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

Abstract

Background Xyloglucan endotransglucosylase/hydrolase (XTH) family plays an important role in cell wall reconstruction and stress resistance in plants. However, the detailed characteristics of XTH family genes and their expression pattern under salt stress have not been reported in poplar. Results In this study, a total of 43 PtrXTH genes were identified from Populus simonii × Populus nigra, and most of them contain two conserved structures (Glyco_hydro_16 and XET_C domain). The promoters of the PtrXTH genes contain mutiple cis-acting elements related to growth and development and stress responses. Collinearity analysis revealed that the XTH genes from poplar has an evolutionary relationship with other six species, including Eucalyptus robusta, Solanum lycopersicum, Glycine max, Arabidopsis, Zea mays and Oryza sativa. Based on RNA-Seq analysis, the PtrXTH genes have different expression patterns in the roots, stems and leaves, and many of them are highly expressed in the roots. In addition, there are11 differentially expressed PtrXTH genes in the roots, 9 in the stems, and 7 in the leaves under salt stress. In addition, the accuracy of RNA-Seq results was verified by RT-qPCR. Conclusion All the results indicated that XTH family genes may play an important role in tissue specificity and salt stress response. This study will lay a theoretical foundation for further study on molecular function of XTH genes in poplar.

The XTH Gene Family in Schima superba: Genome-Wide Identification, Expression Profiles, and Functional Interaction Network Analysis

“…For example, the genes from the ancestral group and Group III were localized in the extracellular space and cell wall, respectively, whereas genes in Group I/II were mainly in the cell wall, cytoplasm, and extracellular space. These findings were similar to those reported in pineapple and poplar ( Li et al, 2019 ; Cheng et al, 2021 ). Moreover, all the genes in Group III contained three introns and four exons, and the types and numbers of conserved motifs within the group were similar.…”

“…Segmental and tandem duplication events did not lead to XTH gene family expansion but might increase functional divergence, which was an essential factor in adapting to environmental changes ( Conant and Wolfe, 2008 ). Of course, segmental and tandem duplication events also are found among poplar XTH family genes ( Cheng et al, 2021 ). Furthermore, the phylogenetic analysis of XTH encoded proteins among the five plants revealed that S. superba and C. sinensis , all belonging to Theaceae, had many more genetic relationships, while Populus and E. grandis had much closer relationships ( Figure 1 ).…”

“…Multigene families of XTHs have been identified in a variety of plant species, including Arabidopsis thaliana (33), Oryza sativa (29), Triticum aestivum (5), Sorghum bicolor (35), Nicotiana tabacum (56), Glycine max (61), Solanum lycopersicum (25), Actinidia deliciosa (14), Malus sieversii (11), Gossypium hirsutum (23), Brassica rapa (53), Brassica oleracea (38), B. juncea (74), and Populus spp. (41; Yokoyama and Nishitani, 2001 ; Yokoyama et al, 2004 ; Geisler-Lee et al, 2006 ; Saladié et al, 2006 ; Liu et al, 2007 ; Atkinson et al, 2009 ; Lee et al, 2010 ; Rai et al, 2016 ; Nawaz et al, 2017 ; Song et al, 2018 ; Wang et al, 2018 ; Li et al, 2020 ; Wu et al, 2020 ; Cheng et al, 2021 ). Based on their phylogenetic relationships, the XTH genes are normally classified into three major groups, Group I, Group II, and Group III, and one minor ancestral group exists differently in species ( Yokoyama and Nishitani, 2001 ; Baumann et al, 2007 ; Michailidis et al, 2009 ; Wang et al, 2018 ; Li et al, 2020 ; Wu et al, 2020 ).…”

A Genome-Wide Association Study of Senegalese Sorghum Seedlings Responding to Pathotype 5 of Sporisorium reilianum

“…Indeed, these genes play an important role in cell wall reconstruction and stress resistance, particularly abiotic stresses. Thirty-five XTH genes have been reported in sorghum [ 17 ]. To the best of our knowledge, no biotic stress related function has been reported, suggesting that this SNP association could be due to switching to the flooded environment to which the seedlings were exposed during the experiment.…”

Identification and expression analysis of xyloglucan endotransglucosylase/hydrolase (XTH) family in grapevine (Vitis vinifera L.)

“…Thus far, the XTH family has been identified and analyzed in species such as Arabidopsis thaliana (33), Hordeum vulgare (24), Glycine max (61), and Nicotiana tabacum (54). ( Nomchit et al, 2010 ; Li et al, 2018 ; Meng et al, 2018 ; Cheng et al, 2021 ; Strohmeier et al, 2004 ; Tiika et al, 2021 ). The XTH family was initially classified into three groups, named groups I, II, and III, in Arabidopsis ( Campbell & Braam, 1999 ).…”