scholarly journals Genome-wide characterization and expression analysis of soybean trihelix gene family

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8753
Author(s):  
Wei Liu ◽  
Yanwei Zhang ◽  
Wei Li ◽  
Yanhui Lin ◽  
Caijie Wang ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Stress Responses ◽  
Selective Pressure ◽  
Plant Immunity ◽  
Environmental Stresses ◽  
Soybean Genome ◽  
Multiple Roles ◽  
Functional Domain ◽  
Genomic Information ◽  
Genome Wide

Trihelix transcription factors play multiple roles in plant growth, development and various stress responses. In this study, we identified 71 trihelix family genes in the soybean genome. These trihelix genes were located at 19 out of 20 soybean chromosomes unevenly and were classified into six distinct subfamilies: GT-1, GT-2, GTγ, SIP1, SH4 and GTδ. The gene structure and conserved functional domain of these trihelix genes were similar in the same subfamily but diverged between different subfamilies. Thirteen segmental duplicated gene pairs were identified and all of them experienced a strong purifying selective pressure during evolution. Various stress-responsive cis-elements presented in the promoters of soybean trihelix genes, suggesting that the trihelix genes might respond to the environmental stresses in soybean. The expression analysis suggests that trihelix genes are involved in diverse functions during soybean development, flood or salinity tolerance, and plant immunity. Our results provide genomic information of the soybean trihelix genes and a basis for further characterizing their roles in response to environmental stresses.

scholarly journals Genome-Wide Analysis of the Trihelix Gene Family and Their Response to Cold Stress in Dendrobium officinale

2021 ◽  
Vol 13 (5) ◽  
pp. 2826
Author(s):  
Yan Tong ◽  
Hui Huang ◽  
YuHua Wang
Keyword(s):  
Stress Responses ◽  
Cold Treatment ◽  
Dendrobium Officinale ◽  
Functional Domain ◽  
Cis Elements ◽  
Genome Wide Analysis ◽  
Functional Studies ◽  
Genome Wide ◽  
Growth Development ◽  
Chinese Medicinal Plant

Trihelix transcription factors play important roles in plant growth, development and various stress responses. In this study, we identified 32 trihelix family genes (DoGT) in the important Chinese medicinal plant Dendrobium officinale. These trihelix genes could be classified into five different subgroups. The gene structure and conserved functional domain of these trihelix genes were similar in the same subfamily but diverged between different subfamilies. Various stresses responsive cis-elements presented in the promoters of DoGT genes, suggesting that the trihelix genes might respond to the environmental stresses. Expressional changes of DoGT genes in three tissues and under cold treatment suggested that trihelix genes were involved in diverse functions during D. officinale development and cold tolerance. This study provides novel insights into the phylogenetic relationships and functions of the D. officinaletrihelix genes, which will aid future functional studies investigating the divergent roles of trihelix genes belonging to other species.

scholarly journals Genome-wide analysis of CrRLK1L genes and their expression profiling during fiber development in cotton

2020 ◽  
Author(s):  
Dongyun Zuo ◽  
Javaria Ashraf ◽  
Hailiang Cheng ◽  
Shang Liu ◽  
Youping Zhang ◽  
...  
Keyword(s):  
Stress Responses ◽  
Plant Immunity ◽  
Fiber Development ◽  
The Other ◽  
Element Analysis ◽  
Specific Expression ◽  
Group Iii ◽  
Group I ◽  
Genome Wide ◽  
Specific Expression Pattern

Abstract Background: Catharanthus roseus receptor-like kinase 1-like (CrRLK1Ls) proteins play important roles in cell growth, plant morphogenesis, reproduction, hormone signaling, plant immunity and stress responses in Arabidopsis. However, not much information is available about their functions during cotton fiber development.Results: We identified a total of 125, 73 and 71 full-length putative CrRLK1L genes in G. hirsutum, G. arboreum and G. raimondii, which are much greater than that of the other plants. The phylogenetic and gene structure analysis divided the cotton CrRLK1L genes into six major groups, among which only group I and II contained AtCrRLK1Ls of Arabidopsis, suggesting that other groups (group III-VI) were expanded by gene duplication during cotton evolution. Genome collinearity analysis revealed that half of the At02 genes in G. hirsutum derived from A02 of G. arboreum, while the other half (GhCrRLK1L6 and GhCrRLK1L7) originated from Dt03 and Dt02 of G. raimondii, indicating segmental duplication between noncorresponding chromosomes during polyploidization of G. hirsutum. In addition, expression and cis-element analysis revealed that only 22 GhCrRLK1Ls showed specific expression pattern during fiber development which are mainly due to the presence of binding sites for NAC, MYB and WRKY transcription factors.Conclusions: This study provides a strong foundation to further explore the molecular mechanism of CrRLK1L genes during fiber development in upland cotton.

Identification and expression analysis of chloroplast ribonucleoproteins (cpRNPs) in Arabidopsis and rice

Genome ◽  
2020 ◽  
Author(s):  
Jiawen Wu ◽  
Huimin Liu ◽  
Shan Lu ◽  
Jian Hua ◽  
Baohong Zou
Keyword(s):  
Expression Analysis ◽  
Stress Responses ◽  
Expression Patterns ◽  
Tissue Expression ◽  
Stability Control ◽  
Rna Recognition Motif ◽  
Chloroplast Targeting ◽  
Genome Wide ◽  
A Genome ◽  
Targeting Signal

Chloroplast ribonucleoproteins (cpRNPs) are implicated in splicing, editing and stability control of chloroplast RNAs as well as in regulating development and stress tolerance. To facilitate a comprehensive understanding of their functions, we carried out a genome-wide identification, curation, and phylogenetic analysis of cpRNP genes in Oryza sativa (rice) and Arabidopsis thaliana (Arabidopsis). Ten cpRNP genes were identified in each of Arabidopsis and rice genomes based on the presence of two RRM (RNA recognition motif) domains and an N-terminal chloroplast targeting signal peptide in the predicted proteins. These proteins are localized to chloroplasts. Gene expression analysis revealed that cpRNPs have differential tissue expression patterns and some cpRNPs are induced by abiotic stresses such as cold, heat and drought. Taken together, our study provides a comprehensive annotation of the cpRNP gene family and their expression patterns in Arabidopsis and rice which will facilitate further studies on their roles in plant growth and stress responses.

scholarly journals Identification and Expression Analysis of SLAC/SLAH Gene Family in Brassica napus L.

2021 ◽  
Vol 22 (9) ◽  
pp. 4671
Author(s):  
Yunyou Nan ◽  
Yuyu Xie ◽  
Ayub Atif ◽  
Xiaojun Wang ◽  
Yanfeng Zhang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Expression Analysis ◽  
Stress Responses ◽  
Structural Characteristics ◽  
Brassica Napus L ◽  
Nitrate Treatment ◽  
Genome Wide ◽  
Slow Type ◽  
Hormone Responses

Slow type anion channels (SLAC/SLAHs) play important roles during anion transport, growth and development, abiotic stress responses and hormone responses in plants. However, there is few report on SLAC/SLAHs in rapeseed (Brassica napus). Genome-wide identification and expression analysis of SLAC/SLAH gene family members were performed in B. napus. A total of 23 SLAC/SLAH genes were identified in B. napus. Based on the structural characteristics and phylogenetic analysis of these members, the SLAC/SLAHs could be classified into three main groups. Transcriptome data demonstrated that BnSLAH3 genes were detected in various tissues of the rapeseed and could be up-regulated by low nitrate treatment in roots. BnSLAC/SLAHs were exclusively localized on the plasma membrane in transient expression of tobacco leaves. These results will increase our understanding of the evolution and expression of the SLAC/SLAHs and provide evidence for further research of biological functions of candidates in B. napus.

scholarly journals Deciphering miRNAs involved in crosstalk between auxin and cold stress in Arabidopsis roots

2020 ◽  
Author(s):  
Mohammad Aslam ◽  
Kenji Sugita ◽  
Yuan Qin ◽  
Abidur Rahman
Keyword(s):  
Stress Response ◽  
Cold Stress ◽  
Expression Analysis ◽  
Stress Responses ◽  
Auxin Signaling ◽  
Potential Candidate ◽  
Wild Type ◽  
Gene Expressions ◽  
Significant Differential Expression ◽  
Genome Wide

Abstract Background: The phytohormone auxin and microRNA-mediated regulation of gene expressions are key regulators for plant growth and development at both optimal and under low-temperature stress conditions. However, the mechanistic link between microRNA and auxin in regulating plant cold stress response remains elusive. Results: To better understand the role of microRNA in the crosstalk between auxin and cold stress responses, we took advantage of the mutants of Arabidopsis thaliana with altered response to auxin transport and signal. Screening of the mutants for root growth recovery after cold stress at 4°C revealed that the auxin signaling mutant, solitary root 1 ( slr1; mutation in Aux/IAA14), shows a hypersensitive response to cold stress. Genome-wide expression analysis of miRNA in wild-type and slr1 mutant roots using next-generation sequencing revealed 180 known and 71 novel cold-responsive microRNAs. Cold stress also increased the abundance of 26 nt-31 nt small RNA population in slr1 compared with wild-type. Comparative analysis of microRNA expression shows significant differential expression of 13 known and 7 novel miRNAs in slr1 at 4°C compared with wild-type. Target gene expression analysis of the members from one potential candidate miRNAs, miR169 revealed the possible involvement of miR169- NF-YA module in the auxin-mediated cold stress response. Conclusions: Taken together, these results indicate that SLR/IAA14, a transcriptional repressor of auxin signaling, plays a crucial role in integrating miRNA in auxin and cold responses.

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