In silico genome wide identification and expression analysis of the WUSCHEL-related homeobox gene family in Medicago sativa

Abstract

Alfalfa (Medicago sativa) is an important food and feed crop which rich in mineral sources. The WUSCHEL-related homeobox (WOX) gene family plays important roles in plant development and identification of putative gene families, their structure, and potential functions is a primary step for not only understanding the genetic mechanisms behind various biological process but also for genetic improvement. A variety of computational tools, including MAFFT, HMMER, hidden Markov models, Pfam, SMART, MEGA, ProtTest, BLASTn, and BRAD, among others, were used. We identified 34 MsWOX genes based on a systematic analysis of the alfalfa plant genome spread in eight chromosomes. This is an expansion of the gene family which we attribute to observed chromosomal duplications. Sequence alignment analysis revealed 61 conserved proteins containing a homeodomain. Phylogenetic study sung reveal five evolutionary clades with 15 motif distributions. Gene structure analysis reveals various exon, intron, and untranslated structures which are consistent in genes from similar clades. Functional analysis prediction of promoter regions reveals various transcription binding sites containing key growth, development, and stress-responsive transcription factor families such as MYB, ERF, AP2, and NAC which are spread across the genes. Most of the genes are predicted to be in the nucleus. Also, there are duplication events in some genes which explain the expansion of the family. The present research provides a clue on the potential roles of MsWOX family genes that will be useful for further understanding their functional roles in alfalfa plants.

Comprehensive Analysis of WUSCEL-Related Homeobox Gene Family in Ramie (Boehmeria nivea) Indicates Its Potential Role in Adventitious Root Development

“…In contrast, genes belonging to different subgroups and clades like BnWOX4/10 (chr13), BnWUS/13B (chr12), and BnWOX9A/9B/14 (chr2) were also located on the same chromosomes. These, however, followed similar patterns with the WOX genes reported in other species like Medicago sativa Triticum aestivum and Hordeum vulgare [17,24].…”

“…In previous studies, a variable number of WOX genes were reported in different plant species, such as 15 in A. thaliana, 13 in rice, 43 in bread wheat, 34 in Medicago sativa, 10 in Jatropha curcas, and 20 in Hevea brasiliensis [22][23][24][25]. Specific expression of the genes in various organs and cells in plants pointed to their crucial roles in organogenesis [15,[26][27][28].…”

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

“…This gene family is implicated in developmental processes including cell division, development, stem cell repair, organ formation, seed formation, tissues, and organ regeneration [ 83 – 86 ]. Recent studies have indicated that WOX genes play a role in the regulation of abiotic stress resistance including drought [ 87 ]. In Glycine max, expression of the WOX gene family has been shown to be induced by drought, heat, cold, and salt stress in [ 84 ], and in Arabidopsis, WOX9 was reported to be expressed in the root tip meristem tissue and promote root cell multiplication which is a mechanism of drought tolerance [ 88 , 89 ].…”

Characterization and expression profiles of WUSCHEL-related homeobox (WOX) gene family in cultivated alfalfa (Medicago sativa L.)

“…This classification is consistent with other reported plants. Even though a previous study identified 34 MsWOXs genes in alfalfa using homeodomain sequences as a query and named them according to their location on the chromosomes [ 54 ], here we identified 14 MsWOXs using comprehensive bioinformatic analysis and named them based on homology to Arabidopsis and Medicago WOX genes (Fig. 1 ), which is helpful to explore novel and established biological functions.…”