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

Abstract

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.

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

“…To explore the phylogenetic relationship and evolutionary pattern of WOX genes in kiwifruit, the neighbor-joining (NJ) tree was constructed using the full-length protein sequences of the identified 17 AcWOXs , 10 AeWOXs , and previously published 15 AtWOXs and 10 OsWOXs ( WOX genes from Arabidopsis and rice). Consistent with previous reports in Arabidopsis , rice, and other species ( Nardmann & Werr, 2012 ; Lin et al, 2013 ; Tang et al, 2017 ; Shafique Khan et al, 2021 ), both AcWOXs and AeWOXs were classified into three clades (the ancient clade, the intermediate clade, and the modern/WUS clade) ( Fig. 2 ).…”

“…The WOX gene family is the core regulator for forming the shoot apical meristem and embryonic development, stem cell maintenance, and various other developmental processes in plants ( Ariel et al, 2007 ; Wu, Chory & Weigel, 2007 ; Deveaux et al, 2008 ; Shimizu et al, 2009 ; van der Graaff, Laux & Rensing, 2009 ; Palovaara et al, 2010 ). Genome-wide identification of the WOX gene family had been accomplished in several plants ( Deveaux et al, 2008 ; Liu et al, 2014b ; Cheng et al, 2014 ; Tang et al, 2017 ; Rahman et al, 2017 ; Li et al, 2018 , 2020 ; Ramkumar et al, 2018 ; Shafique Khan et al, 2021 ). However, genome-wide characterization of the WOX gene family had not been conducted in kiwifruits.…”

“…OsWOX11 , a member of the intermediate clade, was the most reported, responding to abiotic stresses such as drought and cold reviewed in ( Tvorogova et al, 2021 ). Minh-Thu reported that OsWOX13 , an ancient clade WOX gene, enhances drought tolerance and triggers early flowering in rice ( Shafique Khan et al, 2021 ). In poplar, over-expression of PtoWOX13 led to an increased adventitious root (AR) number, deceased AR length or increased AR roughtnees ( Liu et al, 2014b ).…”

“…The WOX subfamily specifically binds to the target region by the homeodomain to activate or depress the expression of the target gene in plants ( Mukherjee, Brocchieri & Bürglin, 2009 ; Jha, Ochatt & Kumar, 2020 ; Tvorogova et al, 2021 ). Genome-wide identification of the WOX subfamily has been performed in several plants, including Arabidopsis, rice, maize, walnut, physic nut, grapes, peach, pear, apricot, coffee, and poplar ( Li et al, 2020 ; Shafique Khan et al, 2021 ).…”

Genome-Wide Identification and Comparative Analysis of WOX Genes in Four Euphorbiaceae Species and Their Expression Patterns in Jatropha curcas

“…Numerous studies have shown that WOX genes play different roles in the development of rice roots, stems, and leaves ( Li et al, 2012 ; Wang et al, 2017 ; Zhou et al, 2017 ). The WOX6 gene plays a significant role in the regulation of seed development, especially for the growth and development of seeds under water-deficient conditions ( Shafique Khan et al, 2021 ). In particular, WOX6 gene in rice regulates the asymmetric expression of auxin, resulting in the appearance of rice tiller horns ( Zhang et al, 2018 ).…”