Genome-Wide Identification and Expression Profiling of 2OGD Superfamily Genes from Three Brassica Plants

Abstract

The 2-oxoglutarate and Fe(II)-dependent dioxygenase (2OGD) superfamily is the second largest enzyme family in the plant genome, and its members are involved in various oxygenation and hydroxylation reactions. Due to their important biochemical significance in metabolism, a systematic analysis of the plant 2OGD genes family is necessary. Here, we identified 160, 179, and 337 putative 2OGDs from Brassica rapa, Brassica oleracea, and Brassica napus. According to their gene structure, domain, phylogenetic features, function, and previous studies, we also divided 676 2OGDs into three subfamilies: DOXA, DOXB, and DOXC. Additionally, homologous and phylogenetic comparisons of three subfamily genes provided valuable insight into the evolutionary characteristics of the 2OGD genes from Brassica plants. Expression profiles derived from the transcriptome and Genevestigator database exhibited distinct expression patterns of the At2OGD, Br2OGD, and Bo2OGD genes in different developmental stages, tissues, or anatomical parts. Some 2OGD genes showed high expression levels in various tissues, such as callus, seed, silique, and root tissues, while other 2OGD genes were expressed at very low levels in other tissues. Analysis of six Bo2OGD genes in different tissues by qRT-PCR indicated that these genes are involved in the metabolism of gibberellin, which in turn regulates plant growth and development. Our working system analysed 2OGD gene families of three Brassica plants and laid the foundation for further study of their functional characterization.

Comprehensive Analysis of the SUV Gene Family in Allopolyploid Brassica napus and Its Diploid Ancestors

“…Before the separation of Brassica and Arabidopsis lineages, the WGD event was experienced, and then another whole-genome triploid (WGT) event was experienced [ 65 , 66 ]. After the WGT event, the gene family menbers changed, and the amplification phenomenon was also identified in the 2OGD gene family [ 67 ]. WGD is closely related to the evolution of plants and the origin of polyploidy and two hypotheses had been proposed to explain the origin and evolution of polyploidy [ 68 ].…”

Hormone biosynthesis and metabolism members of 2OGD superfamily are involved in berry development and respond to MeJA and ABA treatment of Vitis vinifera L

“…Kawai et al first identified the 2OGD superfamily in Arabidopsis , rice, Picea abies , Selaginella moellendorffi , Physcomitrella patens and Chlamydomonas reinhardtii , which own 130, 114, 142, 74, 66 and 41 members respectively [ 3 ]. Followed by the 2OGDs identification in corn [ 38 ], tomato [ 6 ], Salvia miltiorrhiza [ 39 ], Brassica rapa , Brassica oleracea and Brassica napus [ 40 ], which have 103, 159, 132, 160, 179 and 337 members respectively. In this study, 163 Vv2OGD members were identified in grape, which is the third-biggest 2OGD family in identified species, only after Brassica oleracea and Brassica napus .…”

BocODD1 and BocODD2 Regulate the Biosynthesis of Progoitrin Glucosinolate in Chinese Kale

“…The deduced protein sequences of the four BocODDs contained Fe( 2+ ) and the 2-oxoglutarate (2OG)-dependent dioxygenase domain, which catalyze the oxidation of an organic substrate using a dioxygen molecule, mostly by using ferrous iron as the active site cofactor and 2OG as a co-substrate [ 27 ]. The 2OG gene family can be classified into three classes—DOXA, DOXB, and DOXC—based on their amino acid sequences [ 28 ]. The DOXC class is involved in the biosynthesis of various phytochemicals [ 28 ].…”

“…The 2OG gene family can be classified into three classes—DOXA, DOXB, and DOXC—based on their amino acid sequences [ 28 ]. The DOXC class is involved in the biosynthesis of various phytochemicals [ 28 ]. ODDs have been classified into DOXC and catalyze the biosynthesis of goitrogenic 2-hydroxy-3-butenyl glucosinolate in Arabidopsis [ 16 , 28 ].…”

“…The DOXC class is involved in the biosynthesis of various phytochemicals [ 28 ]. ODDs have been classified into DOXC and catalyze the biosynthesis of goitrogenic 2-hydroxy-3-butenyl glucosinolate in Arabidopsis [ 16 , 28 ]. However, there was no difference in the DNA and cDNA sequences between the two Chinese kale genotypes, indicating that the differences in the 2-hydroxy-3-butenyl glucosinolate content were not caused by gene sequences.…”