJA) on the physiological and molecular mechanism of TTL biosynthesis was studied. These results showed that MeJA treatment could improve the TTL contents, soluble sugar, starch, soluble protein, endogenous hormones (ZT, GA3, IAA, and ABA), antioxidant enzymes (catalase, peroxidase, and superoxide dismutase), and the efficiency of photosynthesis in
G. biloba
leaves. A total of 100 differentially expressed genes (DEGs) were identified between the control group and MeJA treatment through RNA-seq analysis. The results indicated that exogenous MeJA treatment upregulated the expression levels of the following genes:
BMY
(beta-amylase) in the starch and sucrose metabolic pathway;
PEX7
(peroxin-7) in the peroxisome pathway;
psbA
(photosystem II reaction center D1 protein),
psbC
(photosystem II CP43 chlorophyll apoprotein),
psaA
(photosystem I P700 chlorophyll a apoprotein A1), and
petF
(photosynthetic electron transport ferredoxin) in the photosynthesis pathway; and
CYP450
(
Gb-16765
) (cytochromeP450).
Conclusions
Exogenous MeJA treatment can promote physiological indexes (photosynthetic efficiency, starch, sucrose, antioxidant enzyme activities, etc.) and then regulating differential genes, thus controlling the synthesis of TTLs.
Terpenoids are the main active components in the Zanthoxylum armatum leaves, which have extensive medicinal value. The Z. armatum leaf is the main by‐product in the Z. armatum industry. However, the ...transcription factors involved in the biosynthesis of terpenoids are rarely reported. This study was performed to identify and classify the APETALA2/ethylene‐responsive factor (AP2/ERF) gene family of Z. armatum. The chromosome distribution, gene structure, conserved motifs, and cis‐acting elements of the promoter of the species were also comprehensively analyzed. A total of 214 ZaAP2/ERFs were identified. From the obtained transcriptome and terpenoid content data, four candidate ZaAP2/ERFs involved in the biosynthesis of terpenoids were selected via correlation and weighted gene co‐expression network analysis. A phylogenetic tree was constructed using 13 AP2/ERFs related to the biosynthesis of terpenoids in other plants. ZaERF063 and ZaERF166 showed close evolutionary relationships with the ERFs in other plant species and shared a high AP2‐domain sequence similarity with the two closest AP2/ERF proteins, namelySmERF8 from Salvia miltiorrhiza and AaERF4 from Artemisia annua. Further investigation into the effects of methyl jasmonate (MeJA) treatment on the content of terpenoids in Z. armatum leaves revealed that MeJA significantly induced the upregulation of ZaERF166 and led to a significant increase in the terpenoids content in Z. armatum leaves, indicating that ZaERF166 might be involved in the accumulation of terpenoids of Z. armatum. Results will be beneficial for the functional characterization of AP2/ERFs in Z. armatum and establishment of the theoretical foundation to increase the production of terpenoids via the manipulation of the regulatory elements and strengthen the development and utilization of Z. armatum leaves.
Core Ideas
A total of 214 APETALA2/ethylene‐responsive factors (AP2/ERFs) have been identified in the genome of Zanthoxylum armatum.
Methyl jasmonate (MeJA) treatment significantly enhanced the content of terpenoids in Z. armatum leaves.
ZaERF166 was significantly upregulated by MeJA induction.
ZaERF166 may be involved in the regulation of terpenoid synthesis in Z. armatum leaves.
As an important spice species in Rutaceae, the Sichuan pepper (Zanthoxylum armatum) can provide pungent and numbing taste, as well as aroma in its mature fruit. Here we assembled a chromosome-level ...genome of green prickly ash which was widely cultivated in a major production area including Chongqing and Sichuan province, China. We generated 712 Gb (∼112 × ) PacBio long reads and 511 Gb (∼82 × ) Hi-C data, and yielded an assembly of 99 pseudochromosomes with total size of 5.32 Gb and contig N50 of 796 kb. The genomic analyses and cytogenetic experiments both indicated that the cultivar ‘Zhuye Huajiao’ was a triploid. We identified a Zanthoxylum-specific whole genome duplication event emerging about 24.8 million years ago (Mya). We also detected a transposition burst event (0.3–0.4 Mya) responsible for the large genome size of Z. armatum. Metabolomic analysis of the Zanthoxylum fruits during development stages revealed profiles of 39 volatile aroma compounds and 528 secondary metabolites, from which six types of sanshools were identified. Based on metabolomic and transcriptomic network analysis, we screened candidate genes encoding long chain acyl-CoA synthetase, fatty acid desaturase, branched-chain amino acid aminotransferase involved in sanshool biosynthesis and three genes encoding terpene synthase during fruit development. The multi-omics data provide insights into the evolution of Zanthoxylum and molecular basis of numbing and aroma flavor of Sichuan pepper.
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