Genome-wide identification and expression profile analysis of the

Abstract

Context Soybean cyst nematode is the most important pest of soybean (Glycine max (L.) Merr.) worldwide, causing serious yield losses. Lignin is a vital component of the cell wall that can provide resistance to cyst nematode. O-Methyltransferase (OMT) is a key enzyme involved in lignin metabolism in the phenylalanine pathway. Aims In this study, the soybean OMT gene family was systematically identified, and the expression response of GmOMT to abiotic and cyst nematode stresses was investigated. Methods In total, 67 OMT genes were obtained from the soybean genome through conserved structural domain alignment. GmOMT expression under abiotic stress of soybean was examined based on next-generation RNA sequencing (RNA-Seq). Comprehensive analysis of the genes was conducted, including gene structure, conserved structure, affinity, chromosomal localisation, functional prediction, Gene Ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis, promoter analysis, and expression pattern analysis. Key results The 67 GmOMT genes were identified and distributed among the 19 chromosomes. The GmOMT genes were classified into two categories: CCOMT subfamily and COMT subfamily. GmOMT genes from the same family shared similar gene structures and conserved structural domains, which have undergone strong purifying selection during evolution. The presence of multiple cis-responsive elements in the promoters of GmOMT genes suggested that members of the soybean OMT family may be involved in growth and developmental activities and resistance to stress in soybean. Conclusions GmOMT expression under abiotic stress showed that some of the genes may play a role in abiotic stress. Of them, GmCCOMT3 and GmCCOMT7 were closely associated with lignin synthesis based on both RNA-Seq and quantitative real-time PCR analysis. Implications These findings are valuable for elucidating the function of GmOMT in lignin metabolism and the relationship with SCN resistance.

Genome-wide identification of the OMT gene family in Cucumis melo L. and expression analysis under abiotic and biotic stress

“…To better understand the role of CmOMTs in the response to abiotic and biotic stresses, we analyzed the type, number, and distribution of cis -acting elements of 21 CmOMTs in the promoter. Light-responsive elements were present in all CmOMTs , suggesting that the expression of CmOMTs may be regulated by light, similar to previous studies on soybeans ( Zhao et al, 2022 ). In addition, the number of hormone-response cis -acting elements and stress-response cis -acting elements suggests that CmOMT family members may be extensively involved in growth, development, and environmental stress.…”

“…Analyses of plant evolutionary relationships have shown that genes with similar intron-exon structures and conserved motif arrangements often have similar functions ( Long, Souza & Gilbert, 1995 ). Most members of the same taxon of the 67 OMTs in soybean have similar gene structures, and the same results have been observed in pomegranate and rice ( Zhang et al, 2021a ; Zhang et al, 2021b ; Zhao et al, 2022 ; Liang et al, 2022 ). In our study, 21 CmOMTs were classified as class I, class II, and class III, which consisted of nine, six, and six members, respectively.…”

“…We performed GO enrichment analysis of the CmOMTs and identified a total of 13 overrepresented terms ( Q -value ≤ 0.05), and they were mainly related to methylation in the biological process category and methyltransferase activity in the molecular function category. The results were similar to the functions of OMTs in soybean and watermelon, thus demonstrating the similar functions of OMTs in different species ( Chang et al, 2021 ; Zhao et al, 2022 ). The specific binding of cis -acting elements with transcription factors in the promoter to regulate gene expression is not only the most important method of biological signal transduction but also an important means by which genes interact with other genes ( Cheng et al, 2019 ).…”

Genetic and evolutionary dissection of melatonin response signaling facilitates the regulation of plant growth and stress responses

“…COMT from soybean, tomato, apple, and grape were separated into clades D and E with distant related indicating the evolutionary constancy of COMTs between species and their functional differentiation. Differential expression patterns of COMT in different tissues of soybean and grape also suggested their functional diversity in response to abiotic stress 98,99 . Similarly, COMT in apple to a common ancestor has undergone duplication, generating two clusters with different functions 100 .…”

“…Differential expression patterns of COMT in different tissues of soybean and grape also suggested their functional diversity in response to abiotic stress. 98,99 Similarly, COMT in apple to a common ancestor has undergone duplication, generating two clusters with different functions. 100 In addition, tandem or segmental duplication of COMT in Arabidopsis implied their conservative functions in coping with abiotic stress.…”