scholarly journals Identification and expression analysis of the WRKY gene family during different developmental stages in Lycium ruthenicum Murr. fruit

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10207
Author(s):  
Richard John Tiika ◽  
Jia Wei ◽  
Rui Ma ◽  
Hongshan Yang ◽  
Guangxin Cui ◽  
...  
Keyword(s):  
Gene Family ◽  
Plant Species ◽  
Zinc Finger ◽  
Developmental Stages ◽  
Quantitative Polymerase Chain Reaction ◽  
Expression Patterns ◽  
Conserved Motif ◽  
Motif Prediction ◽  
Transcriptome Database ◽  
Lycium Ruthenicum

Background The WRKY gene family, one of the major transcription factor families in plants, plays crucial regulatory roles in physiological and biological developmental processes, and the adaptation of plants to the environment. However, the systematic study of WRKY structure, expression profiling, and regulatory functions has not been extensively reported in Lycium ruthenicum, although these aspects have been comprehensively studied in most plant species. Methods In this study, the WRKY genes were identified from a L. ruthenicum transcriptome database by using bioinformatics. The identification, phylogenetic analysis, zinc-finger structures, and conserved motif prediction were extensively explored. Moreover, the expression levels of 23 selected genes with fragments per kilobase of exons per million mapped reads (FPKM) >5 were assayed during different fruit developmental stages with real-time quantitative polymerase chain reaction (RT-qPCR). Results A total of 73 putative WRKY proteins in the L. ruthenicum transcriptome database were identified and examined. Forty-four proteins with the WRKY domain were identified and divided into three major groups with several subgroups, in accordance with those in other plant species. All 44 LrWRKY proteins contained one or two conserved WRKY domains and a zinc-finger structure. Conserved motif prediction revealed conservation of the WRKY DNA-binding domain in L. ruthenicum proteins. The selected LrWRKY genes exhibited discrete expression patterns during different fruit developmental stages. Interestingly, five LrWRKYs (-20, -21, -28, -30, and -31) were expressed remarkably throughout the fruit developmental stages. Discussion Our results reveal the characteristics of the LrWRKY gene family, thus laying a foundation for further functional analysis of the WRKY family in L. ruthenicum.

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.

Identification and expression analysis of E2 ubiquitin-conjugating enzymes in cucumber

2021 ◽  
Author(s):  
Wei Lai ◽  
Zhaoyang Hu ◽  
Chuxia Zhu ◽  
Yingui Yang ◽  
Shiqiang Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Biological Processes ◽  
Protein Ubiquitination ◽  
Genome Wide ◽  
Conjugating Enzymes ◽  
Gene Structures ◽  
Ubiquitin Conjugating Enzymes ◽  
Genome Wide Survey

Protein ubiquitination is one of the most common modifications that can degrade or modify proteins in eukaryotic cells. The E2 ubiquitin-conjugating enzymes (UBCs) are involved in multiple biological processes of eukaryotes and their response to adverse stresses. Genome-wide survey of the UBC gene family has been performed in many plant species but not in cucumber (Cucumis sativus). In this study, a total of 38 UBC family genes (designated as CsUBC1–CsUBC38) were identified in cucumber. The phylogenetic analysis of UBC proteins from cucumber, Arabidopsis and maize indicated that these proteins could be divided into 15 groups. Most of the phylogenetically related CsUBC members had similar conserved motif patterns and gene structures. The CsUBC genes were unevenly distributed on seven chromosomes, and gene duplication analysis indicated that segmental duplication has played a significant role in the expansion of the cucumber UBC gene family. Promoter analysis of these genes resulted in the identification of many hormone-, stress- and development-related cis-elements. The CsUBC genes exhibited differential expression patterns in different tissues and developmental stages of fruit ripening. In addition, a total of 14 CsUBC genes were differentially expressed upon downy mildew (DM) infection compared with the control. Our results lay the foundation for further clarification of the roles of the CsUBC genes in the future.

scholarly journals Identification and Expression Analysis of the NAC Gene Family in Coffea canephora

Agronomy ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 670 ◽  
Author(s):  
Dong ◽  
Jiang ◽  
Yang ◽  
Xiao ◽  
Bai ◽  
...  
Keyword(s):  
Cold Stress ◽  
Gene Family ◽  
Stress Responses ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Coffea Canephora ◽  
Coffee Bean ◽  
Systematic Analysis ◽  
Nac Gene Family ◽  
Basic Features

The NAC gene family is one of the largest families of transcriptional regulators in plants, and it plays important roles in the regulation of growth and development as well as in stress responses. Genome-wide analyses have been performed in diverse plant species, but there is still no systematic analysis of the NAC genes of Coffea canephora Pierre ex A. Froehner. In this study, we identified 63 NAC genes from the genome of C. canephora. The basic features and comparison analysis indicated that the NAC gene members increased via duplication events during the evolution of the plant. Phylogenetic analysis divided the NAC proteins from C. canephora, Arabidopsis and rice into 16 subgroups. Analysis of the expression patterns of CocNACs under cold stress and coffee bean development indicated that 38 CocNACs were differentially expressed under cold stress; six genes may play important roles in the process of cold acclimation, and four genes among 54 CocNACs showing a variety of expression patterns during different developmental stages of coffee beans may be positively related to the bean development. This study can expand our understanding of the functions of the CocNAC gene family in cold responses and bean development, thereby potentially intensifying the molecular breeding programs of Coffea spp. plants.

scholarly journals Identification and Profiling of Conserved MicroRNAs in Different Developmental Stages of Crown Imperial (Fritillaria Imperialis L.) using High-throughput Sequencing

2021 ◽  
Author(s):  
Fereshteh Ahmadi Teshniz ◽  
Behrouz Shiran ◽  
Sadegh Mousavi-Fard ◽  
Hossein Fallahi ◽  
Bojana Banović Đeri
Keyword(s):  
Plant Species ◽  
Abiotic Stresses ◽  
Regulatory Networks ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Practical Application ◽  
Sequencing Technologies ◽  
New Strategies ◽  
Different Tissues

Abstract Novel strategies for improvement of plants’ ornamental and other properties relay on miRNA control of differential plant gene expression modulation. Still, in response to the same abiotic stresses, some conserved miRNA families show different expression patterns in different plant species. In parallel, the use of deep sequencing technologies reveals new levels of complexity of regulatory networks in plants through identification of new miRNAs. These are two major reasons why more studies are needed before envisioned new strategies may take their course in practical application domain. This research revealed 21 conserved miRNAs, matching 15 miRNA families, in Fritilaria imperialis. Among identified conserved miRNA families in crown imperial, miR166, miR169 and miR396 families were the most abundant ones. The expression of seven conserved miRNAs (Fim-miR156b, Fim-miR159, Fim-miR166a-5p, Fim-miR169d-5p, Fim-miR171c, Fim-miR393 and Fim-miR396e-3p) was further investigated in different tissues and three developmental stages, suggesting different roles these miRNAs have in growth and development of crown imperial. Gained knowledge from this research can open the door to find efficient ways to secure crown imperial survival, preservation and utilization and if proven useful may be applied in other plant species as well.

scholarly journals Comparing Time Series Transcriptome Data Between Plants Using A Network Module Finding Algorithm

2019 ◽  
Author(s):  
Jiyoung Lee ◽  
Lenwood S. Heath ◽  
Ruth Grene ◽  
Song Li
Keyword(s):  
Plant Species ◽  
Transcriptome Analysis ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Network Module ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis ◽  
R Programming Language ◽  
Homologous Genes ◽  
R Programming

ABSTRACTComparative transcriptome analysis is the comparison of expression patterns between homologous genes in different species. Since most molecular mechanistic studies in plants have been performed in model species including Arabidopsis and rice, comparative transcriptome analysis is particularly important for functional annotation of genes in other plant species. Many biological processes, such as embryo development, are highly conserved between different plant species. The challenge is to establish one-to-one mapping of the developmental stages between two species. In this protocol, we solve this problem by converting the gene expression patterns into a co-expression network and then apply network module-finding algorithms to the cross-species co-expression network. We describe how to perform such analysis using bash scripts for preliminary data processing and R programming language, which implemented simulated annealing method for module finding. We also provide instructions on how to visualize the resulting co-expression networks across species.

scholarly journals De novo characterization of the Lycium ruthenicum transcriptome and analysis of its digital gene expression profiles during fruit development and ripening

2017 ◽  
Vol 69 (1) ◽  
pp. 181-190 ◽  
Author(s):  
Yong Peng ◽  
Huiqin Ma ◽  
Shangwu Chen
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
De Novo ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Digital Gene Expression ◽  
Orthologous Group ◽  
Functional Studies ◽  
Lycium Ruthenicum

Lycium ruthenicum Murr., which belongs to the family Solanaceae, is a resource plant for Chinese traditional medicine and nutraceutical foods. In this study, RNA sequencing was applied to obtain raw reads of L. ruthenicum fruit at different stages of ripening, and a de novo assembly of its sequence was performed. Approximately 52.45 million 100-bp paired-end raw reads were generated from the samples by deep RNA-seq analysis. These short reads were assembled to obtain 164814 contigs, and the contigs were assembled into 84968 non-redundant unigenes using the Trinity method. Assembled sequences were annotated with gene descriptions, gene ontology, clusters of orthologous group and KEGG (Kyoto Encyclopedia of Genes and Genomes)pathway terms. Digital gene expression analysis was applied to compare gene-expression patterns at different fruit developmental stages. These results contribute to existing sequence resources for Lycium spp. during the fruit-ripening stages, which is valuable for further functional studies of genes involved in L. ruthenicum fruit nutraceutical quality.

Magnetic Bead Adsorption Extraction of Xyloglucan Endoglucosidase/Hydrolase Gene and Its Expression Analysis in Land Cotton

2021 ◽  
Vol 15 (4) ◽  
pp. 478-490
Author(s):  
Xianliang Li ◽  
Hang Liu ◽  
Zhichang Zhao
Keyword(s):  
Gene Family ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Magnetic Bead ◽  
Evolutionary Significance ◽  
Cotton Fibers ◽  
Expression Levels ◽  
Duplication Events ◽  
And Function

The xyloglucan Endotransglucosylase/hydrolase (XTH) genes are proposed to encode enzymes responsible for cleaving and reattaching xyloglucan polymers. Despite prior identification of the XTH gene family in Arabidopsis and rice, the XTH family in upland cotton, a tetraploid plant whose fiber cell is an excellent model for the study of plant cell elongation, is yet uncharacterized. In this study, iron tetroxide based magnetic nanobead (Fe3O4 NPs) was successfully prepared and applied to extract xyloglucan endoglucosidase/hydrolase genes. Analysis of the genes can provide insight into the evolutionary significance and function of the XTH gene family. A total of 41 XTH genes found by searching the phytozomev 10 database were classified into three groups based on their phylogeny and the motifs of individual genes. The 25 and 5 GhXTH genes occurred as clusters resulting from the segmental and tandem duplication. More frequent duplication events in cotton contributed to the expansion of the family. Global microarray analysis of GhXTH gene expression in cotton fibers showed that 18 GhXTH genes could be divided into two clusters and four subclusters based on their expression patterns. Accumulated expression levels were relatively high at the elongation stages of the cotton fibers, suggesting that cotton fiber elongation requires high amounts of the GhXTH protein. The expression profiles of GhXTH3 and GhXTH4 showed by quantitative realtime PCR were similar to those determined by microarray. Additionally, the expression levels of GhXTH3 and GhXTH4 in Gossypium barbadense were higher than those in Gossypium hirsutum at developmental stages, indicating that expression levels of GhXTH3 and GhXTH4 in fibers varied among cultivars differing in fiber length.

scholarly journals Molecular Evolution of the Vacuolar Iron Transporter (VIT) Family Genes in 14 Plant Species

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 144 ◽  
Author(s):  
Jun Cao
Keyword(s):  
Gene Family ◽  
Plant Species ◽  
Tandem Duplication ◽  
Expression Patterns ◽  
Gene Organization ◽  
Development Stages ◽  
Functional Studies ◽  
Iron Transporter ◽  
Group I ◽  
Conserved Gene

The vacuolar iron transporter (VIT) proteins are involved in the storage and transport of iron. However, the evolution of this gene family in plants is unknown. In this study, I first identified 114 VIT genes in 14 plant species and classified these genes into seven groups by phylogenetic analysis. Conserved gene organization and motif distribution implied conserved function in each group. I also found that tandem duplication, segmental duplication and transposition contributed to the expansion of this gene family. Additionally, several positive selection sites were identified. Divergent expression patterns of soybean VIT genes were further investigated in different development stages and under iron stress. Functional network analysis exhibited 211 physical or functional interactions. The results will provide the basis for further functional studies of the VIT genes in plants.

scholarly journals Genome-wide Identification and Abiotic Stress Response Pattern Analysis of NF-Y Gene Family in Peanut (Arachis Hypogaea L.)

2021 ◽  
Author(s):  
Qian Wan ◽  
Lu Luo ◽  
Xiurong Zhang ◽  
Yuying Lv ◽  
Suqing Zhu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Gene Family ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Regulatory Region ◽  
Amino Acid Sequences ◽  
Start Codon ◽  
Abiotic Stress Response ◽  
Specific Expression

AbstractThe nuclear factor Y (NF-Y) transcription factor (TF) family consists of three subfamilies NF-YA, NF-YB and NF-YC. Many studies have proven that NF-Y complex plays multiple essential roles in stress response in Arabidopsis and other plant species. However, little attention has been given to these genes in peanut. In this study, thirty-three AhNF-Y genes were identified in cultivated peanut and they were distributed on 16 chromosomes. A phylogenetic analysis of the NF-Y amino acid sequences indicated that the peanut NF-Y proteins were clustered in pairs at the end of the branches and showed high conservation with previous reported plant NF-Ys. Evolutionary history analysis showed that only segmental duplication contributed to expansion of this gene family. Analysis of the 1500-bp regulatory regions upstream the start codon showed that, except for AhNF-YB6, peanut NF-Ys contained at least one abiotic stress response element in their regulatory region. Expression patterns of peanut NF-Ys in 22 tissues and developmental stages were analyzed. A few NF-Ys showed universal expression patterns, while most NF-Ys showed specific expression patterns. Through RNA-seq and qRT-PCR analyses, expression of six AhNF-Y genes was induced under salt stress in leaves or roots. In addition, AhNF-YA4/8/11, NF-YB4 and NF-YC2/8 also responded to osmotic stress, ABA (abscisic acid) and salicylic acid (SA) treatment.

scholarly journals Genome-Wide Identification and Expression Patterns of the C2H2-Zinc Finger Gene Family Related to Stress Responses and Catechins Accumulation in Camellia sinensis [L.] O. Kuntze

2021 ◽  
Vol 22 (8) ◽  
pp. 4197
Author(s):  
Shiyang Zhang ◽  
Junjie Liu ◽  
Guixian Zhong ◽  
Bo Wang
Keyword(s):  
Gene Family ◽  
Zinc Finger ◽  
Camellia Sinensis ◽  
Stress Responses ◽  
Zinc Finger Protein ◽  
Higher Plants ◽  
Expression Patterns ◽  
Physiological Status ◽  
C2h2 Zinc Finger ◽  
Meja Treatment

The C2H2-zinc finger protein (C2H2-ZFP) is essential for the regulation of plant development and widely responsive to diverse stresses including drought, cold and salt stress, further affecting the late flavonoid accumulation in higher plants. Tea is known as a popular beverage worldwide and its quality is greatly dependent on the physiological status and growing environment of the tea plant. To date, the understanding of C2H2-ZFP gene family in Camellia sinensis [L.] O. Kuntze is not yet available. In the present study, 134 CsC2H2-ZFP genes were identified and randomly distributed on 15 chromosomes. The CsC2H2-ZFP gene family was classified into four clades and gene structures and motif compositions of CsC2H2-ZFPs were similar within the same clade. Segmental duplication and negative selection were the main forces driving the expansion of the CsC2H2-ZFP gene family. Expression patterns suggested that CsC2H2-ZFPs were responsive to different stresses including drought, salt, cold and methyl jasmonate (MeJA) treatment. Specially, several C2H2-ZFPs showed a significant correlation with the catechins content and responded to the MeJA treatment, which might contribute to the tea quality and specialized astringent taste. This study will lay the foundations for further research of C2H2-type zinc finger proteins on the stress responses and quality-related metabolites accumulation in C. sinensis.

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