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

Abstract

Trihelix proteins are the members of gene family encoding transcriptional factors in plants that take part in plant responses to various cellular activities and stresses. The DNA-binding domain of these proteins is a tryptophan enrich tandem repeat forming helix-loop-helix-loop-helix. We retrieved the protein sequence of 28 candidates of trihelix gene family of Arabidopsis thaliana. These 28 proteins are grouped in five subfamilies according to their structural properties. These trihelix members were located on all 5 chromosomes of Arabidopsis with uneven distribution. We characterized diversity in amino acid residues in trihelix domain and found conserved motif in trihelix protein. Further, the gene structure analysis showed the distribution of introns and exons on each gene. The promoter analysis was done and 5 cis-regulatory elements were located on 1 kb of the promoter sequence. Synteny analysis showed the relationship among the trihelix genes. This study will be helpful in providing the in silico genomic information about the trihelix transcriptional factor in Arabidopsis thaliana. Moreover, these findings will be helpful in understanding trihelix family for their diverse role in plant stress and development

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

“…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 ].…”

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

“…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).…”

“…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).…”

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

“…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).…”