scholarly journals Identification of Homeobox Genes Associated with Lignification and Their Expression Patterns in Bamboo Shoots

Biomolecules ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 862 ◽  
Author(s):  
Xiurong Xu ◽  
Yongfeng Lou ◽  
Kebin Yang ◽  
Xuemeng Shan ◽  
Chenglei Zhu ◽  
...  
Keyword(s):  
Storage Time ◽  
Expression Patterns ◽  
Moso Bamboo ◽  
Prolonged Storage ◽  
Phyllostachys Edulis ◽  
Lignin Synthesis ◽  
Positive Expression ◽  
Bamboo Shoots ◽  
Transcriptome Expression ◽  
Intron Distribution

Homeobox (HB) genes play critical roles in regulating various aspects of plant growth and development. However, little is known about HB genes in bamboo. In this study, a total of 115 HB genes (PeHB001–PeHB115) were identified from moso bamboo (Phyllostachys edulis) and grouped into 13 distinct classes (BEL, DDT, HD-ZIP I–IV, KNOX, NDX, PHD, PINTOX, PLINC, SAWADEE, and WOX) based on the conserved domains and phylogenetic analysis. The number of members in the different classes ranged from 2 to 24, and they usually varied in terms of exon–intron distribution pattern and length. There were 20 conserved motifs found in 115 PeHBs, with motif 1 being the most common. Gene ontology (GO) analysis showed that PeHBs had diverse molecular functions, with 19 PeHBs being annotated as having xylem development, xylem, and phloem pattern formation functions. Co-expression network analysis showed that 10 of the 19 PeHBs had co-expression correlations, and three members of the KNOX class were hub proteins that interacted with other transcription factors (TFs) such as MYB, bHLH, and OVATE, which were associated with lignin synthesis. Yeast two-hybridization results further proved that PeHB037 (BEL class) interacted with PeHB057 (KNOX class). Transcriptome expression profiling indicated that all PeHBs except PeHB017 were expressed in at least one of the seven tissues of moso bamboo, and 90 PeHBs were expressed in all the tissues. The qRT-PCR results of the 19 PeHBs showed that most of them were upregulated in shoots as the height increased. Moreover, a KNOX binding site was found in the promoters of the key genes involved in lignin synthesis such as Pe4CL, PeC3H, PeCCR, and PeCOMT, which had positive expression correlations with five KNOX genes. Similar results were found in winter bamboo shoots with prolonged storage time, which was consistent with the degree of lignification. These results provide basic data on PeHBs in moso bamboo, which will be helpful for future functional research on PeHBs with positive regulatory roles in the process of lignification.

scholarly journals Transcriptome Reveals the Specificity of Phyllostachys edulis ‘Pachyloen’ Shoots at Different Developmental Stages

Forests ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 861 ◽  
Author(s):  
Yaping Hu ◽  
Ying Zhang ◽  
Jie Zhou ◽  
Guibing Wang ◽  
Qirong Guo
Keyword(s):  
Metabolic Pathways ◽  
Developmental Stages ◽  
Moso Bamboo ◽  
Biological Processes ◽  
Phyllostachys Edulis ◽  
Monthly Basis ◽  
Bamboo Shoots ◽  
Tyrosine Metabolism ◽  
Culm Wall ◽  
Cellular Components

Phyllostachys edulis ‘Pachyloen’ can have a stalk wall thickness of up to 2.5 cm at a height of 1.3 m, which is 1.8 times that of normal Moso bamboo (Phyllostachys edulis); this serves as an excellent cultivar, comprising both wood and bamboo shoots. We collected bamboo shoot samples of Phyllostachys edulis ‘Pachyloen’ and Moso bamboo on a monthly basis from September to April and used transcriptome sequencing to explore the differences in their development. The results showed that there were 666–1839 Phyllostachys edulis ‘Pachyloen’-specific genes at different developmental stages enriched in 20 biological processes, 15 cellular components, 12 molecular functions, and 137 metabolic pathways, 52 of which were significant. Among these, 27 metabolic pathways such as tyrosine metabolism and their uniquely expressed genes were found to play important roles in the thickening of Phyllostachys edulis ‘Pachyloen’. This study provides insights into the mechanisms underlying the thickening of the culm wall of Phyllostachys edulis ‘Pachyloen’.

scholarly journals Genome-Wide Investigation of the NAC Gene Family and Its Potential Association with the Secondary Cell Wall in Moso Bamboo

Biomolecules ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 609 ◽  
Author(s):  
Shan ◽  
Yang ◽  
Xu ◽  
Zhu ◽  
Gao
Keyword(s):  
Cell Wall ◽  
Gene Family ◽  
Secondary Cell Wall ◽  
Expression Patterns ◽  
Wood Property ◽  
Moso Bamboo ◽  
Functional Studies ◽  
Bamboo Shoots ◽  
Potential Association ◽  
Nac Gene Family

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 PeNACs were identified and characterized in moso bamboo (Phyllostachys edulis). Based on their gene structures and conserved motifs, the PeNACs were divided into 11 groups according to their homologs in Arabidopsis. PeNACs were expressed variously in different tissues of moso bamboo, suggesting their functional diversity. Fifteen PeNACs associated with the SCW were selected for co-expression analysis and validation. It was predicted that 396 genes were co-expressed with the 15 PeNACs, 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 PeNACs were upregulated with a trend of rising first and then decreasing except PeNAC37, which increased continuously. These results indicated that these PeNACs might play important roles in SCW biosynthesis and lignification in bamboo shoots. Seven of 15 PeNACs had been found positively co-expressed with seven PeMYBs, and they had similar expression patterns with those of the PeMYBs in bamboo shoots. The targeted sites of miR164 were found in 16 PeNACs, of which three PeNACs associated with SCW were validated to have an opposite expression trend to that of miR164 in growing bamboo shoots. In addition, three PeNACs were selected and verified to have self-activation activities. These results provide comprehensive information of the NAC gene family in moso bamboo, which will be helpful for further functional studies of PeNACs to reveal the molecular regulatory mechanisms of bamboo wood property.

scholarly journals Genome-wide identification and expression analysis of dirigent-jacalin genes from plant chimeric lectins in Moso bamboo (Phyllostachys edulis)

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248318
Author(s):  
Ruifang Ma ◽  
Bin Huang ◽  
Jialu Chen ◽  
Zhinuo Huang ◽  
Peiyao Yu ◽  
...  
Keyword(s):  
Stress Response ◽  
Growth And Development ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Protein Structures ◽  
Moso Bamboo ◽  
Dimensional Structure ◽  
Phyllostachys Edulis ◽  
Plant Lectins ◽  
J Proteins

Dirigent-jacalin (D-J) genes belong to the plant chimeric lectin family, and play vital roles in plant growth and resistance to abiotic and biotic stresses. To explore the functions of the D-J family in the growth and development of Moso bamboo (Phyllostachys edulis), their physicochemical properties, phylogenetic relationships, gene and protein structures, and expression patterns were analyzed in detail. Four putative PeD-J genes were identified in the Moso bamboo genome, and microsynteny and phylogenetic analyses indicated that they represent a new branch in the evolution of plant lectins. PeD-J proteins were found to be composed of a dirigent domain and a jacalin-related lectin domain, each of which contained two different motifs. Multiple sequence alignment and homologous modeling analysis indicated that the three-dimensional structure of the PeD-J proteins was significantly different compared to other plant lectins, primarily due to the tandem dirigent and jacalin domains. We surveyed the upstream putative promoter regions of the PeD-Js and found that they mainly contained cis-acting elements related to hormone and abiotic stress response. An analysis of the expression patterns of root, leaf, rhizome and panicle revealed that four PeD-J genes were highly expressed in the panicle, indicating that they may be required during the formation and development of several different tissue types in Moso bamboo. Moreover, PeD-J genes were shown to be involved in the rapid growth and development of bamboo shoots. Quantitative Real-time PCR (qRT PCR) assays further verified that D-J family genes were responsive to hormones and stresses. The results of this study will help to elucidate the biological functions of PeD-Js during bamboo growth, development and stress response.

scholarly journals Genome-wide identification of growth-regulating factors in moso bamboo (Phyllostachys edulis): in silico and experimental analyses

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7510 ◽  
Author(s):  
Yanan Shi ◽  
Huanlong Liu ◽  
Yameng Gao ◽  
Yujiao Wang ◽  
Min Wu ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Purifying Selection ◽  
Synonymous Substitution ◽  
Moso Bamboo ◽  
Bimolecular Fluorescence Complementation ◽  
Pcr Analysis ◽  
Hormone Regulation ◽  
In Planta ◽  
Phyllostachys Edulis ◽  
Specific Expression

Growth-regulating factor (GRF), a small plant-specific transcription factor (TF) family, is extensively involved in the regulation of growth and developmental processes. However, the GRF family has not been comprehensively studied in moso bamboo (Phyllostachys edulis), a typical non-timber forest member. Here, 18 GRF genes were identified and characterized from the moso bamboo genome, and they clustered into three subfamilies (A, B and C). PeGRF genes were analyzed to determine their gene structures, conserved motifs and promoter. The non-synonymous/synonymous substitution ratios of paralogous and orthologous were less than 1, indicating that the GRF family mainly experienced purifying selection during evolution. According to the analysis of tissue-specific expression patterns, the participation of moso bamboo GRFs might be required during the formation and development of these five tissues. Moreover, PeGRF proteins might be involved in the regulation of plant development in biological processes. The qRT-PCR analysis demonstrated that PeGRF genes played essential roles in combating hormonal stresses and they might be involved in hormone regulation. PeGRF11, a nuclear localized protein as assessed by a subcellular localization assay, could interact with PeGIF3 in yeast and in planta according to yeast two-hybridization and bimolecular fluorescence complementation assays (BiFC) assays. But PeGRF11, as a TF, had no transcriptional activity in yeast. These results provide useful information for future functional research on the GRF genes in moso bamboo.

scholarly journals Genome-Wide Analysis and Expression Profiling of the Heat Shock Factor Gene Family in Phyllostachys edulis during Development and in Response to Abiotic Stresses

Forests ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 100 ◽  
Author(s):  
Lihua Xie ◽  
Xiangyu Li ◽  
Dan Hou ◽  
Zhanchao Cheng ◽  
Jun Liu ◽  
...  
Keyword(s):  
Heat Shock ◽  
Gene Family ◽  
Protein Interaction ◽  
Structural Characteristics ◽  
Quantitative Polymerase Chain Reaction ◽  
Expression Patterns ◽  
Cold Treatment ◽  
Moso Bamboo ◽  
Phyllostachys Edulis ◽  
Class A

Heat shock transcription factors (Hsfs) play crucial roles in regulating plant responses to heat and other stresses, as well as in plant development. As the largest monopodial bamboo species in the world, how to adapt to various stresses under the background of global climate change is very important for the sustainable development of bamboo forest. However, our understanding of the function of Hsfs in moso bamboo (Phyllostachys edulis) is limited. In this study, a total of 22 non-redundant Hsf genes were identified in the moso bamboo genome. Structural characteristics and phylogenetic analysis revealed that members of the PheHsf family can be clustered into three classes (A, B and C). Furthermore, PheHsfs promoters contained a number of stress-, hormone- and development-related cis-acting elements. Transcriptome analysis indicated that most PheHsfs participate in rapid shoot growth and flower development in moso bamboo. Moreover, the expression patterns of all 12 members of class A were analyzed under various stresses (heat, drought, salt and cold treatment) through Figurereal-time quantitative polymerase chain reaction (qRT-PCR). Within the class A PheHsf members, PheHsfA1a was expressed mainly during moso bamboo development. Expression of four PheHsfA4s and one PheHsfA2 (PheHsfA4a-1, PheHsfA4a-2, PheHsfA4d-1, PheHsfA4d-2, and PheHsfA2a-2) was up-regulated in response to various stresses. PheHsfA2a-2, PheHsfA4d-1 and PheHsfA4d-2 were strongly induced respectively by heat, drought and NaCl stress. Through co-expression analysis we found that two hub genes PheHsfA4a-2 and PheHsfA4a-1 were involved in a complex protein interaction network. Based on the prediction of protein interaction networks, five PheHsfAs (PheHsfA4a-1, PheHsfA4a-2, PheHsfA4d-1, PheHsfA4d-2, and PheHsfA2a-2) were predicted to play an important role in flower and shoot development and abiotic stress response of moso bamboo. This study provides an overview of the complexity of the PheHsf gene family and a basis for analyzing the functions of PheHsf genes of interest.

scholarly journals Identification and expression analysis of the glycosyltransferase GT43 family members in bamboo reveal their potential function in xylan biosynthesis during rapid growth

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zhen Li ◽  
Xinyue Wang ◽  
Kebin Yang ◽  
Chenglei Zhu ◽  
Tingting Yuan ◽  
...  
Keyword(s):  
Cell Wall ◽  
Rapid Growth ◽  
Expression Patterns ◽  
Staining Intensity ◽  
Moso Bamboo ◽  
Strong Positive Correlation ◽  
Abiotic Stress Response ◽  
Bamboo Shoots ◽  
Genes Encoding ◽  
Xylan Biosynthesis

Abstract Background 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. Results 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. Conclusions 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.

scholarly journals The BBX gene family in Moso bamboo (Phyllostachys edulis): identification, characterization and expression profiles

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ruifang Ma ◽  
Jialu Chen ◽  
Bin Huang ◽  
Zhinuo Huang ◽  
Zhijun Zhang
Keyword(s):  
Gene Family ◽  
Target Genes ◽  
Zinc Finger Protein ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Moso Bamboo ◽  
Model Organisms ◽  
Phyllostachys Edulis ◽  
Sequence Alignments ◽  
Specific Expression

Abstract Background The BBX (B-box) family are zinc finger protein (ZFP) transcription factors that play an essential role in plant growth, development and response to abiotic stresses. Although BBX genes have been characterized in many model organisms, genome-wide identification of the BBX family genes have not yet been reported in Moso bamboo (Phyllostachys edulis), and the biological functions of this family remain unknown. Result In the present study, we identified 27 BBX genes in the genome of Moso bamboo, and analysis of their conserved motifs and multiple sequence alignments revealed that they all shared highly similar structures. Additionally, phylogenetic and homology analyses indicated that PeBBX genes were divided into three clusters, with whole-genome duplication (WGD) events having facilitated the expansion of this gene family. Light-responsive and stress-related cis-elements were identified by analyzing cis-elements in the promoters of all PeBBX genes. Short time-series expression miner (STEM) analysis revealed that the PeBBX genes had spatiotemporal-specific expression patterns and were likely involved in the growth and development of bamboo shoots. We further explored the downstream target genes of PeBBXs, and GO/KEGG enrichment analysis predicted multiple functions of BBX target genes, including those encoding enzymes involved in plant photosynthesis, pyruvate metabolism and glycolysis/gluconeogenesis. Conclusions In conclusion, we analyzed the PeBBX genes at multiple different levels, which will contribute to further studies of the BBX family and provide valuable information for the functional validation of this family.

Characterization of moso bamboo (Phyllostachys edulis) Dof transcription factors in floral development and abiotic stress responses

Genome ◽  
2018 ◽  
Vol 61 (3) ◽  
pp. 151-156 ◽  
Author(s):  
Zhanchao Cheng ◽  
Dan Hou ◽  
Jun Liu ◽  
Xiangyu Li ◽  
Lihua Xie ◽  
...  
Keyword(s):  
Stress Responses ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Regulatory Element ◽  
Expression Patterns ◽  
Moso Bamboo ◽  
Phyllostachys Edulis ◽  
Element Analysis ◽  
Specific Expression

The Dof transcription factor (TF) family belongs to a class of plant-specific TFs and is involved in plant growth, development, and response to abiotic stresses. However, there are only very limited reports on the characterization of Dof TFs in moso bamboo (Phyllostachys edulis). In the present research, PheDof TFs showed specific expression profiles based on RNA-seq data analyses. The co-expression network indicated that PheDof12, PheDof14, and PheDof16 might play vital roles during flower development. Cis-regulatory element analysis of these PheDof genes suggested diverse functions. Expression patterns of 12 selected genes from seven different classes under three abiotic stresses (cold, salt, and drought) are further investigated by quantitative real-time PCR. This work will provide useful information for functional analysis and regulation mechanisms of Dof TFs in moso bamboo.

scholarly journals The accuracy of gypsum casts obtained from the disinfected extended-pour alginate impressions through prolonged storage times

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Rania A. Sharif ◽  
Khalid M. Abdelaziz ◽  
Najla M. Alshahrani ◽  
Fatimah S. Almutairi ◽  
Mohrah A. Alaseri ◽  
...  
Keyword(s):  
Dimensional Stability ◽  
Storage Time ◽  
Prolonged Storage ◽  
Time Intervals ◽  
Superior Surface ◽  
Stability Data ◽  
Surface Detail ◽  
Storage Times ◽  
One Way Anova ◽  
Chemical Disinfection

Abstract Background Manufacturers of the extended-pour alginates claimed their dimensional stability through prolonged storage. No data confirmed the ability of these materials to maintain their dimensions and the reproduced oral details following their chemical disinfection. Therefore, this study evaluated the dimensional stability and surface detail reproduction of gypsum casts obtained from disinfected extended-pour alginate impressions through different storage time intervals. Methods Two hundred and forty three hydrocolloid impressions were made from one conventional (Tropicalgin) and two extended-pour (Hydrogum 5 and Chromaprint premium) alginates. These impressions were subjected to none, spray and immersion disinfection before their storage in 100% humidity for 0, 72 and 120 h. The dimensional stability and the surface detail reproduction were indirectly evaluated under low angle illumination on the resulted gypsum casts. At α = 0.05, the parametric dimensional stability data were analyzed using One-Way ANOVA and Tukey’s comparisons, while the nonparametric detail reproduction data were analyzed using KrusKal Wallis and Mann–Whitney's tests. Results All gypsum casts exhibited a degree of expansion; however, the recorded expansion values did not differ between test categories (P > 0.05). Generally, casts obtained from spray-disinfected impressions showed lower detail accuracy (P < 0.05). Immersion-disinfected extended-pour alginates produced casts with better detail accuracy following 120 h of storage (P < 0.05). Conclusion All alginates materials offer comparable cast dimensions under different testing circumstances. Extended-pour alginates offer casts with superior surface details following their immersion disinfection and 120 h of storage. Spray-disinfection using 5.25% sodium hypochlorite affects the surface details of casts obtained from conventional and extended-pour alginates adversely.

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