Genome-wide identification, evolution and function analysis of UGTs superfamily in cotton

Abstract

Glycosyltransferases mainly catalyse the glycosylation reaction in living organisms and widely exists in plants. UGTs have been identified from G. raimondii, G. arboreum and G. hirsutum. However, Genome-wide systematic analysis of UGTs superfamily have not been studied in G. barbadense. 752 UGTs were identified from four cotton species and grouped into 18 clades, of which R was newly discovered clades. Most UGTs were clustered at both ends of the chromosome and showed a heterogeneous distribution. UGT proteins were widely distributed in cells, with the highest distribution in chloroplasts. UGTs of the same clade shared similar intron/exon structural features. During evolution, the gene family has undergone strong selection for purification. UGTs were significantly enriched in “transcriptional activity (GO:0016758)” and “metabolic processes (GO:0008152)”. Genes from the same clade differed in function under various abiotic stresses. The analysis of cis-acting element and qRT–PCR may indicate that GHUGTs play important roles in plant growth, development and abiotic stress. We further found that GHUGT74-2 plays an important role under submergence. The study broadens the understanding of UGTs in terms of gene characteristics, evolutionary processes, and gene function in cotton and provides a new way to systematically and globally understand the structure–function relationship of multigene families in the evolutionary process.

Systematic identification of TPS genes in Gossypium and their characteristics in response to flooding stress

“…The number of TPSs from allotetraploid cotton was less than twice that of diploid cotton, which might be due to gene deletions during the evolutionary process of forming allotetraploid cotton. Gene loss is also present in the evolution of the GRX, AHL and UGT gene families ( Malik et al., 2020 ; Zhao et al., 2020 ; Sun et al., 2022 ).…”

GhLCYε-3 characterized as a lycopene cyclase gene responding to drought stress in cotton

“…Genome sequences of four Gossypium species including G. hirsutum , ZJU; G. barbadense , HAU; G. arboreum , CRI; and G. raimondii, JGI were used to identify the gene family [21] . Protein sequences of tetraploid ( G. barbadense and G. hirsutum ) and diploid ( G. arboreum and G. raimondii ) cotton varieties were downloaded from Cotton FGD ( https://cottonfgd.org ) [22] . Additionally, genome datas of six other plants, A. thaliana, Vitis vinifera (V. vinifera), Populus trichocarpa (P. trichocarpa), Theobroma cacao (T. cacao), Oryza sativa (O. sativa) and Zea mays (Z. mays) were downloaded from the Phytozome V12.1 online site ( https://phytozome-next.jgi.doe.gov/ ) [23] .…”

“…The protein sequences were entered into the online MEME software to predicted the LCYs conserved motif sequence, The analysis was set to allow a maximum of 15 motifs, and other parameters were kept at default settings ( http://meme-suite.org/tools/meme ) [22] . Genome-wide annotation files and General Feature Format (GFF) files for four different cotton cultivars were acquired from CottonFGD ( http://www.cottonfgd.net/ ).…”

Molecular Identification and Characterization of UDP-glycosyltransferase (UGT) Multigene Family in Pomegranate

“…It was previously thought that group Q was specific to monocots, such as maize [54] and wheat [52]; however, the occurrence of Q members in Malus × domestica [41], Epimedium pubescens [35], and Triticum aestivum [52] suggested that group Q was not exclusive to monocots. Only one UGT in group R was found in Camellia sinensis [33] and other four species (Lotus japonicus, Medicago truncatula, Phaseolus vulgaris, and Trifolium pratense) [38], while there were 4, 4, and 6 UGT members belonging to the R group in P. granatum, Malus × domestica [41], and Gossypium raimondii [37], respectively, suggesting that group R may make an important contribution to the glycosylation of specific metabolites. Quantitatively, PgUGTs were concentrated in groups A, D, E, G, and L, indicating that members of these five groups expanded more rapidly than any other groups during plant evolution, as described by Caputi et al [7].…”