Nitrogen is a macronutrient element for plant growth and development. Circular RNAs (circRNAs) serve as pivotal regulators for the coordination between nutrient supply and plant demand. Moso bamboo ...(Phyllostachys edulis) is an excellent plant with fast growth, and the mechanism of the circRNA-target module in response to nitrogen remains unclear.
Deep small RNA sequencing results of moso bamboo seedlings under different concentrations of KNO
(N0 = 0 mM, N6 = 6 mM, N18 = 18 mM) were used to identify circRNAs. A total of 549 circRNAs were obtained, of which 309 were generated from corresponding parental coding genes including 66 new ones. A total of 536 circRNA-parent genes were unevenly distributed in 24 scaffolds and were associated with root growth and development. Furthermore, 52 differentially expressed circRNAs (DECs) were obtained, including 24, 33 and 15 DECs from three comparisons of N0 vs. N6, N0 vs. N18 and N6 vs. N18, respectively. Based on integrative analyses of the identified DECs, differentially expressed mRNAs (DEGs), and miRNAs (DEMs), a competitive endogenous RNA (ceRNA) network was constructed, including five DECs, eight DEMs and 32 DEGs. A regulatory module of PeSca_6:12,316,320|12,372,905-novel_miR156-PH02Gene35622 was further verified by qPCR and dual-luciferase reporter assays.
The results indicated that circRNAs could participate in multiple biological processes as miRNA sponges, including organ nitrogen compound biosynthesis and metabolic process regulation in moso bamboo. Our results provide valuable information for further study of circRNAs in moso bamboo under fluctuating nitrogen conditions.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The 14-3-3 protein family plays an important role in regulating plant growth and development. The genes of the 14-3-3 family have been reported in multiple species. However, little is known about the ...14-3-3 gene family in bamboo. In this study, a total of 58 genes belonging to the 14-3-3 family were identified in three representative bamboo species, i.e., Olyra latifolia, Phyllostachys edulis, and Bonia amplexicaulis, whose encoding proteins were grouped into ε and non-ε groups by phylogeny analysis with 14-3-3 proteins from Arabidopsis thaliana and Oryza sativa. The 14-3-3s had diverse gene structures and motif characteristics among the three bamboo species. Collinearity analysis suggested that the genes of the 14-3-3 family in bamboo had undergone a strong purification selection during evolution. Tissue-specific expression analysis showed the expression of Pe14-3-3s varied in different tissues of P. edulis, suggesting that they had functional diversity during growth and development. Co-expression analysis showed that four Pe14-3-3s co-expressed positively with eight ribosomal genes. Yeast two-hybrid (Y2H) assays showed that Pe14-3-3b/d could interact with Pe_ribosome-1/5/6, and qPCR results demonstrated that Pe14-3-3b/d and Pe_ribosome-1/5/6 had similar expression trends with the increase in shoot height, which further confirmed that they would work together to participate in the shoot growth and development of bamboo. Additionally, the transgenic Arabidopsis plants overexpressing Pe14-3-3b had longer roots, a larger stem diameter, an earlier bolting time and a faster growth rate than wild-type Arabidopsis, indicating that Pe14-3-3b acted as a growth promoter. Our results provide comprehensive information on 14-3-3 genes in bamboo and highlight Pe14-3-3b as a potential target for bamboo improvement.
The Kelch repeat F-box (KFB) protein is an important E3 ubiquitin ligase that has been demonstrated to perform an important post-translational regulatory role in plants by mediating multiple ...biological processes. Despite their importance, KFBs have not yet been identified and characterized in bamboo. In this study, 19 PeKFBs were identified with F-box and Kelch domains; genes encoding these PeKFBs were unevenly distributed across 12 chromosomes of moso bamboo. Phylogenetic analysis indicated that the PeKFBs were divided into eight subclades based on similar gene structures and highly conserved motifs. A tissue-specific gene expression analysis showed that the
s were differentially expressed in various tissues of moso bamboo. All the promoters of the
s contained stress-related
-elements, which was supported by the differentially expression of
s of moso bamboo under drought and cold stresses. Sixteen proteins were screened from the moso bamboo shoots' cDNA library using PeKFB9 as a bait through a yeast two-hybrid (Y2H) assay. Moreover, PeKFB9 physically interacted with PeSKP1-like-1 and PePRX72-1, which mediated the activity of peroxidase in proteolytic turnover. Taken together, these findings improved our understanding of PeKFBs, especially in response to stresses, and laid a foundation for revealing the molecular mechanism of PeKFB9 in regulating lignin polymerization by degrading peroxidase.
Plants employ an array of photoprotection mechanisms to alleviate the harmful effects of high light intensity. The violaxanthin cycle, which is associated with non-photochemical quenching (NPQ), ...involves violaxanthin de-epoxidase (VDE), and zeaxanthin epoxidase (ZEP) and is one of the most rapid and efficient mechanisms protecting plants under high light intensity. Woody bamboo is a class of economically and ecologically important evergreen grass species widely distributed in tropical and subtropical areas. However, the function of VDE in bamboo has not yet been elucidated. In this study, we found that high light intensity increased NPQ and stimulated the de-epoxidation of violaxanthin cycle components in moso bamboo (
Phyllostachys edulis
), whereas, samples treated with the VDE inhibitor (dithiothreitol) exhibited lower NPQ capacity, suggesting that violaxanthin cycle plays an important role in the photoprotection of bamboo. Further analysis showed that not only high light intensity but also extreme temperatures (4 and 42°C) and drought stress upregulated the expression of
PeVDE
in bamboo leaves, indicating that
PeVDE
is induced by multiple abiotic stresses. Overexpression of
PeVDE
under the control of the
CaMV 35S
promoter in
Arabidopsis
mutant
npq1
mutant could rescue its NPQ, indicating that
PeVDE
functions in dissipating the excess absorbed light energy as thermal energy in bamboo. Moreover, compared with wild-type (Col-0) plants, the transgenic plants overexpressing
PeVDE
displayed enhanced photoprotection ability, higher NPQ capacity, slower decline in the maximum quantum yield of photosystem II (
F
v
/
F
m
) under high light intensity, and faster recovery under optimal conditions. These results suggest that
PeVDE
positively regulates the response to high light intensity in bamboo plants growing in the natural environment, which could improve their photoprotection ability through the violaxanthin cycle and NPQ.
Moso bamboo (Phyllostachys edulis) is an economically and ecologically important nontimber forestry species. Further development of this species as a sustainable bamboo resource has been hindered by ...a lack of population genome information. Here, we report a moso bamboo genomic variation atlas of 5.45 million single-nucleotide polymorphisms (SNPs) from whole-genome resequencing of 427 individuals covering 15 representative geographic areas. We uncover low genetic diversity, high genotype heterozygosity, and genes under balancing selection underlying moso bamboo population adaptation. We infer its demographic history with one bottleneck and its recently small population without a rebound. We define five phylogenetic groups and infer that one group probably originated by a single-origin event from East China. Finally, we conduct genome-wide association analysis of nine important property-related traits to identify candidate genes, many of which are involved in cell wall, carbohydrate metabolism, and environmental adaptation. These results provide a foundation and resources for understanding moso bamboo evolution and the genetic mechanisms of agriculturally important traits.
Fargesia macclureana (Poaceae) is a woody bamboo species found on the Qinghai-Tibet Plateau (QTP) approximately 2000 ~ 3800 m above sea level. It rarely blossoms in the QTP, but it flowered 20 days ...after growing in our lab, which is in a low-altitude area outside the QTP. To date, little is known regarding the molecular mechanism of bamboo flowering, and no studies of flowering have been conducted on wild bamboo plants growing in extreme environments. Here, we report the first de novo transcriptome sequence for F. macclureana to investigate the putative mechanisms underlying the flowering time control used by F. macclureana to adapt to its environment.
Illumina deep sequencing of the F. macclureana transcriptome generated 140.94 Gb of data, assembled into 99,056 unigenes. A comprehensive analysis of the broadly, specifically and differentially expressed unigenes (BEUs, SEUs and DEUs) indicated that they were mostly involved in metabolism and signal transduction, as well as DNA repair and plant-pathogen interactions, which may be of adaptive importance. In addition, comparison analysis between non-flowering and flowering tissues revealed that expressions of FmFT and FmHd3a, two putative F. macclureana orthologs, were differently regulated in NF- vs F- leaves, and carbohydrate metabolism and signal transduction were two major KEGG pathways that DEUs were enriched in. Finally, we detected 9296 simple sequence repeats (SSRs) that may be useful for further molecular marker-assisted breeding.
F. macclureana may have evolved specific reproductive strategies for flowering-related pathways in response to photoperiodic cues to ensure long vegetation growing period. Our findings will provide new insights to future investigations into the mechanisms of flowering time control and adaptive evolution in plants growing at high altitudes.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Invertases (INVs) can irreversibly hydrolyze sucrose into fructose and glucose, which play principal roles in carbon metabolism and responses to various stresses in plants. However, little is known ...about the INV family in bamboos, especially their potential function in drought stress. In this study, 29
PeINV
s were identified in moso bamboo (
Phyllostachys edulis
). They were clustered into alkaline/neutral invertase (NINV) and acid invertase (AINV) groups based on the gene structures, conserved motifs, and phylogenetic analysis results. The collinearity analysis showed nine segmental duplication pairs within
PeINV
s, and 25 pairs were detected between
PeINV
s and
OsINV
s.
PeINV
s may have undergone strong purification selection during evolution, and a variety of stress and phytohormone-related regulatory elements were found in the promoters of
PeINV
s. The tissue-specific expression analysis showed that
PeINV
s were differentially expressed in various moso bamboo tissues, which suggested that they showed functional diversity. Both the RNA-seq and quantitative real-time PCR results indicated that four
PeINV
s were significantly upregulated under drought stress. Co-expression network and Pearson’s correlation coefficient analyses showed that these
PeINV
s co-expressed positively with sugar and water transport genes (
SWTG
s), and the changes were consistent with sugar content. Overall, we speculate that the identified
PeINV
s are spatiotemporally expressed, which enables them to participate in moso bamboo growth and development. Furthermore,
PeINV
s, together with
SWTG
s, also seem to play vital roles in the response to drought stress. These results provide a comprehensive information resource for
PeINV
s, which will facilitate further study of the molecular mechanism underlying
PeINV
s involvement in the response to drought stress in moso bamboo.
Bamboo is a perennial and renewable biomass forest resource and its leaf flavonoid is an antioxidant for biological and pharmacological research. The established genetic transformation and gene ...editing systems in bamboo are significantly limited by the dependence on bamboo regeneration capability. The way to improve the flavonoid content in bamboo leaves through biotechnology is still not feasible.
Here, we developed an in-planta, Agrobacterium-mediated gene expression method for exogenous genes via wounding and vacuum in bamboo. We demonstrated that the RUBY served as a reporter efficiently expressed in bamboo leaves and shoots, albeit unable to integrate into the chromosome. We have also developed a gene editing system by creating an in situ mutant of the bamboo violaxanthin de-epoxidase (PeVDE) gene in bamboo leaves, with lower NPQ values under the fluorometer, which can serve as a native reporter for gene editing. Furthermore, the bamboo leaves with increased flavonoid content were achieved by knocking out the cinnamoyl-CoA reductase genes.
Our method can be applied for the functional characterization of novel genes in a short time and is helpful for bamboo leaf flavonoid biotechnology breeding in the future.
Xylan is one of the most abundant hemicelluloses and can crosslink cellulose and lignin to increase the stability of cell walls. A number of genes encoding glycosyltransferases play vital roles in ...xylan biosynthesis in plants, such as those of the GT43 family. However, little is known about glycosyltransferases in bamboo, especially woody bamboo which is a good substitute for timber.
A total of 17 GT43 genes (PeGT43-1 ~ PeGT43-17) were identified in the genome of moso bamboo (Phyllostachys edulis), which belong to three subfamilies with specific motifs. The phylogenetic and collinearity analyses showed that PeGT43s may have undergone gene duplication, as a result of collinearity found in 12 pairs of PeGT43s, and between 17 PeGT43s and 10 OsGT43s. A set of cis-acting elements such as hormones, abiotic stress response and MYB binding elements were found in the promoter of PeGT43s. PeGT43s were expressed differently in 26 tissues, among which the highest expression level was found in the shoots, especially in the rapid elongation zone and nodes. The genes coexpressed with PeGT43s were annotated as associated with polysaccharide metabolism and cell wall biosynthesis. qRT-PCR results showed that the coexpressed genes had similar expression patterns with a significant increase in 4.0 m shoots and a peak in 6.0 m shoots during fast growth. In addition, the xylan content and structural polysaccharide staining intensity in bamboo shoots showed a strong positive correlation with the expression of PeGT43s. Yeast one-hybrid assays demonstrated that PeMYB35 could recognize the 5' UTR/promoter of PeGT43-5 by binding to the SMRE cis-elements.
PeGT43s were found to be adapted to the requirement of xylan biosynthesis during rapid cell elongation and cell wall accumulation, as evidenced by the expression profile of PeGT43s and the rate of xylan accumulation in bamboo shoots. Yeast one-hybrid analysis suggested that PeMYB35 might be involved in xylan biosynthesis by regulating the expression of PeGT43-5 by binding to its 5' UTR/promoter. Our study provides a comprehensive understanding of PeGT43s in moso bamboo and lays a foundation for further functional analysis of PeGT43s for xylan biosynthesis during rapid growth.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
NAC (NAM, ATAF, and CUC) transcription factors (TFs) are implicated in the transcriptional regulation of diverse processes and have been characterized in a number of plant species. However, NAC TFs ...are still not well understood in bamboo, especially their potential association with the secondary cell wall (SCW). Here, 94
s were identified and characterized in moso bamboo (
). Based on their gene structures and conserved motifs, the PeNACs were divided into 11 groups according to their homologs in
.
s were expressed variously in different tissues of moso bamboo, suggesting their functional diversity. Fifteen
s associated with the SCW were selected for co-expression analysis and validation. It was predicted that 396 genes were co-expressed with the 15
s, in which 16 and 55 genes were involved in the lignin catabolic process and cellulose biosynthetic process respectively. As the degree of lignification in the growing bamboo shoots increased, all 15
s were upregulated with a trend of rising first and then decreasing except
, which increased continuously. These results indicated that these
s might play important roles in SCW biosynthesis and lignification in bamboo shoots. Seven of 15
s had been found positively co-expressed with seven
s, and they had similar expression patterns with those of the
s in bamboo shoots. The targeted sites of miR164 were found in 16
s, of which three
s associated with SCW were validated to have an opposite expression trend to that of miR164 in growing bamboo shoots. In addition, three
s were selected and verified to have self-activation activities. These results provide comprehensive information of the
gene family in moso bamboo, which will be helpful for further functional studies of
s to reveal the molecular regulatory mechanisms of bamboo wood property.
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