Genome-Wide Identification of WOX Gene Family and Expression Analysis during Rejuvenational Rhizogenesis in Walnut (Juglans regia L.)

Evolutionary analysis of genes from WOX family and their expression profile in grape (Vitis vinifera) under different stresses

The WUSCHEL-related homeobox (WOX) transcription factor family plays critical roles in plant growth, development, and stress adaptation, but the biological functions in response to various stress of the WOX gene family have not been extensively researched in grapevine (Vitis vinifera ). In this study, 12 grapevine WOXs were identified from the grapevine genome. Quantitative PCR and microarray expression profiling found that the expression of WOXs had an obvious tissue-specific pattern. Conjoint analysis between various tissues and treated materials indicated VvWUS1 expression is associated with expression of genes from grapevine rupestris stem pitting-associated virus; and VvWOX3 with grapevine fanleaf virus. The gene expression patterns of the WOXs in grape were different under salt stress, with VvWOX8/9 , VvWUS1 , and VvWOX3 responding more strongly to salt stress than control by 18.20-, 9.50-, and 9.19-fold. This study further improves understanding of the evolution and function of the WOX gene family, and offers a theoretical framework and reference for breeding grapevine to better tolerate adversity and permit cultivation of seedlings free of viruses.

Genome-wide analysis of the WOX gene family and the role of EjWUSa in regulating flowering in loquat (Eriobotrya japonica)

The WUSCHEL (WUS)-related homeobox (WOX) gene family plays a crucial role in stem cell maintenance, apical meristem formation, embryonic development, and various other developmental processes. However, the identification and function of WOX genes have not been reported in perennial loquat. In this study, 18 EjWOX genes were identified in the loquat genome. Chromosomal localization analysis showed that 18 EjWOX genes were located on 12 of 17 chromosomes. Gene structure analysis showed that all EjWOX genes contain introns, of which 11 EjWOX genes contain untranslated regions. There are 8 pairs of segmental duplication genes and 0 pairs of tandem duplication genes in the loquat WOX family, suggesting that segmental duplications might be the main reason for the expansion of the loquat WOX family. A WOX transcription factor gene named EjWUSa was isolated from loquat. The EjWUSa protein was localized in the nucleus. Protein interactions between EjWUSa with EjWUSa and EjSTM were verified. Compared with wild-type Arabidopsis thaliana, the 35S::EjWUSa transgenic Arabidopsis showed early flowering. Our study provides an important basis for further research on the function of EjWOX genes and facilitates the molecular breeding of loquat early-flowering varieties.

Genome-wide identification and expression profiling of WUSCHEL-related homeobox (WOX) genes confer their roles in somatic embryogenesis, growth and abiotic stresses in banana

Plant-specific WUSCHEL-related homeobox (WOX) transcription factors are known to be involved in plant developmental processes, especially in embryogenesis. In this study, a total of thirteen WOX members were identified in the banana (Musa acuminata) genome (MaWOX) and characterized for in-silico analysis. Phylogenetic analysis revealed that these genes were divided into three clades (ancient, intermediate and modern) which reflected the evolutionary history of WOX families. Furthermore, modern clade members have shown higher variations in gene structural features and carried unique conserved motifs (motif 3 and motif 4) when compared to the members of other clades. The differential expression of all 13 MaWOX was observed in early (embryogenic cell suspension (ECS), multiplying ECS, germinating embryos, young leaflet and node of germinated plantlets) and late (unripe fruit peel and pulp, ripe fruit peel and pulp) developmental stages of banana cultivar Grand Naine. The maximum expression of MaWOX6 (18 fold) and MaWOX13 (120 fold) was found during somatic embryogenesis and in unripe fruit pulp, respectively. Moreover, numerous cis-elements responsive to drought, cold, ethylene, methyl jasmonate (MeJA), abscisic acid (ABA) and gibberellic acid (GA) were observed in all MaWOX promoter regions. The subsequent expression analysis under various abiotic stresses (cold, drought and salt) revealed maximum expression of the MaWOX3 (830 fold), MaWOX8a (30 fold) and MaWOX11b (105 fold) in salt stress. It gives evidence about their possible role in salt stress tolerance in banana. Hence, the present study provides precise information on the MaWOX gene family and their expression in various tissues and stressful environmental conditions that may help to develop climate-resilient banana plants.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03387-w.

Characterization of walnut JrWOX11 and its overexpression provide insights into adventitious root formation and development and abiotic stress tolerance

The well-developed root system enables plant survival under various environmental stresses. WUSCHEL-RELATED HOMEOBOX GENE 11 (WOX11) plays a critical role in adventitious root formation and development in rice, Arabidopsis, and easy-to-root tree poplar. However, in difficult-to-root trees, the knowledge of WOX11 during adventitious root formation and development remains scarce. In this study, the JrWOX11 gene was isolated from a difficult-to-root tree walnut and heterologously expressed in the "84K" poplar. The results showed that JrWOX11 contained a similar structure and sequence to the homologous genes in rice, Arabidopsis, and poplar, but had different numbers and types of motifs and cis-elements. JrWOX11 lacked the motif GGAIQY compared to that in easy-to-root trees. In addition, JrWOX11 expression was induced by ABA, PEG, and NaCl treatments. Overexpression of JrWOX11 in poplar promoted root initiation and significantly increased adventitious root (ARs) number, lateral roots (LRs) number, and root hair (RH) length. Furthermore, the aboveground biomass was notably increased under NaCl and PEG treatments in transgenic plants. When NaCl and PEG were removed, the survival rate, aerial shoot development, and de novo root organogenesis were also markedly enhanced in transgenic shoot cuttings. The study provides valuable information on the differences between JrWOX11 and the homologous genes in rice, Arabidopsis, and poplar, and supports the critical role of JrWOX11 in the formation of AR and tolerance to salt and osmotic stresses.

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

The WUSCHEL-Related Homeobox (WOX) family is a type of homeobox transcription factor superfamily and its members perform many functions ranging from plant embryonic growth to organ formation in plants. Although the WOX proteins have been identified and characterized in many plant species, genome-wide identification and characterization of WOX proteins in the Phaseolus vulgaris genome has been performed for the first time in this study. Accordingly, 18 WOX proteins were identified using bioinformatics tools and biochemical/physicochemical properties of these proteins were investigated. Phvul-WOX genes were found to be categorized into three major phylogenetic groups according to the phylogenetic analysis and a total of five segmental duplication events were detected after duplication analysis. Moreover, the Phvul-WOX genes were found to be expressed in different plant tissues at different levels and some stress-related miRNAs have been found to target the Phvul-WOX genes based on miRNA analysis. Additionaly, MDA content, total protein level and catalase enzyme activity analyses were conducted in two P. vulgaris cultivars namely Yakutiye cv. and Zulbiye cv. subjected to 150 mM salt stress. Next, these cultivars were used for screening the expression levels of Phvul-WOX-1, Phvul-WOX-9, Phvul-WOX-11, Phvul-WOX-15 and Phvul-WOX-16 genes in response to salt stress. The insights gained from this study may be of assistance to the researchers who work in this area.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01208-1.

In silico identification, characterization expression profile of WUSCHEL-Related Homeobox (WOX) gene family in two species of kiwifruit

The WUSCHEL (WUS)-related homeobox (WOX) gene family is a class of plant-specific transcriptional factors and plays a crucial role in forming the shoot apical meristem and embryonic development, stem cell maintenance, and various other developmental processes. However, systematic identification and characterization of the kiwifruit WOX gene family have not been studied. This study identified 17 and 10 WOX genes in A. chinensis (Ac) and A. eriantha (Ae) genomes, respectively. Phylogenetic analysis classified kiwifruit WOX genes from two species into three clades. Analysis of phylogenetics, synteny patterns, and selection pressure inferred that WOX gene families in Ac and Ae had undergone different evolutionary patterns after whole-genome duplication (WGD) events, causing differences in WOX gene number and distribution. Ten conserved motifs were identified in the kiwifruit WOX genes, and motif architectures of WOXs belonging to different clades highly diverged. The cis-element analysis and expression profiles investigation indicated the functional differentiation of WOX genes and identified the potential WOXs in response to stresses. Our results provided insight into general characters, evolutionary patterns, and functional diversity of kiwifruit WOXs.

Rejuvenation remodels transcriptional network to improve rhizogenesis in mature Juglans tree

Adventitious rooting of walnut species (Juglans L.) is known to be rather difficult, especially for mature trees. The adventitious root formation (ARF) capacities of mature trees can be significantly improved by rejuvenation. However, the underlying gene regulatory networks (GRNs) of rejuvenation remain largely unknown. To characterize such regulatory networks, we carried out the transcriptomic study using RNA samples of the cambia and peripheral tissues on the bottom of rejuvenated and mature walnut (Juglans hindsii × J. regia) cuttings during the ARF. The RNA sequencing data suggested that zeatin biosynthesis, energy metabolism and substance metabolism were activated by rejuvenation, whereas photosynthesis, fatty acid biosynthesis and the synthesis pathways for secondary metabolites were inhibited. The inter- and intra-module GRNs were constructed using differentially expressed genes. We identified 35 hub genes involved in five modules associated with ARF. Among these hub genes, particularly, beta-glucosidase-like (BGLs) family members involved in auxin metabolism were overexpressed at the early stage of the ARF. Furthermore, BGL12 from the cuttings of Juglans was overexpressed in Populus alba × P. glandulosa. Accelerated ARF and increased number of ARs were observed in the transgenic poplars. These results provide a high-resolution atlas of gene activity during ARF and help to uncover the regulatory modules associated with the ARF promoted by rejuvenation.

Genome-Wide Identification and Expression Profiling of the WOX Gene Family in Citrus sinensis and Functional Analysis of a CsWUS Member

WUSCHEL-related homeobox (WOX) transcription factors (TFs) are well known for their role in plant development but are rarely studied in citrus. In this study, we identified 11 putative genes from the sweet orange genome and divided the citrus WOX genes into three clades (modern/WUSCHEL(WUS), intermediate, and ancient). Subsequently, we performed syntenic relationship, intron-exon organization, motif composition, and cis-element analysis. Co-expression analysis based on RNA-seq and tissue-specific expression patterns revealed that CsWOX gene expression has multiple intrinsic functions. CsWUS homolog of AtWUS functions as a transcriptional activator and binds to specific DNA. Overexpression of CsWUS in tobacco revealed dramatic phenotypic changes, including malformed leaves and reduced gynoecia with no seed development. Silencing of CsWUS in lemon using the virus-induced gene silencing (VIGS) system implied the involvement of CsWUS in cells of the plant stem. In addition, CsWUS was found to interact with CsCYCD3, an ortholog in Arabidopsis (AtCYCD3,1). Yeast one-hybrid screening and dual luciferase activity revealed that two TFs (CsRAP2.12 and CsHB22) bind to the promoter of CsWUS and regulate its expression. Altogether, these results extend our knowledge of the WOX gene family along with CsWUS function and provide valuable findings for future study on development regulation and comprehensive data of WOX members in citrus.

Genome-wide characterization and expression and co-expression analysis suggested diverse functions of WOX genes in bread wheat

WUSCHEL-related homeobox (WOX) genes belong to the homeobox superfamily, are plant-specific and play vital functions in the growth and development. Herein, we identified a total of 43 TaWOX genes in the allohexaploid (AABBDD) genome of Triticum aestivum L. These genes were distributed on the various chromosomes of each subgenome (A, B and D). The phylogenetic analysis showed the clustering of TaWOXs into three clades: ancient, intermediate and modern or WUS. The gene and protein structures including exon/intron organization, intron phases, and domain and motif distribution were found to be conserved in each phylogenetic clade. The subcellular localization was predicted as nuclear. The Ka/Ks analyses suggested the purifying selection of paralogous genes. The differential expression profiling of various TaWOXs in numerous tissue developmental stages and different layers of grains suggested their role in growth and development. Moreover, a few genes exhibited modulated expression during abiotic and biotic stress conditions, which revealed their roles in stress response. The occurrence of various cis-acting regulatory elements further confirmed their role in plant development and stress tolerance. The co-expression analyses suggested the interactions of these genes with other genes, involved in various processes including plant development, signalling and stress responses. The present study reported several characteristic features of TaWOXs genes that can be useful for further characterization in future studies.