Genome-wide analysis and expression profiling of DNA-binding with one zinc finger (Dof) transcription factor family in potato

Venkatesh, Jelli; Park, Se Won

doi:10.1016/j.plaphy.2015.05.010

Cited by 88 publications

(69 citation statements)

References 70 publications

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“…In this study, we analyzed the structure, phylogenetic relationships, chromosomal locations, sub-cellular localization, gene duplication events, cis-elements, and expression patterns of Dof genes in wheat (TaDofs); 108 TaDof genes were identified. Dof genes were previously identified in several species, including Arabidopsis (36 genes) [9], rice (30) [9], tomato (34) [11], soybean (78) [40], corn (46) [13], potato (35) [41], chrysanthemum (20) [42], and foxtail genomes (36) [43]. A larger number of TaDof genes were detected, but this was likely caused by the allohexaploid genome of wheat.…”

Section: A Large Number Of Tadof Genes Are Present In Common Wheatmentioning

confidence: 99%

Genome-Wide Identification, Structure Characterization, and Expression Profiling of Dof Transcription Factor Gene Family in Wheat (Triticum aestivum L.)

Fang

Jiang

et al. 2020

Agronomy

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DNA binding with one finger (Dof) proteins are plant-specific transcription factors with crucial roles in plant growth and stress response. Even so, little is known about them in wheat. In this study, 108 wheat Dof (TaDof) genes across 21 chromosomes were detected. Although variable in sequence length, molecular weight, and isoelectric point, all TaDof proteins contained conserved zinc-finger structures and were phylogenetically divided into 7 sub-groups. Exon/intron and motif analyses suggested that TaDof structures and conserved motifs were similar within sub-groups but diverse among sub-groups. Many segmental duplications were identified and Ka/Ks and inter-species synthetic analyses indicated that polyploidization was main reason for increased number of TaDofs. Prediction and experimental confirmation revealed that TaDofs functioned as transcription factors in the nucleus. Expression pattern profiling showed that TaDofs specifically affected growth and development, and biotic and abiotic stress responses. Wheat miRNAs and cis-regulator were predicted as essential players in molding TaDofs expression patterns. qRT-PCR analysis revealed that TaDofs were induced by salt and drought stresses. Customized annotation revealed that TaDofs were widely involved in phytohormone response, defense, growth and development, and metabolism. Our study provided a comprehensive understanding to wheat TaDofs.

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Section: A Large Number Of Tadof Genes Are Present In Common Wheatmentioning

confidence: 99%

Genome-Wide Identification, Structure Characterization, and Expression Profiling of Dof Transcription Factor Gene Family in Wheat (Triticum aestivum L.)

Fang

Jiang

et al. 2020

Agronomy

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“…As shown in Supplementary material 1, which illustrates the intron/exon gene structure, the positions and phases of most Dof gene introns are conserved between sorghum and cotton [38]. There are 78 GmDof genes in soybean (genome size 1100 Mb) [39], 34 SlDof genes in tomato (genome size 900 Mb) [40], 76 BraDof genes in Chinese cabbage (genome size 485 Mb) [41], 35 StDof genes in potato (genome size 844 Mb) [42], 42 MtDof genes in Medicago truncatula (genome size 500 Mb) [43], and 46 DcDof genes in carrot (genome size 421.5 Mb) [44], while the number of known GhDof genes in G. hirsutum L. has increased to 114. G. hirsutum L. (AD 1 , 2n = 4x = 52, genome size 2.5 Gb) is an allotetraploid plant species with a D-subgenome and A-subgenome.…”

Section: Ghdof Genes Are Amplified By Segmental Duplicationmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of the Dof Transcription Factor Gene Family in Gossypium hirsutum L.

Liu

et al. 2018

Agronomy

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Gossypium hirsutum L. is a worldwide economical crop; however, premature leaf senescence reduces its production and quality which is regulated by stresses, hormones, and genes. DNA binding with the one zinc finger (Dof) transcription factors (TFs) participate widely in plant development and responses to biotic and abiotic stresses, but there have been few reports of these TFs in cotton. Here, we perform a genome-wide study of G. Hirsutum L. Dof (GhDof) genes and analyze their phylogeny, duplication, and expression. In total, 114 GhDof genes have been identified and classified into nine subgroups (A, B1, B2.2, B2.1, C1, C2.1, C2.2, D1, and D2) based on phylogenetic analysis. An MCScanX analysis showed that the GhDof genes expanded due to segmental duplications. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that GhDofD9.6 was not only differentially expressed between CCRI10 (with premature senescence) and Liao4086 (without premature senescence) but also responded to salinity stress; GhDofA5.7, GhDofA7.4, GhDofA8.2, GhDof11.1, GhDofD7.2, and GhDofD11.3 signfificantly responded to cold (4 °C) stress. This work lays the foundation for further analysis of the function of GhDof genes in G. hirsutum, which will be helpful for improving the production and quality of cotton.

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“…21,22 In terms of family composition, the first genome-wide report for Dof genes was for Arabidopsis, which presented 36 Dof-encoding genes and one pseudogene. 1 Thereafter, many studies identifying Dof genes have been reported, with 30 members in rice, 24 41 in poplar, 25 26 in barley, 26 19 in moss, 27 12 in the fern Selaginella moellendorffiii , 27 10 in loblolly pine, 27 31 in wheat, 28 27 in Brachypodium distachyon , 29 10 in pine, 30 34 in tomato, 31 78 in soybean, 32 25 in sugarcane, 33 76 in Chinese cabbage, 34 46 in maize, 35 35 in potato 36 and 46 in carrot. 37 …”

Section: Introductionmentioning

confidence: 99%

Transcriptome analyses of the Dof-like gene family in grapevine reveal its involvement in berry, flower and seed development

et al. 2016

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The Dof (DNA-binding with one finger) protein family spans a group of plant transcription factors involved in the regulation of several functions, such as plant responses to stress, hormones and light, phytochrome signaling and seed germination. Here we describe the Dof-like gene family in grapevine (Vitis vinifera L.), which consists of 25 genes coding for Dof. An extensive in silico characterization of the VviDofL gene family was performed. Additionally, the expression of the entire gene family was assessed in 54 grapevine tissues and organs using an integrated approach with microarray (cv Corvina) and real-time PCR (cv Pinot Noir) analyses. The phylogenetic analysis comparing grapevine sequences with those of Arabidopsis, tomato, poplar and already described Dof genes in other species allowed us to identify several duplicated genes. The diversification of grapevine DofL genes during evolution likely resulted in a broader range of biological roles. Furthermore, distinct expression patterns were identified between samples analyzed, corroborating such hypothesis. Our expression results indicate that several VviDofL genes perform their functional roles mainly during flower, berry and seed development, highlighting their importance for grapevine growth and production. The identification of similar expression profiles between both approaches strongly suggests that these genes have important regulatory roles that are evolutionally conserved between grapevine cvs Corvina and Pinot Noir.

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Genome-wide analysis and expression profiling of DNA-binding with one zinc finger (Dof) transcription factor family in potato

Cited by 88 publications

References 70 publications

Genome-Wide Identification, Structure Characterization, and Expression Profiling of Dof Transcription Factor Gene Family in Wheat (Triticum aestivum L.)

Genome-Wide Identification, Structure Characterization, and Expression Profiling of Dof Transcription Factor Gene Family in Wheat (Triticum aestivum L.)

Genome-Wide Identification and Expression Analysis of the Dof Transcription Factor Gene Family in Gossypium hirsutum L.

Transcriptome analyses of the Dof-like gene family in grapevine reveal its involvement in berry, flower and seed development

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