GENOME-WIDE ANALYSIS OF TRIHELIX TRANSCRIPTION FACTOR GENE FAMILY IN Arabidopsis thaliana

Yasmeen, Erum; Riaz, Muhammad Waheed; Sultan, Shaiq; Azeem, Farrukh; Abbas, Amjad; Riaz, Kashif; Ali, Muhammad Amjad

doi:10.21162/pakjas/16.3347

Cited by 14 publications

(12 citation statements)

References 26 publications

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“…Among the 40 SbTH genes, 8 (20.0%) contained the GT1 domain, 23 (57.5%) contained the Myb_DNA-binding domain and 9 (22.5%) contained both GT1 domain and Myb DNA-binding domain. The ratio of SbTH genes to total genes in the S. bicolor genome was about 0.12% [ 18 ], which is similar to that of Arabidopsis (0.11%) [ 19 , 20 ], soybean (0.14%) [ 21 , 22 ], and rice (0.10%) [ 23 , 24 ] but more that than of tomato (0.05%) [ 12 , 25 ], chrysanthemum (0.04%) [ 26 , 27 ], wheat (0.08%) [ 28 , 29 ], and buckwheat (0.06%) [ 30 , 31 ].…”

Section: Resultsmentioning

confidence: 99%

Genome-wide identification and expression profile analysis of trihelix transcription factor family genes in response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]

Duan

Zhang

et al. 2021

BMC Genomics

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Background Transcription factors, including trihelix transcription factors, play vital roles in various growth and developmental processes and in abiotic stress responses in plants. The trihelix gene has been systematically studied in some dicots and monocots, including Arabidopsis, tomato, chrysanthemum, soybean, wheat, corn, rice, and buckwheat. However, there are no related studies on sorghum. Results In this study, a total of 40 sorghum trihelix (SbTH) genes were identified based on the sorghum genome, among which 34 were located in the nucleus, 5 in the chloroplast, 1 (SbTH38) in the cytoplasm, and 1 (SbTH23) in the extracellular membrane. Phylogenetic analysis of the SbTH genes and Arabidopsis and rice trihelix genes indicated that the genes were clustered into seven subfamilies: SIP1, GTγ, GT1, GT2, SH4, GTSb8, and orphan genes. The SbTH genes were located in nine chromosomes and none on chromosome 10. One pair of tandem duplication gene and seven pairs of segmental duplication genes were identified in the SbTH gene family. By qPCR, the expression of 14 SbTH members in different plant tissues and in plants exposed to six abiotic stresses at the seedling stage were quantified. Except for the leaves in which the genes were upregulated after only 2 h exposure to high temperature, the 12 SbTH genes were significantly upregulated in the stems of sorghum seedlings after 24 h under the other abiotic stress conditions. Among the selected genes, SbTH10/37/39 were significantly upregulated, whereas SbTH32 was significantly downregulated under different stress conditions. Conclusions In this study, we identified 40 trihelix genes in sorghum and found that gene duplication was the main force driving trihelix gene evolution in sorghum. The findings of our study serve as a basis for further investigation of the functions of SbTH genes and providing candidate genes for stress-resistant sorghum breeding programmes and increasing sorghum yield.

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Section: Resultsmentioning

confidence: 99%

Genome-wide identification and expression profile analysis of trihelix transcription factor family genes in response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]

Duan

Zhang

et al. 2021

BMC Genomics

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“…Recently, a new subfamily, GTδ was formed in tomato (Solanum lycopersicum) and rice (Yu et al, 2015;. In the present study, the classification of the soybean trihelix gene family has been renewed according to their new classification in Arabidopsis, tomato and rice ( Figure 3) (Kaplan et al, 2012;Yasmeen et al, 2016;Yu et al, 2015;. All of the 71 soybean trihelix genes were classified into 6 subfamilies (GT-1, GT-2, SH4, SIP1, GTγ and GTδ).…”

Section: Characterization Of the Soybean Trihelix Genesmentioning

confidence: 85%

“…v1 and performing a different search method. To date, the soybean trihelix family is the second largest known trihelix gene family (next to the wheat trihelix family composed of 94 trihelix genes) (Xiao et al, 2019) compared with other plants, such as Arabidopsis (28), rice (41) tomato (36), Brassica rapa (52), Chrysanthemum (20) and tartary buckwheat (31) (Yasmeen et al, 2016;Yu et al, 2015;Wang et al, 2017;Wang et al, 2018;Ma et al, 2019).…”

Section: Characterization Of the Soybean Trihelix Genesmentioning

confidence: 99%

Peer Review #1 of "Genome-wide characterization and expression analysis of soybean trihelix gene family (v0.1)"

2020

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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. 13 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 comprehensive genomic information of the soybean trihelix genes and a basis for further characterizing their roles in response to environmental stresses.

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“…In plants, a number of genes are up regulated in response to abiotic stresses and the products of these genes encourage plant survival in adverse environmental conditions (Ali et al, 2017;Rasul et al, 2017). These stress inducible genes could promote stress tolerance directly or by controlling other genes (Yasmeen et al, 2016). Transcription factors (TFs) belong to a class of genes that modulate the expression of their target genes through binding with cis-regulatory elements present in the promoter region (Nakashima et al, 2009).…”

Section: Analysis Of Putative Cis-regulatory Elements In Aqp Promotersmentioning

confidence: 99%

Drought affects aquaporins gene expression in important pulse legume chickpea (Cicer arietinum L.)

Azeem¹,

Ahmed²,

Atif³

et al. 2018

PAK.J.BOT.

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Aquaporins (AQPs) mediate cross membrane transport of water and other solutes in plants. AQPs also enhance plant performance under environmental stresses including water shortage. Chickpea (Cicer arietinum L.) is the most important pulse legume for the people of semi-arid tropics. To understand the evolutionary relationships and role of AQPs in drought tolerance in chickpea, the current study involves an evolutionary analysis coupled with expression analysis and promoter analysis of selected AQPs. A total of 503 non-redundant AQP genes have been studied in 11 plant species including mosses (Physcomitrella patens), monocots (Oryza sativa and Zea mays) and dicots (Solanum lycopersicum, Populus trichocarpa, Gossypium hirsutum, Glycine max, Arabidopsis thaliana, Brassica rapa, Solanum tubrosum and Cicer arietinum). Phylogenetic analysis demonstrated a clear divergence of AQP subfamilies as paralogous groups and possible evolutionary direction of AQP subfamilies. Semi-quantitative RT-PCR analysis depicted involvement of PIP2; 2 and NIP6; 3 in increasing plant drought stress tolerance and of SIP1; 1 and PIP2; 3 with a contrary role. In silico promoter analysis identified a 49 bp conserved motif among six AQPs and several abiotic stresses related cis-elements. The present study is a very first step in deciphering AQPs role in drought stress tolerance with a special perspective from evolutionary relationships and gene expression regulation.

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GENOME-WIDE ANALYSIS OF TRIHELIX TRANSCRIPTION FACTOR GENE FAMILY IN Arabidopsis thaliana

Cited by 14 publications

References 26 publications

Genome-wide identification and expression profile analysis of trihelix transcription factor family genes in response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]

Genome-wide identification and expression profile analysis of trihelix transcription factor family genes in response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]

Peer Review #1 of "Genome-wide characterization and expression analysis of soybean trihelix gene family (v0.1)"

Drought affects aquaporins gene expression in important pulse legume chickpea (Cicer arietinum L.)

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