scholarly journals Genome-Wide Analysis of the Homeobox Gene Family and Identification of Drought-Responsive Members in Populus trichocarpa

Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2284
Author(s):  
Jing Hou ◽  
Yan Sun ◽  
Lei Wang ◽  
Yuanzhong Jiang ◽  
Ningning Chen ◽  
...  
Keyword(s):  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Dominant Gene ◽  
Homeobox Gene ◽  
Regulatory Elements ◽  
Virus Induced Gene Silencing ◽  
Motif Analysis ◽  
Significant Information ◽  
Spatio Temporal ◽  
Poplar Seedlings

Homeobox (HB) genes play critical roles in the regulation of plant morphogenesis, growth and development. Here, we identified a total of 156 PtrHB genes from the Populus trichocarpa genome. According to the topologies and taxonomy of the phylogenetic tree constructed by Arabidopsis thaliana HB members, all PtrHB proteins were divided into six subgroups, namely HD-ZIP, ZF-HD, HB-PHD, TALE, WOX and HB-OTHERS. Multiple alignments of conserved homeodomains (HDs) revealed the conserved loci of each subgroup, while gene structure analysis showed similar exon–intron gene structures, and motif analysis indicated the similarity of motif number and pattern in the same subgroup. Promoter analysis indicated that the promoters of PtrHB genes contain a series of cis-acting regulatory elements involved in responding to various abiotic stresses, indicating that PtrHBs had potential functions in these processes. Collinearity analysis revealed that there are 96 pairs of 127 PtrHB genes mainly distributing on Chromosomes 1, 2, and 5. We analyzed the spatio-temporal expression patterns of PtrHB genes, and the virus-induced gene silencing (VIGS) of PtrHB3 gene resulted in the compromised tolerance of poplar seedlings to mannitol treatment. The bioinformatics on PtrHB family and preliminary exploration of drought-responsive genes can provide support for further study of the family in woody plants, especially in drought-related biological processes. It also provides a direction for developing new varieties of poplar with drought resistance. Overall, our results provided significant information for further functional analysis of PtrHB genes in poplar and demonstrated that PtrHB3 is a dominant gene regulating tolerance to water stress treatment in poplar seedlings.

scholarly journals The DUBs Family in Populus: Identification, Characterization, Evolution and Expression Patterns

2020 ◽  
Author(s):  
Wenqing Zheng ◽  
Liang Du
Keyword(s):  
Abiotic Stress ◽  
Expression Profiles ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Genome Structure ◽  
Regulatory Elements ◽  
Abiotic Stress Response ◽  
Motif Analysis ◽  
Duplication Events ◽  
The Stability

Abstract Background: The deubiquitinases (DUB) family are a class of enzymes that regulate the stability or reverse the ubiquitination modification of many proteins in the cell, participating in cell cycle regulation, cell division and differentiation, various physiological activities such as DNA damage repair, growth and development, and response to stress. However, little is known about these genes in the woody plants. Results: In the present study, 88 DUB genes were identified in woody model plant Populus trichocarpa, including 44 PtrUBP, 3 PtrUCH, 23 PtrOTU, 4 PtrMJD, and 14 PtrJAMM with similar domains. According to the phylogenetic analysis, the 44 PtrUBP genes were classified into 14 subfamily, three PtrUCHs were classified into two groups, 23 PtrOTUs had six groups, four PtrMJDs had two groups, and 14 PtrJAMMs had six groups. The structure and motif analysis indicated that the same subfamily had similar genome structure and motif distribution characteristics. Ks/Ka analysis showed that the segmental duplication events played a major role in the expansion of Populus DUB genes. Synteny analysis of Populus DUB genes and four other species provided deep perception into the evolutionary traits of DUB genes. Expression profiles derived from transcriptome data exhibited distinct expression patterns of DUB genes in various tissues. Based on the result of promoter cis-regulatory elements analysis, we selected 16 representative PtrUBP genes to test their response to different hormonal treatments. The results showed that most of PtrUBPs were upregulated in the ABA, SA, and MeJA treatments, implying that their potential roles in abiotic stress response in Populus. Conclusion: The results in this study broaden our understanding of the DUB gene family in plants, and the analysis of the structure, conserved elements, and expression patterns of the DUBs provide a solid foundation for exploring their specific functions in Populus as well as indicate potential role of PtrUBP gene in abiotic stress.

scholarly journals Genome-wide identification and expression analysis of Raffinose synthetase family in cotton

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ruifeng Cui ◽  
Xiaoge Wang ◽  
Waqar Afzal Malik ◽  
Xuke Lu ◽  
Xiugui Chen ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Plant Leaves ◽  
Motif Analysis ◽  
Expression Levels ◽  
Genome Wide ◽  
Salt And Drought Stress ◽  
Key Genes ◽  
Stress Gene

Abstract Background The Raffinose synthetase (RAFS) genes superfamily is critical for the synthesis of raffinose, which accumulates in plant leaves under abiotic stress. However, it remains unclear whether RAFS contributes to resistance to abiotic stress in plants, specifically in the Gossypium species. Results In this study, we identified 74 RAFS genes from G. hirsutum, G. barbadense, G. arboreum and G. raimondii by using a series of bioinformatic methods. Phylogenetic analysis showed that the RAFS gene family in the four Gossypium species could be divided into four major clades; the relatively uniform distribution of the gene number in each species ranged from 12 to 25 based on species ploidy, most likely resulting from an ancient whole-genome polyploidization. Gene motif analysis showed that the RAFS gene structure was relatively conservative. Promoter analysis for cis-regulatory elements showed that some RAFS genes might be regulated by gibberellins and abscisic acid, which might influence their expression levels. Moreover, we further examined the functions of RAFS under cold, heat, salt and drought stress conditions, based on the expression profile and co-expression network of RAFS genes in Gossypium species. Transcriptome analysis suggested that RAFS genes in clade III are highly expressed in organs such as seed, root, cotyledon, ovule and fiber, and under abiotic stress in particular, indicating the involvement of genes belonging to clade III in resistance to abiotic stress. Gene co-expressed network analysis showed that GhRFS2A-GhRFS6A, GhRFS6D, GhRFS7D and GhRFS8A-GhRFS11A were key genes, with high expression levels under salt, drought, cold and heat stress. Conclusion The findings may provide insights into the evolutionary relationships and expression patterns of RAFS genes in Gossypium species and a theoretical basis for the identification of stress resistance materials in cotton.

scholarly journals Genome-Wide Analysis and Characterization of the Aux/IAA Family Genes Related to Floral Scent Formation in Hedychium coronarium

2019 ◽  
Vol 20 (13) ◽  
pp. 3235 ◽  
Author(s):  
Yanguo Ke ◽  
Farhat Abbas ◽  
Yiwei Zhou ◽  
Rangcai Yu ◽  
Yuechong Yue ◽  
...  
Keyword(s):  
Gene Family ◽  
Developmental Stages ◽  
Floral Scent ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Virus Induced Gene Silencing ◽  
Cut Flowers ◽  
Flower Opening ◽  
Hedychium Coronarium

Auxin plays a key role in different plant growth and development processes, including flower opening and development. The perception and signaling of auxin depend on the cooperative action of various components, among which auxin/indole-3-acetic acid (Aux/IAA) proteins play an imperative role. In a recent study, the entire Aux/IAA gene family was identified and comprehensively analyzed in Hedychium coronarium, a scented species used as an ornamental plant for cut flowers. Phylogenetic analysis showed that the Aux/IAA gene family in H. coronarium is slightly contracted compared to Arabidopsis, with low levels of non-canonical proteins. Sequence analysis of promoters showed numerous cis-regulatory elements related to various phytohormones. HcIAA genes showed distinct expression patterns in different tissues and flower developmental stages, and some HcIAA genes showed significant responses to auxin and ethylene, indicating that Aux/IAAs may play an important role in linking hormone signaling pathways. Based on the expression profiles, HcIAA2, HcIAA4, HcIAA6 and HcIAA12, were selected as candidate genes and HcIAA2 and HcIAA4 were screened for further characterization. Downregulation of HcIAA2 and HcIAA4 by virus-induced gene silencing in H. coronarium flowers modified the total volatile compound content, suggesting that HcIAA2 and HcIAA4 play important roles in H. coronarium floral scent formation. The results presented here will provide insights into the putative roles of HcIAA genes and will assist the elucidation of their precise roles during floral scent formation.

scholarly journals The DUB family in Populus: identification, characterization, evolution and expression patterns

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wenqing Zheng ◽  
Liang Du
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Gene Structure ◽  
Expression Profiles ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Foliar Spray ◽  
Regulatory Elements ◽  
Limited Information ◽  
Abiotic Stress Response

Abstract Background The deubiquitinase (DUB) family constitutes a group of proteases that regulate the stability or reverse the ubiquitination of many proteins in the cell. These enzymes participate in cell-cycle regulation, cell division and differentiation, diverse physiological activities such as DNA damage repair, growth and development, and response to stress. However, limited information is available on this family of genes in woody plants. Results In the present study, 88 DUB family genes were identified in the woody model plant Populus trichocarpa, comprising 44 PtrUBP, 3 PtrUCH, 23 PtrOTU, 4 PtrMJD, and 14 PtrJAMM genes with similar domains. According to phylogenetic analysis, the PtrUBP genes were classified into 16 groups, the PtrUCH genes into two, the PtrOTU genes into eight, the PtrMJD genes into two, and the PtrJAMM genes into seven. Members of same subfamily had similar gene structure and motif distribution characteristics. Synteny analysis of the DUB family genes from P. thrchocarpa and four other plant species provided insight into the evolutionary traits of DUB genes. Expression profiles derived from previously published transcriptome data revealed distinct expression patterns of DUB genes in various tissues. On the basis of the results of analysis of promoter cis-regulatory elements, we selected 16 representative PtrUBP genes to treatment with abscisic acid, methyl jasmonate, or salicylic acid applied as a foliar spray. The majority of PtrUBP genes were upregulated in response to the phytohormone treatments, which implied that the genes play potential roles in abiotic stress response in Populus. Conclusions The results of this study broaden our understanding of the DUB family in plants. Analysis of the gene structure, conserved elements, and expression patterns of the DUB family provides a solid foundation for exploration of their specific functions in Populus and to elucidate the potential role of PtrUBP gene in abiotic stress response.

scholarly journals Genome-Wide Analysis of OPR Family Genes in Cotton Identified a Role for GhOPR9 in Verticillium dahliae Resistance

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1134
Author(s):  
Shichao Liu ◽  
Ruibin Sun ◽  
Xiaojian Zhang ◽  
Zili Feng ◽  
Feng Wei ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Regulatory Elements ◽  
Virus Induced Gene Silencing ◽  
Biotic And Abiotic Stresses ◽  
Cis Acting ◽  
Protein Motifs ◽  
Genome Wide ◽  
Duplication Events ◽  
Polyethylene Glycol 6000 ◽  
Similar Gene

The 12-oxo-phytodienoic acid reductases (OPRs) have been proven to play a major role in plant development and growth. Although the classification and functions of OPRs have been well understood in Arabidopsis, tomato, rice, maize, and wheat, the information of OPR genes in cotton genome and their responses to biotic and abiotic stresses have not been reported. In this study, we found 10 and 9 OPR genes in Gossypium hirsutum and Gossypium barbadense, respectively. They were classified into three groups, based on the similar gene structure and conserved protein motifs. These OPR genes just located on chromosome 01, chromosome 05, and chromosome 06. In addition, the whole genome duplication (WGD) or segmental duplication events contributed to the evolution of the OPR gene family. The analyses of cis-acting regulatory elements of GhOPRs showed that the functions of OPR genes in cotton might be related to growth, development, hormone, and stresses. Expression patterns showed that GhOPRs were upregulated under salt treatment and repressed by polyethylene glycol 6000 (PEG6000). The expression patterns of GhOPRs were different in leaf, root, and stem under V. dahliae infection. GhOPR9 showed a higher expression level than other OPR genes in cotton root. The virus-induced gene silencing (VIGS) analysis suggested that knockdown of GhOPR9 could increase the susceptibility of cotton to V. dahliae infection. Furthermore, GhOPR9 also modulated the expressions of jasmonic acid (JA) pathway-regulated genes under the V. dahliae infection. Overall, our results provided the evolution and potential functions of the OPR genes in cotton. These findings suggested that GhOPR9 might play an important role in cotton resistance to V. dahliae.

scholarly journals Distal and proximal cis-regulatory elements sense X-chromosomal dosage and developmental state at the Xist locus

2021 ◽  
Author(s):  
Rutger A.F. Gjaltema ◽  
Till Schwämmle ◽  
Pauline Kautz ◽  
Michael Robson ◽  
Robert Schöpflin ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Embryonic Stem ◽  
Developmental State ◽  
Regulatory Elements ◽  
Developmental Time ◽  
Proximal Region ◽  
Spatial Proximity ◽  
Enhancer Activity ◽  
Regulatory Regions ◽  
Spatio Temporal

AbstractDevelopmental genes such as Xist, the master regulator of X-chromosome inactivation (XCI), are controlled by complex cis-regulatory landscapes, which decode multiple signals to establish specific spatio-temporal expression patterns. Xist integrates information on X-chromosomal dosage and developmental stage to trigger XCI at the primed pluripotent state in females only. Through a pooled CRISPR interference screen in differentiating mouse embryonic stem cells, we identify functional enhancer elements of Xist during the onset of random XCI. By quantifying how enhancer activity is modulated by X-dosage and differentiation, we find that X-dosage controls the promoter-proximal region in a binary switch-like manner. By contrast, differentiation cues activate a series of distal elements and bring them into closer spatial proximity of the Xist promoter. The strongest distal element is part of an enhancer cluster ∼200 kb upstream of the Xist gene which is associated with a previously unannotated Xist-enhancing regulatory transcript, we named Xert. Developmental cues and X-dosage are thus decoded by distinct regulatory regions, which cooperate to ensure female-specific Xist upregulation at the correct developmental time. Our study is the first step to disentangle how multiple, functionally distinct regulatory regions interact to generate complex expression patterns in mammals.

scholarly journals Genome-wide identification and characterization of Solanum tuberosum BiP genes reveals the role of the promoter architecture in BiP gene diversity

2020 ◽  
Author(s):  
Venura Herath ◽  
Mathieu Gayral ◽  
Nirakar Adhikari ◽  
Rita Miller ◽  
Jeanmarie Verchot
Keyword(s):  
Solanum Tuberosum ◽  
Gene Diversity ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Linear Distribution ◽  
Potato Genome ◽  
Unfolded Protein ◽  
Promoter Architecture ◽  
Spatio Temporal ◽  
The Unfolded Protein Response

AbstractThe endoplasmic reticulum (ER) immunoglobulin binding proteins (BiPs) are molecular chaperones involved in normal protein maturation and refolding malformed proteins through the unfolded protein response (UPR). Plants BiPs belong to a multi-gene family contributing to development, immunity, and responses to environmental stresses. This study identified three BiP homologues in the Solanum tuberosum (potato) genome using phylogenetic, amino acid sequence, 3-D protein modeling and gene structure analysis. These analyses revealed that StBiP1 and StBiP2 grouped with AtBiP2, whereas StBiP3 grouped with AtBiP3. While the protein sequences and folding structures are highly similar, these StBiPs are distinguishable by their expression patterns in different tissues and in response to environmental stressors such as treatment with heat, chemicals, or virus elicitors of UPR. Ab initio promoter analysis revealed that potato and Arabidopsis BiP1 and BiP2 promoters were highly enriched with cis regulatory elements (CREs) linked to developmental processes, whereas BiP3 promoters were enriched with stress-related CREs. The frequency and linear distribution of these CREs produced two phylogenetic branches that further resolve the groups identified through gene phylogeny and exon/intron phase analysis. These data reveal that the CRE architecture of BiP promoters potentially define their spatio -temporal expression patterns under developmental and stress related cues.

scholarly journals Spatio-temporal expression of phytoglobin: a determining factor in the NO specification of cell fate

2019 ◽  
Vol 70 (17) ◽  
pp. 4365-4377 ◽  
Author(s):  
Claudio Stasolla ◽  
Shuanglong Huang ◽  
Robert D Hill ◽  
Abir U Igamberdiev
Keyword(s):  
Cell Fate ◽  
Growth And Development ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Cell Behavior ◽  
Cell Tissue ◽  
Organ Specific ◽  
Response To Stress ◽  
Spatio Temporal ◽  
Determining Factor

AbstractPlant growth and development rely on the orchestration of cell proliferation, differentiation, and ultimately death. After varying rounds of divisions, cells respond to positional cues by acquiring a specific fate and embarking upon distinct developmental pathways which might differ significantly from those of adjacent cells exposed to diverse cues. Differential cell behavior is most apparent in response to stress, when some cells might be more vulnerable than others to the same stress condition. This appears to be the case for stem cells which show abnormal features of differentiation and ultimately signs of deterioration at the onset of specific types of stress such as hypoxia and water deficit. A determining factor influencing cell behavior during growth and development, and cell response during conditions of stress is nitric oxide (NO), the level of which can be regulated by phytoglobins (Pgbs), known scavengers of NO. The modulation of NO by Pgbs can be cell, tissue, and/or organ specific, as revealed by the expression patterns of Pgbs dictated by the presence of distinct cis-regulatory elements in their promoters. This review discusses how the temporal and spatial Pgb expression pattern influences NO-mediated responses and ultimately cell fate acquisition in plant developmental processes.

scholarly journals Complex Analysis of Retroposed Genes’ Contribution to Human Genome, Proteome and Transcriptome

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 542
Author(s):  
Magdalena Regina Kubiak ◽  
Michał Wojciech Szcześniak ◽  
Izabela Makałowska
Keyword(s):  
Complex Analysis ◽  
Genomic Sequence ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Protein Domain ◽  
Gene Duplications ◽  
Protein Coding ◽  
Spatio Temporal ◽  
Recombination Hot Spots ◽  
Cis And Trans

Gene duplication is a major driver of organismal evolution. One of the main mechanisms of gene duplications is retroposition, a process in which mRNA is first transcribed into DNA and then reintegrated into the genome. Most gene retrocopies are depleted of the regulatory regions. Nevertheless, examples of functional retrogenes are rapidly increasing. These functions come from the gain of new spatio-temporal expression patterns, imposed by the content of the genomic sequence surrounding inserted cDNA and/or by selectively advantageous mutations, which may lead to the switch from protein coding to regulatory RNA. As recent studies have shown, these genes may lead to new protein domain formation through fusion with other genes, new regulatory RNAs or other regulatory elements. We utilized existing data from high-throughput technologies to create a complex description of retrogenes functionality. Our analysis led to the identification of human retroposed genes that substantially contributed to transcriptome and proteome. These retrocopies demonstrated the potential to encode proteins or short peptides, act as cis- and trans- Natural Antisense Transcripts (NATs), regulate their progenitors’ expression by competing for the same microRNAs, and provide a sequence to lncRNA and novel exons to existing protein-coding genes. Our study also revealed that retrocopies, similarly to retrotransposons, may act as recombination hot spots. To our best knowledge this is the first complex analysis of these functions of retrocopies.

scholarly journals GimmeMotifs: an analysis framework for transcription factor motif analysis

2018 ◽  
Author(s):  
Niklas Bruse ◽  
Simon J. van Heeringen
Keyword(s):  
Dna Sequences ◽  
Motif Discovery ◽  
High Throughput Sequencing ◽  
Performance Metrics ◽  
De Novo ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Ensemble Method ◽  
Regulatory Sequences ◽  
Motif Analysis

AbstractBackgroundTranscription factors (TFs) bind to specific DNA sequences, TF motifs, in cis-regulatory sequences and control the expression of the diverse transcriptional programs encoded in the genome. The concerted action of TFs within the chromatin context enables precise temporal and spatial expression patterns. To understand how TFs control gene expression it is essential to model TF binding. TF motif information can help to interpret the exact role of individual regulatory elements, for instance to predict the functional impact of non-coding variants.FindingsHere we present GimmeMotifs, a comprehensive computational framework for TF motif analysis. Compared to the previously published version, this release adds a whole range of new functionality and analysis methods. It now includes tools for de novo motif discovery, motif scanning and sequence analysis, motif clustering, calculation of performance metrics and visualization. Included with GimmeMotifs is a non-redundant database of clustered motifs. Compared to other motif databases, this collection of motifs shows competitive performance in discriminating bound from unbound sequences. Using our de novo motif discovery pipeline we find large differences in performance between de novo motif finders on ChIP-seq data. Using an ensemble method such as implemented in GimmeMotifs will generally result in improved motif identification compared to a single motif finder. Finally, we demonstrate maelstrom, a new ensemble method that enables comparative analysis of TF motifs between multiple high-throughput sequencing experiments, such as ChIP-seq or ATAC-seq. Using a collection of ~200 H3K27ac ChIP-seq data sets we identify TFs that play a role in hematopoietic differentiation and lineage commitment.ConclusionGimmeMotifs is a fully-featured and flexible framework for TF motif analysis. It contains both command-line tools as well as a Python API and is freely available at: https://github.com/vanheeringen-lab/gimmemotifs.

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