Genome-wide identification, and phylogenetic and expression profiling analyses, of XTH gene families in Brassica rapa L. and Brassica oleracea L.

Abstract

Background Xyloglucan endotransglucosylase/hydrolase genes (XTHs) are a multigene family and play key roles in regulating cell wall extensibility in plant growth and development. Brassica rapa and Brassica oleracea contain XTHs, but detailed identification and characterization of the XTH family in these species, and analysis of their tissue expression profiles, have not previously been carried out. Results In this study, 53 and 38 XTH genes were identified in B. rapa and B. oleracea respectively, which contained some novel members not observed in previous studies. All XTHs of B. rapa, B. oleracea and Arabidopsis thaliana could be classified into three groups, Group I/II, III and the Early diverging group, based on phylogenetic relationships. Gene structures and motif patterns were similar within each group. All XTHs in this study contained two characteristic conserved domains (Glyco_hydro and XET_C). XTHs are located mainly in the cell wall but some are also located in the cytoplasm. Analyses of the mechanisms of gene family expansion revealed that whole-genome triplication (WGT) events and tandem duplication (TD) may have been the major mechanisms accounting for the expansion of the XTH gene family. Interestingly, TD genes all belonged to Group I/II, suggesting that TD was the main reason for the largest number of genes being in these groups. B. oleracea had lost more of the XTH genes, the conserved domain XET_C and the conserved active-site motif EXDXE compared with B. rapa, consistent with asymmetrical evolution between the two Brassica genomes. A majority of XTH genes exhibited different tissue-specific expression patterns based on RNA-seq data analyses. Moreover, there was differential expression of duplicated XTH genes in the two species, indicating that their functional differentiation occurred after B. rapa and B. oleracea diverged from a common ancestor. Conclusions We carried out the first systematic analysis of XTH gene families in B. rapa and B. oleracea. The results of this investigation can be used for reference in further studies on the functions of XTH genes and the evolution of this multigene family.

Genome-wide Identification and Expression Analysis of the Eyloglucan Endotransglucosylase/hydrolase Gene Family in Poplar

“…XET_C contained the motif 5 and motif 10. This results were similar to the previous study (Wu et al 2020).…”

“…As shown in the Fig. 1, the evolutionary tree could be divided into 4 groups (Group / , Group A, Group B and Early diverging group), which was similar to Brassica rapa (Wu et al 2020). We found that the Group / contained the most members with 33 members.…”

Genome-wide identification and expression analysis of the xyloglucan endotransglucosylase/hydrolase gene family in poplar

“…As shown in the Fig. 1 , the XTH family could be divided into 4 groups (GroupI/II, Group IIIA, Group IIIB and Early diverging group), which was similar to that in Brassica rapa [ 9 ]. And the GroupI/IIcontained the most members with 33 members.…”

“…Moreover, a small part of outlier group (early diverting) was found in detailed clade [ 7 , 8 ]. In summary, XTH family is divided into I / II, IIIA, IIIB and the early diverting groups [ 9 ].…”

Identification and response analysis of xyloglucan endotransglycosylase/hydrolases (XTH) family to fluoride and aluminum treatment in Camellia sinensis

“…7 ). Studies showed that the expression of AtXTH5 was also significantly upregulated under Al stress [ 31 ]. The expression levels of CsXTH 5 and CsXTH13 decreased when Al 3+ concentration increased to 4 mM (Fig.…”