The genome-wide characterization of WOX gene family in Phaseolus vulgaris L. during salt stress

Akbulut, Simay Ezgi; Okay, Aybüke; Aksoy, Taner; Aras, Sümer; Büyük, İlker

doi:10.1007/s12298-022-01208-1

Cited by 10 publications

(7 citation statements)

References 55 publications

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“…1 B). They were dispersed on different chromosomes, consistent with previous studies [ 34 , 50 , 51 ]. The number of introns is similar in both the Ancient and Intermediate clades of WOX family genes, as previously reported in banana and C. sinensis plants [ 47 ].…”

Section: Discussionsupporting

confidence: 92%

Identification of WUSCHEL-related homeobox gene and truncated small peptides in transformation efficiency improvement in Eucalyptus

Zhang,

Liu,

Ren

et al. 2023

BMC Plant Biol

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Background The WUSCHEL-related Homeobox (WOX) genes, which encode plant-specific homeobox (HB) transcription factors, play crucial roles in regulating plant growth and development. However, the functions of WOX genes are little known in Eucalyptus, one of the fastest-growing tree resources with considerable widespread cultivation worldwide. Results A total of nine WOX genes named EgWOX1-EgWOX9 were retrieved and designated from Eucalyptus grandis. From the three divided clades marked as Modern/WUS, Intermediate and Ancient, the largest group Modern/WUS (6 EgWOXs) contains a specific domain with 8 amino acids: TLQLFPLR. The collinearity, cis-regulatory elements, protein-protein interaction network and gene expression analysis reveal that the WUS proteins in E. grandis involve in regulating meristems development and regeneration. Furthermore, by externally adding of truncated peptides isolated from WUS specific domain, the transformation efficiency in E. urophylla × E. grandis DH32-29 was significant enhanced. The transcriptomics data further reveals that the use of small peptides activates metabolism pathways such as starch and sucrose metabolism, phenylpropanoid biosynthesis and flavonoid biosynthesis. Conclusions Peptides isolated from WUS protein can be utilized to enhance the transformation efficiency in Eucalyptus, thereby contributing to the high-efficiency breeding of Eucalyptus.

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Section: Discussionsupporting

confidence: 92%

Identification of WUSCHEL-related homeobox gene and truncated small peptides in transformation efficiency improvement in Eucalyptus

Zhang,

Liu,

Ren

et al. 2023

BMC Plant Biol

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“…The WOX9 gene may have a role in plants including the regulation of developmental processes. The WOX family is the homeobox transcription factor superfamily playing many functions in embryonic growth to organ formation in plants [83]. This gene family is implicated in developmental processes including cell division, development, stem cell repair, organ formation, seed formation, tissues, and organ regeneration [83][84][85][86].…”

Section: Discussionmentioning

confidence: 99%

“…The WOX family is the homeobox transcription factor superfamily playing many functions in embryonic growth to organ formation in plants [83]. This gene family is implicated in developmental processes including cell division, development, stem cell repair, organ formation, seed formation, tissues, and organ regeneration [83][84][85][86]. Recent studies have indicated that WOX genes play a role in the regulation of abiotic stress resistance including drought [87].…”

Section: Discussionmentioning

confidence: 99%

Comprehensive in silico analysis of the underutilized crop tef (Eragrostis tef (Zucc.) Trotter) genome reveals drought tolerance signatures

Bekele-Alemu,

Ligaba-Osena

2023

BMC Plant Biol

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Background Tef (Eragrostis tef) is a C4 plant known for its tiny, nutritious, and gluten-free grains. It contains higher levels of protein, vitamins, and essential minerals like calcium (Ca), iron (Fe), copper (Cu), and zinc (Zn) than common cereals. Tef is cultivated in diverse ecological zones under diverse climatic conditions. Studies have shown that tef has great diversity in withstanding environmental challenges such as drought. Drought is a major abiotic stress severely affecting crop productivity and becoming a bottleneck to global food security. Here, we used in silico-based functional genomic analysis to identify drought-responsive genes in tef and validated their expression using quantitative RT-PCR. Results We identified about 729 drought-responsive genes so far reported in six crop plants, including rice, wheat, maize, barley, sorghum, pearl millet, and the model plant Arabidopsis, and reported 20 genes having high-level of GO terms related to drought, and significantly enriched in several biological and molecular function categories. These genes were found to play diverse roles, including water and fluid transport, resistance to high salt, cold, and drought stress, abscisic acid (ABA) signaling, de novo DNA methylation, and transcriptional regulation in tef and other crops. Our analysis revealed substantial differences in the conserved domains of some tef genes from well-studied rice orthologs. We further analyzed the expression of sixteen tef orthologs using quantitative RT-PCR in response to PEG-induced osmotic stress. Conclusions The findings showed differential regulation of some drought-responsive genes in shoots, roots, or both tissues. Hence, the genes identified in this study may be promising candidates for trait improvement in crops via transgenic or gene-editing technologies.

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“…We found that, although the AktWOX genes have wide differences at the DNA sequence level, mainly reflected in the number of introns and sequence length, the physical and chemical properties of the proteins they encode are extremely similar, including similar protein lengths and molecular weights and the instability and hydrophilicity of the protein structure (Table 1). Moreover, these characteristics of WOX genes in A. trifoliata are very similar to those of monocots, including wheat [15] and four Euphorbiaceae plants [39], as well as core dicots, including A. thaliana [16] and Phaseolus vulgaris [40]. This indicates that WOX genes are highly conserved during evolution, and the gain and loss of introns/exons are the driving forces for the evolution of this gene family.…”

Section: The Aktwox Gene Structure Is Extremely Conserved During Evol...mentioning

confidence: 66%

Global Analysis of the WOX Transcription Factor Family in Akebia trifoliata

Chen,

Yang,

Zhang

et al. 2023

CIMB

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Akebia trifoliata is an economically important, self-incompatible fruit tree in the Lardizabalaceae family. Asexual propagation is the main strategy used to maintain excellent agronomic traits. However, the generation of adventitious roots during asexual propagation is very difficult. To study the important role of the WUSCHEL-related homeobox (WOX) transcription factor in adventitious root growth and development, we characterized this transcription factor family in the whole genome of A. trifoliata. A total of 10 AktWOXs were identified, with the following characteristics: length (657~11,328 bp), exon number (2~5), isoelectric point (5.65~9.03), amino acid number (176~361 AA) and molecular weight (20.500~40.173 kDa), and their corresponding expression sequence could also be detectable in the public transcriptomic data for A. trifoliata fruit. A total of 10 AktWOXs were classified into modern (6), intermediate (2) and ancient clades (2) and all AktWOXs had undergone strong purifying selection during evolution. The expression profile of AktWOXs during A. trifoliata adventitious root formation indicated that AktWOXs play an important role in the regulation of adventitious root development. Overall, this is the first study to identify and characterize the WOX family in A. trifoliata and will be helpful for further research on A. trifoliata adventitious root formation.

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The genome-wide characterization of WOX gene family in Phaseolus vulgaris L. during salt stress

Cited by 10 publications

References 55 publications

Identification of WUSCHEL-related homeobox gene and truncated small peptides in transformation efficiency improvement in Eucalyptus

Identification of WUSCHEL-related homeobox gene and truncated small peptides in transformation efficiency improvement in Eucalyptus

Comprehensive in silico analysis of the underutilized crop tef (Eragrostis tef (Zucc.) Trotter) genome reveals drought tolerance signatures

Global Analysis of the WOX Transcription Factor Family in Akebia trifoliata

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