scholarly journals Genome-wide characterization of the auxin response factor (ARF) gene family of litchi (Litchi chinensis Sonn.): phylogenetic analysis, miRNA regulation and expression changes during fruit abscission

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6677 ◽  
Author(s):  
Yanqing Zhang ◽  
Zaohai Zeng ◽  
Chengjie Chen ◽  
Caiqin Li ◽  
Rui Xia ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Expression Patterns ◽  
Flower Formation ◽  
Auxin Response ◽  
Dimerization Domain ◽  
Litchi Chinensis ◽  
Regulatory Pathways ◽  
Fruit Abscission ◽  
Genome Wide ◽  
A Genome

Auxin response factors (ARFs) play fundamental roles in modulating various biological processes including fruit development and abscission via regulating the expression of auxin response genes. Currently, little is known about roles of ARFs in litchi (Litchi chinensis Sonn.), an economically important subtropical fruit tree whose production is suffering from fruit abscission. In this study, a genome-wide analysis of ARFs was conducted for litchi, 39 ARF genes (LcARFs) were identified. Conserved domain analysis showed that all the LcARFs identified have the signature B3 DNA-binding (B3) and ARF (Aux_rep) domains, with only 23 members having the dimerization domain (Aux_IAA). The number of exons in LcARF genes ranges from 2 to 16, suggesting a large variation for the gene structure of LcARFs. Phylogenetic analysis showed that the 39 LcARFs could be divided into three main groups: class I, II, and III. In total, 23 LcARFs were found to be potential targets of small RNAs, with three conserved and one novel miRNA-ARF (miRN43-ARF9) regulatory pathways discovered in litchi. Expression patterns were used to evaluate candidate LcARFs involved in various developmental processes, especially in flower formation and organ abscission. The results revealed that most ARF genes likely acted as repressors in litchi fruit abscission, that is, ARF2D/2E, 7A/7B, 9A/9B, 16A/16B, while a few LcARFs, such as LcARF5A/B, might be positively involved in this process. These findings provide useful information and resources for further studies on the roles of ARF genes in litchi growth and development, especially in the process of fruit abscission.

scholarly journals Genome-Wide Phylogenetic Analysis, Expression Pattern, and Transcriptional Regulatory Network of the Pig C/EBP Gene Family

2021 ◽  
Vol 17 ◽  
pp. 117693432110413
Author(s):  
Chaoxin Zhang ◽  
Tao Wang ◽  
Tongyan Cui ◽  
Shengwei Liu ◽  
Bing Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Phylogenetic Analysis ◽  
Regulatory Network ◽  
Target Genes ◽  
Transcriptional Regulatory Network ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Genome Wide ◽  
A Genome

The CCAAT/enhancer binding protein (C/EBP) transcription factors (TFs) regulate many important biological processes, such as energy metabolism, inflammation, cell proliferation etc. A genome-wide gene identification revealed the presence of a total of 99 C/EBP genes in pig and 19 eukaryote genomes. Phylogenetic analysis showed that all C/EBP TFs were classified into 6 subgroups named C/EBPα, C/EBPβ, C/EBPδ, C/EBPε, C/EBPγ, and C/EBPζ. Gene expression analysis showed that the C/EBPα, C/EBPβ, C/EBPδ, C/EBPγ, and C/EBPζ genes were expressed ubiquitously with inconsistent expression patterns in various pig tissues. Moreover, a pig C/EBP regulatory network was constructed, including C/EBP genes, TFs and miRNAs. A total of 27 feed-forward loop (FFL) motifs were detected in the pig C/EBP regulatory network. Based on the RNA-seq data, gene expression patterns related to FFL sub-network were analyzed in 27 adult pig tissues. Certain FFL motifs may be tissue specific. Functional enrichment analysis indicated that C/EBP and its target genes are involved in many important biological pathways. These results provide valuable information that clarifies the evolutionary relationships of the C/EBP family and contributes to the understanding of the biological function of C/EBP genes.

scholarly journals Genome-wide transcriptional profiling uncovers a similar oligodendrocyte-related transcriptional response to acute and chronic alcohol drinking in the amygdala

2021 ◽  
Author(s):  
Sharvari Narendra ◽  
Claudia Klengel ◽  
Bilal Hamzeh ◽  
Drasti Patel ◽  
Joy Otten ◽  
...  
Keyword(s):  
Gene Expression ◽  
Alcohol Drinking ◽  
Brain Area ◽  
Transcriptional Profiling ◽  
Expression Patterns ◽  
Transcriptional Response ◽  
Histone Deacetylation ◽  
Regulatory Pathways ◽  
Genome Wide ◽  
A Genome

AbstractAlcohol intake progressively increases after prolonged consumption of alcohol, but relatively few new therapeutics targeting development of alcohol use disorder (AUD) have been validated. Here, we conducted a genome-wide RNA-sequencing (RNA-seq) analysis in mice exposed to different modes (acute vs chronic) of ethanol drinking. We focused on transcriptional profiles in the amygdala including the central and basolateral subnuclei, a brain area previously implicated in alcohol drinking and seeking, demonstrating distinct gene expression patterns and canonical pathways induced by both acute and chronic intake. Surprisingly, both drinking modes triggered similar transcriptional changes, including up-regulation of ribosome-related/translational pathways and myelination pathways, and down-regulation of chromatin binding and histone modification. Notably, multiple genes that were significantly regulated in mouse amygdala with alcohol drinking, including Atp2b1, Slc4a7, Nfkb1, Nts, and Hdac2, among others had previously been associated with human AUD via GWAS or other genomic studies. In addition, analyses of hub genes and upstream regulatory pathways predicted that voluntary ethanol consumption affects epigenetic changes via histone deacetylation pathways, oligodendrocyte and myelin function, and oligodendrocyte-related transcriptional factor, Sox17.Overall, our results suggest that the transcriptional landscape in the central and basolateral subnuclei of the amygdala is sensitive to voluntary alcohol drinking. They provide a unique resource of gene expression data for future translational studies examining transcriptional mechanisms underlying the development of AUD due to alcohol consumption.

Bioinformatics analysis of the auxin response factor gene family in Prunus persica

2019 ◽  
Vol 99 (2) ◽  
pp. 232-242
Author(s):  
Liping Guo ◽  
Jianzhou Gao ◽  
Jaime A. Teixeira da Silva ◽  
Xiaonan Yu
Keyword(s):  
Phylogenetic Analysis ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Promoter Region ◽  
Prunus Persica ◽  
Expression Patterns ◽  
Auxin Response ◽  
Comprehensive Overview ◽  
A Genome

Auxin plays an important role in various aspects of plant growth and development. Auxin response factors (ARFs) are plant-specific transcription factors that regulate the expression of auxin-responsive genes by binding with auxin response elements (AuxinREs) in the promoter region of such genes. In this study, a genome-wide analysis of the ARF genes in Prunus persica was carried out using the latest updated genomics data of this plant. A total of 17 ARF genes were identified and were named PpARF1 to PpARF17. A comprehensive overview of these PpARFs was undertaken, including a phylogenetic analysis and analysis of gene structures, conserved motifs and domains, chromosome location, cis-elements in the promoter region, and gene expression patterns. The 17 PpARF genes were distributed over eight chromosomes. All identified PpARF proteins had an ARF domain and a typical B3-DNA-binding domain that consisted of two α-helixes and seven β-sheets. Some of the PpARF proteins also had an Aux/IAA domain. Phylogenetic analysis categorized PpARF proteins into four groups. PpARF genes had many elements related to stress responses in the promotor region and showed distinct expression levels in leaves and roots. The present study provides basic information about the ARF gene family in Prunus persica and enables further verification of candidate genes related to plant growth.

scholarly journals Genome-Wide Investigation of the Auxin Response Factor Gene Family in Tartary Buckwheat (Fagopyrum tataricum)

2018 ◽  
Vol 19 (11) ◽  
pp. 3526 ◽  
Author(s):  
Moyang Liu ◽  
Zhaotang Ma ◽  
Anhu Wang ◽  
Tianrun Zheng ◽  
Li Huang ◽  
...  
Keyword(s):  
Fruit Development ◽  
Expression Patterns ◽  
Auxin Response Factor ◽  
Tartary Buckwheat ◽  
Structure Evolution ◽  
Response Factor ◽  
Auxin Response ◽  
Fagopyrum Tataricum ◽  
Genome Wide ◽  
A Genome

Auxin signaling plays an important role in plant growth and development. It responds to various developmental and environmental events, such as embryogenesis, organogenesis, shoot elongation, tropical growth, lateral root formation, flower and fruit development, tissue and organ architecture, and vascular differentiation. However, there has been little research on the Auxin Response Factor (ARF) genes of tartary buckwheat (Fagopyrum tataricum), an important edible and medicinal crop. The recent publication of the whole-genome sequence of tartary buckwheat enables us to study the tissue and expression profile of the FtARF gene on a genome-wide basis. In this study, 20 ARF (FtARF) genes were identified and renamed according to the chromosomal distribution of the FtARF genes. The results showed that the FtARF genes belonged to the related sister pair, and the chromosomal map showed that the duplication of FtARFs was related to the duplication of the chromosome blocks. The duplication of some FtARF genes shows conserved intron/exon structure, which is different from other genes, suggesting that the function of these genes may be diverse. Real-time quantitative PCR analysis exhibited distinct expression patterns of FtARF genes in various tissues and in response to exogenous auxin during fruit development. In this study, 20 FtARF genes were identified, and the structure, evolution, and expression patterns of the proteins were studied. This systematic analysis laid a foundation for the further study of the functional characteristics of the ARF genes and for the improvement of tartary buckwheat crops.

Sign in / Sign up

Export Citation Format

Share Document