Genome-wide characterization of 2- oxoglutarate and Fe(II)-dependent dioxygenase family genes in tomato during growth cycle and their roles in metabolism

- In addition, type I flavone synthase (FNSI) belongs to the 2ODD family and contributes to the biosynthesis of flavones, but this protein has not been characterized in tomato..
- The Sl2ODD s in the same clade showed similar intron/exon distributions and conserved motifs.
- The Sl2ODD s were unevenly distributed across the 12 chromosomes, with different expression patterns among major tissues and at different developmental stages of the tomato growth cycle.
- We found that the Sl2ODD expression patterns were consistent with their functions during the tomato growth cycle .
- These results indicated the significance of Sl2ODDs in tomato growth and metabolism.
- Conclusions: Our study provided a comprehensive understanding of the tomato 2ODD family and demonstrated the significant roles of these family members in plant metabolism.
- We also suggest that no FNSI genes in tomato contribute to the biosynthesis of flavones..
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- Analysis of the genomes of six model plant species showed that more than 500 pu- tative 2OGDs could be classified into three major clas- ses: DOXAs, DOXBs and DOXCs [2].
- DOXA class enzymes, including plant homologs of Escherichia coli (E.coli) AlkB, are involved in the oxidative demethylation of alkylated nucleic acids and histones [3].
- 2ODDs are also involved in the biosynthesis of second- ary metabolites that have substantial biological and me- dicinal value.
- Moreover, a genome-wide study of Salvia miltiorrhiza found that 2ODD plays a crucial role in the biosynthesis of tanshi- nones [10], and 2ODDs in tobacco (Nicotiana tabacum) have been functionally characterized as being involved in the biosynthesis of colorful flavonoids [11]..
- The biosynthesis pathway of flavonoids in the Sola- naceae has been extensively studied [15, 16].
- OsFNSI was identified using parsley FNSI as bait and is the first FNSI found outside of the Apiaceae family [21].
- A comprehensive analysis of the 2ODD family in tomato has not been performed.
- Genome-wide identification and phylogenetic analysis of 2ODDs in tomato.
- The number of amino acid residues of the predicted Sl2ODDs ranged from 248 to 418, with corre- sponding molecular weights from 28.4 to 47.7 kDa (Table S1).
- was accurate enough for used in the estimation of the function of several unknown genes.
- For instance, twenty of the 25 members in clade 1 are GAOXs (Fig.
- Gene structure and protein motif analysis of Sl2ODDs To gain further insight into the structural diversity of to- mato 2ODDs, we used the online software GSDS 2.0 to analyze the exon-intron structure of 2ODDs based on the genome sequence and the corresponding coding DNA sequences of the 2ODDs in tomato (Fig.
- Overall, the conserved motif composition and gene structure of the 2ODD mem- bers, together with the phylogenetic tree results, strongly supported the classification reliability..
- b Conserved motifs of Sl2ODDs.
- Each motif is represented in the colored box: motif 1 (khaki), motif 2 (dark khaki), motif 3 (slate blue), motif 4 (gold), motif 5 (yellow green), motif 6 (midnight blue), motif 7 (cadet blue), motif 8 (saddle brown), motif 9 (deep pink), motif 10 (dark violet), motif 11 (dark red), motif 12 (cyan), motif 13 (peach puff), motif 14 (dark salmon), and motif 15 (orchid).
- c Exon and intron gene structures of Sl2ODDs .
- d The exon number distributions of Sl2ODDs.
- Chromosomal distribution and synteny analysis of Sl2ODDs.
- The 128 Sl2ODD members (excluding Solyc00g031030, Solyc10g026520, and Solyc03g095920, which are identi- fied using the MicroTom Metabolic Network (MMN) dataset based on ITAG 3.0 but absent in the updated ITAG 4.0 gene models) are widely distributed across the 12 tomato chromosomes.
- Chromosome 2 has the largest number of Sl2ODDs (25/128).
- We detected duplicated genes in the Sl2ODD family using the MCScanX package.
- Expression pattern of Sl2ODDs.
- To dissect the potential roles of Sl2ODDs involved in specific plant secondary metabolism, the expression patterns of Sl2ODD genes were investigated using the recently published MMN dataset [25].
- The expression patterns of the remaining 122 Sl2ODDs could be divided into four clusters (Fig.
- A total of 46 Sl2ODDs were mainly expressed in the flowering stage (F45) and the roots.
- for example, nearly half of the clade 3 genes (13/27) were expressed signifi- cantly in the roots.
- 3 Schematic representations for the distribution and duplication of Sl2ODD genes in the tomato genome.
- a The distribution of Sl2ODDs in chromosomes.
- Different colors of Sl2ODD s indicate their subfamilies shown in the Fig.1.
- b The interchromosomal relationships of Sl2ODDs .
- Gray lines indicate all synteny blocks in the tomato genome and the black lines indicate duplicated Sl2ODD gene pairs.
- Potential roles of Sl2ODDs in metabolism.
- 4 Expression patterns of Sl2ODDs during major tomato growth stages and tissues.
- GA3OXs, GA2OXs) that belong to the 2ODD family and contribute to structural modification.
- GA2OXs play a role in GA catabolism re- sponsible for GA deactivation via C-2 hydroxylation of the GA backbone.
- In the present study, a total of 19.
- Analysis of Sl2ODDs involved in gibberellin biosynthesis and catabolism pathway.
- a Expression profiles of 19 GAox genes during the tomato life cycle.
- putative GAOX coding genes, including 5 GA20OXs, 3 GA3OXs, and 11 GA2OXs, were found in the tomato genome (Fig.
- The expression of SlGAOXs had obvious tissue specifi- city corresponding to significant expression in the roots, stems, flowers, and fruits (Fig.
- Overexpression of GA2OX1 resulted in the reduction in endogenous GAs and led to a decrease in tomato ger- mination rate and fruit weight [26].
- As GAs have a broad impact on plant growth, according to the expression profile, the different GA2OX homologs in tomato may function in different tissues and periods of plants..
- Ethylene output by organs increases dramatically at specific stages of the plant growth cycle, such as fertilization, ripening, senescence, abscission, and re- sponse to stresses [36].
- ACC is then converted into ethylene by ACO, a member of the 2ODD family..
- The expression model of the seven ACOs during to- mato fruit development has been reported previously [29].
- ACO1 was mainly expressed in the fruits, sug- gesting the well-known regulatory effect of ethylene on fruit ripening [29].
- The expression patterns of seven ACOs were different, indicating that their roles in the plant may be diverse..
- GAME11 participates in the initial synthesis process of SGAs and was highly expressed in the roots, leaves, flowers, and immature green fruits (Fig.
- In contrast, GAME31 was mainly expressed at the tomato fruit ripening stage and catalyzes the first important step in the chemical shift after maturation within nonbitter.
- 6 Characterization of Sl2ODDs involved in ethylene biosynthesis pathway.
- a Expression profiles of 7 ACO genes throughout the tomato life cycle.
- Interestingly, we found that the different expression patterns between GAME11 and GAME31 resulted in the appropriate func- tion at the right time.
- The upstream SGA metabolites accu- mulated mainly in the leaves (L45) and green fruits, which is in line with the expression pattern of the.
- The con- tent of downstream SGAs decreases gradually after the Br period along with the expression of the downstream biosynthesis-related gene GAME31.
- a Coexpression analysis of two GAME genes belonging to the 2ODD family with major SGAs across the tomato life cycle.
- FNSI, F3H, flavonol synthase (FLS), and anthocyanidin synthase (ANS) are flavonoid dioxy- genases and belong to the 2ODD family.
- Based on the MMN data, we conducted a coexpression analysis of genes and compounds of the flavonoid pathway.
- Although the flavonoid pathway of plants has been studied [15, 16], the key enzyme FNS responsible for the production of flavones, which compose the largest sub- group of flavonoids, has not been reported in the Sola- naceae thus far.
- Two candidates (Solyc03g080190 and Solyc06g073080) along with other FNSIs (ZmFNSI, OsFNSI, AtDMR6) were distributed in the same group.
- 8 Characterization of Sl2ODDs in flavonoids biosynthesis pathway.
- a Coexpression analysis of genes and flavonoids across the tomato life cycle.
- So far, there is no evidence of the presence of FNSI (Flavone synthase I) in tomato.
- The other four candidates, Solyc02g068310, Solyc05g018130, F3H, and FLS exhibited coexpression patterns together with those of the accumulation of up- stream compounds (Fig.
- The expression of these six potential genes may lead to FNS activity in tomato..
- In this study, a total of 131 2ODDs were identified in the tomato genome, and their phylogenetic relationships,.
- b Coexpression analysis of potential SlFNSIs and flavonoids across the tomato life cycle.
- a Schematic diagram of the reactions of eriodictyol under the action of different enzymes.
- The expression profile suggested that Sl2ODDs were widely distributed in dif- ferent tissues and stages, revealing their importance for normal organismal function during the tomato growth cycle.
- Our results highlighted their irreplaceable roles in the biosynthesis of gibberellins, ethylene, steroidal glycoalkaloids, and flavonoids.
- Our findings promote the understanding of the evolu- tion and function of 2ODDs in tomato, and therefore provide a reference for further research, especially for the genetic improvement of the tomato flavonoid pathway..
- annotation/ITAG4.0_release/) [46] and combined the annotation data of the recently established MicroTom Metabolic Network (MMN, https://www.sciencedirect..
- com/science/article/pii/S to identify 2ODD genes in the Solanum lycopersicum gen- ome.
- The other parameters were set to the defaults.
- The characteristics of the 2ODD structures with motif compositions were visualized by EvolView..
- All 2ODDs were mapped to the 12 tomato chromosomes based on physical location information from the data- base of the tomato genome using MG2C 2.1 (http://mg2 c.iask.in/mg2c_v2.1/) [52].
- Expression patterns of Sl2ODDs.
- Distributions of 54 tandem duplicated Sl2ODD genes in the tomato genome.
- The funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript..
- The datasets generated and analyzed during the current study are available in the Sol Genomics Network repository (Tomato Genome version SL4.0 and Annotation ITAG4.0, ftp://ftp.solgenomics.net/tomato_genome/annotation/.
- The accession numbers are included in the figures..
- Evolution and diversity of the 2-oxoglutarate- dependent dioxygenase superfamily in plants.
- Evolutionary and functional analyses of the 2-oxoglutarate-dependent dioxygenase genes involved in the flavonoid biosynthesis pathway in tobacco.
- Current understanding of the pathways of flavonoid biosynthesis in model and crop plants.
- Differential expression of two cytochrome P450s involved in the biosynthesis of flavones and anthocyanins in chemo-varietal forms of Perilla frutescens.
- A specialized flavone biosynthetic pathway has evolved in the medicinal plant, Scutellaria baicalensis.
- The characterization of transgenic tomato overexpressing gibberellin 20-oxidase reveals induction of parthenocarpic fruit growth, higher yield, and alteration of the gibberellin biosynthetic pathway.
- A critical evaluation of the role of ethylene and MADS transcription factors in the network controlling fleshy fruit ripening..
- Rewiring of the Fruit Metabolome in Tomato Breeding.
- Genome-wide analysis of the potato Hsp20 gene family: identification, genomic organization and expression profiles in response to heat stress..
- 20 years of the SMART protein domain annotation resource.
- 4-Coumarate 3- hydroxylase in the lignin biosynthesis pathway is a cytosolic ascorbate peroxidase

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