Genome-Wide Analysis of WUSCHEL-Related Homeobox Gene Family in Sacred Lotus (Nelumbo nucifera)

Abstract

WUSCHEL-related homeobox (WOX) is a plant-specific transcription factor (TF), which plays an essential role in the regulation of plant growth, development, and abiotic stress responses. However, little information is available on the specific roles of WOX TFs in sacred lotus (Nelumbo nucifera), which is a perennial aquatic plant with important edible, ornamental, and medicinal values. We identified 15 WOX TFs distributing on six chromosomes in the genome of N. nucifera. A total of 72 WOX genes from five species were divided into three clades and nine subclades based on the phylogenetic tree. NnWOXs in the same subclades had similar gene structures and conserved motifs. Cis-acting element analysis of the promoter regions of NnWOXs found many elements enriched in hormone induction, stress responses, and light responses, indicating their roles in growth and development. The Ka/Ks analysis showed that the WOX gene family had been intensely purified and selected in N. nucifera. The expression pattern analysis suggested that NnWOXs were involved in organ development and differentiation of N. nucifera. Furthermore, the protein–protein interaction analysis showed that NnWOXs might participate in the growth, development, and metabolic regulation of N. nucifera. Taken together, these findings laid a foundation for further analysis of NnWOX functions.

Genome-wide prediction and functional analysis of WOX genes in blueberry

“…It was found that members of maize, barley and Arabidopsis as herbaceous plants appeared to cluster with each other, such as AtWOX11 and AtWOX12 in Arabidopsis at the Intermediate Clade, HvWOX7 and HvWOX8 in barley, ZmWOX21 and ZmWOX23 in maize. Similarly, clustering phenomena have also been observed in Nelumbo nucifera, such as NnWOX6 and NnWOX9 , NnWOX1 and NnWOX4 [ 38 ]. Previous studies have found that the relationship between GmWOXs and PvWOXs is closer, possibly due to the fact that lotus root and soybean both belong to the legume family [ 5 ].…”

“…To investigate the structural diversity of VdWOX genes, the distribution of exons and introns was analyzed. Gene structure analysis revealed that the number of introns among members of the VdWOX gene family ranges from 1 to 3, a phenomenon also observed in lotus and soybean [ 5 , 38 ]. Specifically, SVdWOX9 , VdWOX10 , VdWOX11 and VdWOX12 contain two exons, VdWOX2 and VdWOX8 contain four exons, while the remaining six members contain three exons each (Fig.…”

“…The WOX gene family plays an important role in regulating plant growth and development, stress resistance, and plant hormone signal transduction [ 6 , 38 ]. The promoter of VdWOX contains cis acting elements related to plant growth and development, hormones, and stress resistance.…”

Genome-Wide Identification and Co-Expression Networks of WOX Gene Family in Nelumbo nucifera

“…The number of WOX members varies in these plants. Although genome-wide identification of the WOX members in lotus were preliminarily studied [ 39 ], the regulatory interactions of NnWOXs genes need further investigation. With increasing genomics research on lotus [ 30 , 48 ], the Nelumbo Genome Database provided a great platform to investigate the whole-genome analysis of transcription factors [ 35 ].…”

“…Several transcription factor families were identified in lotus, such as MADS-box [ 36 ], WRKY [ 37 ], and YABBY [ 38 ]. Although a previous study conducted a preliminary analysis of the WOX gene family in lotus [ 39 ], the interactions of WOX genes is still largely unknown. Therefore, we describe WOX genes systematically in N. nucifera and construct the co-expressed networks to find vital interactions regarding NnWOX genes during plant growth and development.…”