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 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 Genome-wide identification of the 14-3-3 gene family and its participation in floral transition by interacting with TFL1/FT in Apple

2020 ◽  
Author(s):  
Xiya Zuo ◽  
Shixiang Wang ◽  
Wen Xiang ◽  
Huiru Yang ◽  
Muhammad Mobeen Tahir ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Floral Transition ◽  
Bimolecular Fluorescence Complementation ◽  
Pcr Analysis ◽  
Transcriptional Responses ◽  
Genome Database ◽  
Reverse Transcription Pcr ◽  
Conserved Core

Abstract Background: Apple (Malus domestica Borkh.) is one of the most popular cultivated fruit crops in China. Apple floral transition is an important process but liable to be affected by various environmental factors. The 14-3-3 proteins are involved in regulating diverse biological processes in plants, and some 14-3-3 members play vital roles in flowering. However, little information was available about the 14-3-3 members in apple.Results: In the current study, we identified eighteen 14-3-3 gene family members from the apple genome database, designated MdGF14a to MdGF14r. The isoforms possess a conserved core region comprising nine antiparallel α-helices and divergent N and C termini. According to their structural and phylogenetic features, Md14-3-3 proteins could be classified into two major evolutionary branches, the epsilon (ɛ) group and the non-epsilon (non-ɛ) group. Moreover, expression profiles derived from transcriptome data and quantitative real-time reverse transcription PCR analysis showed diverse expression patterns of Md14-3-3 genes in various tissues and in response to different sugars and hormone treatments during the floral transition phase. Four Md14‑3-3 isoforms (MdGF14a, MdGF14d, MdGF14i, and MdGF14j) exhibiting prominent transcriptional responses to sugars and hormones were selected for further investigation. Furthermore, yeast two-hybrid and bimolecular fluorescence complementation experiments showed that the four Md14-3-3 proteins interact with key floral integrators, MdTFL1 (TERMINAL FLOWER1) and MdFT (FLOWERING LOCUS T). Subcellular localization of four selected Md14-3-3 proteins demonstrated their localization in both the cytoplasm and nucleus.Conclusion: We identified the Md14-3-3s family in apple comprehensively. Certain Md14-3-3 genes are expressed predominantly during the apple floral transition stage, and may participate in the regulation of flowering through association with flower control genes. Our results provide a preliminary framework for further investigation into the roles of Md14-3-3s in floral transition.

scholarly journals Genome-wide identification of the 14-3-3 gene family and its participation in floral transition by interacting with TFL1/FT in Apple

2020 ◽  
Author(s):  
Xiya Zuo ◽  
Shixiang Wang ◽  
Wen Xiang ◽  
Huiru Yang ◽  
Muhammad Mobeen Tahir ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Economic Value ◽  
Floral Transition ◽  
Bimolecular Fluorescence Complementation ◽  
Pcr Analysis ◽  
Transcriptional Responses ◽  
Genome Database ◽  
Reverse Transcription Pcr

Abstract Background: Apple (Malus domestica Borkh.) is a popular cultivated fruit crop with high economic value in China. Apple floral transition is an important process but liable to be affected by various environmental factors. The 14-3-3 proteins are involved in regulating diverse biological processes in plants, and some 14-3-3 members play vital roles in flowering. However, little information was available about the 14-3-3 members in apple.Results: In the current study, we identified eighteen 14-3-3 gene family members from the apple genome database, designated MdGF14a to MdGF14r. The isoforms possess a conserved core region comprising nine antiparallel α-helices and divergent N and C termini. According to their structural and phylogenetic features, Md14-3-3 proteins could be classified into two major evolutionary branches, the epsilon (ɛ) group and the non-epsilon (non-ɛ) group. Moreover, expression profiles derived from transcriptome data and quantitative real-time reverse transcription PCR analysis showed diverse expression patterns of Md14-3-3 genes in various tissues and in response to different sugars and hormone treatments during the floral transition phase. Four Md14‑3-3 isoforms (MdGF14a, MdGF14d, MdGF14i, and MdGF14j) exhibiting prominent transcriptional responses to sugars and hormones were selected for further investigation. Furthermore, yeast two-hybrid and bimolecular fluorescence complementation experiments showed that the four Md14-3-3 proteins interact with key floral integrators, MdTFL1 (TERMINAL FLOWER1) and MdFT (FLOWERING LOCUS T). Subcellular localization of four selected Md14-3-3 proteins demonstrated their localization in both the cytoplasm and nucleus.Conclusion: We identified the Md14-3-3s family in apple comprehensively. Certain Md14-3-3 genes are expressed predominantly during the apple floral transition stage, and may participate in the regulation of flowering through association with flower control genes. Our results provide a preliminary framework for further investigation into the roles of Md14-3-3s in floral transition.

scholarly journals Molecular Mechanism of Xylogenesis in Moso Bamboo (Phyllostachys edulis) Shoots during Cold Storage

Polymers ◽  
2018 ◽  
Vol 11 (1) ◽  
pp. 38 ◽  
Author(s):  
Changtao Li ◽  
Lingling Xuan ◽  
Yuming He ◽  
Jie Wang ◽  
Hui Zhang ◽  
...  
Keyword(s):  
Cell Wall ◽  
Cold Storage ◽  
Cinnamyl Alcohol Dehydrogenase ◽  
Moso Bamboo ◽  
Transcriptomic Analysis ◽  
Pcr Analysis ◽  
Phyllostachys Edulis ◽  
Related Enzyme ◽  
Cold Chamber ◽  
Xylan Biosynthesis

A bamboo shoot is the immature stem of the woody grass and a nutritious and popular vegetable in East Asia. However, it undergoes a rapid xylogenesis process right after harvest, even being stored in a cold chamber. To investigate the molecular regulation mechanisms of xylogenesis in Moso bamboo (Phyllostachys edulis) shoots (MBSes) during cold storage, the measurement of cell wall polymers (cellulose, hemicellulose, and lignin) and related enzyme activities (phenylalanine ammonia lyase (PAL), cinnamyl alcohol dehydrogenase (CAD), peroxidase (POD), and xylan xylosyltransferase (XylT)) and transcriptomic analysis were performed during cold storage. It was noticed that cellulose and lignin contents increased, while hemicellulose content exhibited a downward trend. PAL, CAD, and POD activity presented an upward trend generally in MBS when stored at 4 °C for 16 days. XylT activity showed a descending trend during the stages of storage, but slightly increased during the 8th to 12th days after harvest at 4 °C. Transcriptomic analysis identified 72, 28, 44, and 31 functional unigenes encoding lignin, cellulose, xylan biosynthesis enzymes, and transcription factors (TFs), respectively. Many of these secondary cell wall (SCW)-related genes showed higher expression levels in the later period of cold storage. Quantitative RT-PCR analysis of the selected genes conformed to the expression pattern. Our study provides a comprehensive analysis of MBS secondary wall biosynthesis at the molecular level during the cold storage process. The results give insight into the xylogenesis process of this economically important vegetable and shed light on solving this problem of the post-harvest industry.

scholarly journals Genome-Wide Analysis of Multiple Organellar RNA Editing Factor Family in Poplar Reveals Evolution and Roles in Drought Stress

2019 ◽  
Vol 20 (6) ◽  
pp. 1425 ◽  
Author(s):  
Dongli Wang ◽  
Sen Meng ◽  
Wanlong Su ◽  
Yu Bao ◽  
Yingying Lu ◽  
...  
Keyword(s):  
Drought Stress ◽  
Rna Editing ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Structural Features ◽  
Specific Expression ◽  
Poplar Genome ◽  
Physiological Processes ◽  
Genome Wide

Poplar (Populus) is one of the most important woody plants worldwide. Drought, a primary abiotic stress, seriously affects poplar growth and development. Multiple organellar RNA editing factor (MORF) genes—pivotal factors in the RNA editosome in Arabidopsis thaliana—are indispensable for the regulation of various physiological processes, including organelle C-to-U RNA editing and plasmid development, as well as in the response to stresses. Although the poplar genome sequence has been released, little is known about MORF genes in poplar, especially those involved in the response to drought stress at the genome-wide level. In this study, we identified nine MORF genes in the Populus genome. Based on the structural features of MORF proteins and the topology of the phylogenetic tree, the P. trichocarpa (Ptr) MORF family members were classified into six groups (Groups I–VI). A microsynteny analysis indicated that two (22.2%) PtrMORF genes were tandemly duplicated and seven genes (77.8%) were segmentally duplicated. Based on the dN/dS ratios, purifying selection likely played a major role in the evolution of this family and contributed to functional divergence among PtrMORF genes. Moreover, analysis of qRT-PCR data revealed that PtrMORFs exhibited tissue- and treatment-specific expression patterns. PtrMORF genes in all group were involved in the stress response. These results provide a solid foundation for further analyses of the functions and molecular evolution of MORF genes in poplar, and, in particular, for improving the drought resistance of poplar by genetics manipulation.

scholarly journals Genome-Wide Analysis of the YABBY Transcription Factor Family in Rapeseed (Brassica napus L.)

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 981
Author(s):  
Jichun Xia ◽  
Dong Wang ◽  
Yuzhou Peng ◽  
Wenning Wang ◽  
Qianqian Wang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Brassica Species ◽  
Pcr Analysis ◽  
Sequencing Data ◽  
Functional Identification ◽  
Brassica Napus L ◽  
Intron Structure ◽  
Duplication Events

The YABBY family of plant-specific transcription factors play important regulatory roles during the development of leaves and floral organs, but their functions in Brassica species are incompletely understood. Here, we identified 79 YABBY genes from Arabidopsis thaliana and five Brassica species (B. rapa, B. nigra, B. oleracea, B. juncea, and B. napus). A phylogenetic analysis of YABBY proteins separated them into five clusters (YAB1–YAB5) with representatives from all five Brassica species, suggesting a high degree of conservation and similar functions within each subfamily. We determined the gene structure, chromosomal location, and expression patterns of the 21 BnaYAB genes identified, revealing extensive duplication events and gene loss following polyploidization. Changes in exon–intron structure during evolution may have driven differentiation in expression patterns and functions, combined with purifying selection, as evidenced by Ka/Ks values below 1. Based on transcriptome sequencing data, we selected nine genes with high expression at the flowering stage. qRT-PCR analysis further indicated that most BnaYAB family members are tissue-specific and exhibit different expression patterns in various tissues and organs of B. napus. This preliminary study of the characteristics of the YABBY gene family in the Brassica napus genome provides theoretical support and reference for the later functional identification of the family genes.

scholarly journals Genome-wide analysis and expression characteristics of small auxin-up RNA (SAUR) genes in moso bamboo (Phyllostachys edulis)

Genome ◽  
2017 ◽  
Vol 60 (4) ◽  
pp. 325-336 ◽  
Author(s):  
Qingsong Bai ◽  
Dan Hou ◽  
Long Li ◽  
Zhanchao Cheng ◽  
Wei Ge ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
Shoot Growth ◽  
Subcellular Location ◽  
Moso Bamboo ◽  
Pcr Analysis ◽  
Phyllostachys Edulis ◽  
Comprehensive Overview ◽  
Genome Wide ◽  
Gene Structures

Moso bamboo (Phyllostachys edulis) is well known for its rapid shoot growth. Auxin exerts pleiotropic effects on plant growth. The small auxin-up RNA (SAUR) genes are early auxin-responsive genes involved in plant growth. In total, 38 SAUR genes were identified in P. edulis (PheSAUR). A comprehensive overview of the PheSAUR gene family is presented, including the gene structures, phylogeny, and subcellular location predictions. A transcriptome analysis indicated that 37 (except PheSAUR18) of the PheSAUR genes were expressed during shoot growth process and that the PheSAUR genes were differentially expressed. Furthermore, quantitative real-time PCR analysis indicated that all of the PheSAUR genes could be induced in different tissues of seedlings and that 37 (except PheSAUR41) of the PheSAUR genes were up-regulated after indole-3-acetic acid (IAA) treatment. These results reveal a comprehensive overview of the PheSAUR gene family and may pave the way for deciphering their functions during bamboo development.

scholarly journals Genome-wide identification and analyses of the AHL gene family in cotton (Gossypium)

2019 ◽  
Author(s):  
Lanjie Zhao ◽  
Youjun Lu ◽  
Wei Chen ◽  
Jinbo Yao ◽  
Yan Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Orthologous Gene ◽  
Potential Functions ◽  
Pcr Analysis ◽  
Type I ◽  
Clade B ◽  
Genome Wide

Abstract Background: Members of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED ( AHL ) family are involved in various plant biological processes via protein-DNA and protein-protein interaction. However, no the systematic identification and analysis of AHL gene family have been reported in cotton. Results: To investigate the potential functions of AHLs in cotton, genome-wide identification, expressions and structure analysis of the AHL gene family were performed in this study. 48, 51 and 99 AHL genes were identified from the G.raimondii, G.arboreum and G.hirsutum genome, respectively. Phylogenetic analysis revealed that the AHLs in cotton evolved into 2 clades, Clade-A with 4-5 introns and Clade-B with intronless (excluding AHL 20-2). Based on the composition of the AT-hook motif(s) and PPC/DUF 296 domain, AHL proteins were classified into three types (Type-I/-II/-III), with Type-I AHLs forming Clade-B, and the other two types together diversifying in Clade-A. The detection of synteny and collinearity showed that the AHLs expanded with the WGD in cotton, and the sequence structure of AHL20-2 showed the tendency of increasing intron in three different Gossypium spp . The ratios of non-synonymous (Ka) and synonymous (Ks) substitution rates of orthologous gene pairs revealed that the AHL genes of G.hirsutum had undergone through various selection pressures, purifying selection mainly in A-subgenome and positive selection mainly in D-subgenome. Examination of their expression patterns showed most of AHLs of Clade-B expressed predominantly in stem, while those of Clade-A in ovules, suggesting that the AHLs within each clade shared similar expression patterns with each other. qRT-PCR analysis further confirmed that some GhAHLs higher expression in stems and ovules. Conclusion: In this study, 48, 51 and 99 AHL genes were identified from three cotton genomes respectively. AHLs in cotton were classified into two clades by phylogenetic relationship and three type based on the composition of motif and domain. The AHLs expanded with segmental duplication, not tandem duplication. The expression profiles of GhAHLs revealed abundant differences in expression levels in various tissues and at different stages of ovules development. Our study provided significant insights into the potential functions of AHLs in regulating the growth and development in cotton.

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