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Genome-wide computational analysis of the dirigent gene family in Solanum lycopersicum

Proteome Science volume 22, Article number: 10 (2024) Cite this article

Abstract

Background

Dirigent (DIR) genes play a key role in the development of organic products in plants. They confer conformational influence on processes that lack stereoselectivity and regioselectivity through processes that are mostly understood. They are required to produce lignans, which are a unique and widely distributed family of plant secondary metabolites with intriguing pharmacological characteristics and potential role in plant development. DIR genes are implicated in the process of lignification and protect plants from environmental stresses, including biotic and abiotic stresses. Nevertheless, no research has been performed on the DIR gene family in Solanum lycopersicum. This study provides detailed information on the DIR gene family in S. lycopersicum.

Methods and results

The conserved domain analysis, phylogenetic analysis, evolutionary adaptation, cis-acting elements, proteomic analysis, signal peptide detection, transmembrane potential analysis, sequence identity and similarity analysis, gene assembly, genomic localization, duplication of gene analysis, and evolutionary linkage of 31 potential DIR genes were studied. All these analyses provide a deep understanding of DIR genes in the S. lycopersicum genome that will provide a useful reference for further functional analysis of the DIR genes in S. lycopersicum.

Conclusion

This research provides an in-depth and comprehensive explanation of the detailed process and structural characterization of DIR genes in the genome of S. lycopersicum, laying the groundwork for future plant genetic engineering and crop development exploration. This work will provide valuable information for identifying DIR genes in higher plants and support future research on the DIR gene family.

Background

The name dirigent (DIR) originates from the Latin word dirigere, which means guide or align, and DIR protein was discovered for the very first time in Forsythia intermedia [1]. In the pharmacological direction of E-coniferyl alcohol stereospecific interactions, DIR proteins from Forsythia suspensa [2], mayapple [3], and western red cedar [4] produce the enantiomer pinoresinol, which is effectively used in the plant defense system. DIR along with the disease resistance response (DRR) gene family possess a DIR-conserved domain [5], and they are thought to regulate the oxygen radical bonding of monolignol plant phenolic compounds in plants to produce lignans and lignins [6]; hence, DIR is implicated in disease resistance adaptations [7].

Lignan has antifungal effects, both constitutively and inducibly, and is considered to be mainly involved in plant defense reactions [8]. Lignin accumulation is thought to act as a protective factor in the defensive reaction against microbial infection [9]. According to the study [10], a thicker morphology of leaf tissue includes lignin, which functions as a protective barrier against microbial attack. Lignin protects the recipient by acting as a nondegradable protective lining for pathogens. Lignin is indeed an essential chemical found largely in terminally specialized cells of supporting and water-conducting components, and it is principally involved as an exoskeleton, a waterway in the xylem, and insect and microbe defense [11].

Determining the roles of the DIR gene family in physiological and biological processes could be a useful approach for evaluating and enhancing crop defense responses against environmental stresses. Nevertheless, recently, no research has been performed on the DIR gene family of S. lycopersicum. As a result, the contribution of this work is to identify and analyze the DIR gene family of S. lycopersicum using a genome-wide strategy. Following computational analysis, a total of 31 DIR genes from the S. lycopersicum genome were retrieved. After that, promoter analysis, gene structure analysis, unique motif identification, tertiary configuration identification, chromosomal dispersal, gene duplication, synteny analysis, phylogenetic analysis, and potential membrane analysis were performed to study the DIR gene family in S. lycopersicum.

Methodology

Retrieval of dirigent sequences

The S. lycopersicum DIR genes were retrieved from the seed file (PF03018) (https://www.ebi.ac.uk/interpro/entry/pfam), and in the Phytozome13 (S. lycopersicum ITAG4.0) database (https://phytozome.jgi.doe.gov/) [12] against the S. lycopersicum genome with the default parameters. The Arabidopsis thaliana DIR genes were retrieved from The Arabidopsis Information Resource (TAIR) via the BLAST approach. The protein’s conserved domain was validated using (https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi) the conserved domain database in an automated way after redundant and repetitive segments were eliminated once at a time [13, 14].

Structural characterization and phylogenetic evaluation

The ClustalW tool was used to conduct multiple sequence alignments of sequences. The protein sequences were analyzed with the ExPASy ProtParam tool to determine the protein coding sequence (CDS) length, total number of units, aliphatic index, instability index, grand average of hydropathicity (GRAVY), protein molecular weight, and hypothetical isoelectric point (http://web.expasy.org/protparam/). Using the online tool Gene Structure Display Server (GSDS), the exon/intron regions of specific DIR genes in S. lycopersicum were studied [15,16,17]. The tool MEME (http://meme-suite.org/tools/meme) was used with the parameters Zero or one occurrence per sequence (Zoops), a minimum width of motifs of six and a maximum of 50, and a total number of motifs per sequence of 15 to analyze the motifs of S. lycopersicum DIR genes, and the results were visualized using TBtools (TBtools v1.09854). Subcellular localization analysis was assessed using WoLF PSORT (https://wolfpsort.hgc.jp/) [18]. The WoLF PSORT findings were evaluated using a heatmap plot generated with the TBtools (v1.09854) [19] program. N-glycosylation sites (ASNs) of the DIR sequence were found online via the NetNGlyc 1.0 server (http://www.cbs.dtu.dk/services/NetNGlyc/).

To perform a phylogenetic analysis of the S. lycopersicum DIR gene family, MEGA X (http://www.megasoftware.net/)(20) was used. After aggregation and separation, the differentially expressed genes were divided into different subclasses, and a full dendrogram encompassing Arabidopsis thaliana and S. lycopersicum was constructed using MEGA X. ClustalW (http://www.ebi.ac.uk/clustalw/) [21] with general parameters was used to realign all of the segments first. Since not all S. lycopersicum DIR gene family members are exactly equivalent, gaps were removed, and a more cautious phylogenetic tree was built to improve the study’s reliability. MEGA X was used to generate both phylogenetic trees, which were created using the neighbor-joining [22] approach, and bootstrapping tests, which involved 1000 repetitions [23].

Evolutionary adaptation and chromosomal localization

The S. lycopersicum DIR genes were mapped to the respective S. lycopersicum chromosomes using the Phenogram online program [24] (http://visualization.ritchielab.org/phenograms/plot).

The TBtools program (v1.09854; http://cj-chen.github.io/tbtools/) was used to retrieve chromosome sequence data, as it was used to locate all of the S. lycopersicum DIR genes according to their spatial relationship and chromosomal positions, as well as duplicated regions [25]. The ratios of Ks to Ka were calculated using the TBtools program with default settings (v1.09854). The divergence period of the gene pairs was calculated using the rate of substitutions per synonymous site per year. (Yuan et al., 2015) T = Ks/2x (x = 6.56 109).

Analysis of cis-acting elements in the promoter regions

The presence of cis-acting elements in the S. lycopersicum DIR gene family was studied using the TBtools program (http://cj-chen.github.io/tbtools/) [19]. The upstream region (up to 2 kb and 200 base pairs) of the S. lycopersicum DIR genes were retrieved from the S. lycopersicum genome and saved in FASTA file format. PlantCARE was used to submit and evaluate the data (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/) [26].

Proteomic analysis and signal peptide prediction

The linkage associations of all the DIR family genes in S. lycopersicum were constructed by integrating all the DIR genes of S. lycopersicum into the freely accessible tool string database (https://string-db.org/) [27], with the following criteria: (i) minimum confidence: high (score: 0.07), and (ii) the maximum number of potential interconnections: 5, with all the unconnected sequences being eliminated. To illustrate consensus, all S. lycopersicum DIR genes in S. lycopersicum were mapped using the string database to evaluate their cooccurrence with other closely related taxa. The web hosting server Phyre2 (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index) [28] was used to predict the tertiary conformations and homologs of S. lycopersicum DIR genes, as reported previously [29]. The presence of signal peptides and the locations of their cleavage sites within the given sequences were predicted using the SignalP 6.0 server online tool (https://services.healthtech.dtu.dk/services/SignalP-6.0/) [30].

Transmembrane potential analysis and sequence identity and similarity analysis

All-amino-acid alignments were evaluated in the TMHMM Server, v. 2.0 (http://www.cbs.dtu.dk/services/TMHMM/) online program for analyzing the possible transmembrane mechanisms implicated in all S. lycopersicum DIR genes. To assess sequence similarity, all of the amino acid sequences were submitted to the online program SIAS (http://imed.med.ucm.es/Tools/sias.html) with the baseline model of the BLOSUM62 method with gap consequences.

(1) The cost of establishing the gap, Po (0-100), is 10.

(2) The cost of expanding the gap, Pe (0-100), is 50.

Synteny analysis

The DIR genes in Arabidopsis thaliana and S. lycopersicum were assessed using the Circoletto (http://bat.ina.certh.gr/tools/circoletto/) online program, which employs Circos to identify two sequence datasets. DIR genes of S. lycopersicum were aligned to Arabidopsis thaliana DIR genes. An E value of 10 to -40 (Strict) was used to perform a genome preservation assessment from total local pairings. The S. lycopersicum DIR protein sequences and Arabidopsis thaliana DIR protein sequences were utilized to search their respective protein repositories, with the best hits obtained based on the E value.

Results

Confirmation of DIR genes in S. Lycopersicum

The DIR sequences from the model organism Arabidopsis thaliana and the seed file (PF03018) were used as keywords in a BLASTp homology search against the S. lycopersicum genome to determine all possible closely related sequences in Phytozome v13 (https://phytozome-next.jgi.doe.gov). By eliminating other repetitive sequences, a maximum of 31 DIR genes, labeled SlDIR1 to SlDIR31, were retrieved from the S. lycopersicum genome. All the SlDIRs (S. lycopersicum DIR genes) genes belonged to the DIR group according to the annotation of Phytozome v13 and also matched with their Arabidopsis thaliana orthologs. Subsequently, the existence of a preserved DIR motif was confirmed utilizing SMART and Pfam screening of all SlDIRs. TBtool was used to further confirm the presence of a DIR domain in all SlDIRs genes, as shown in Fig. 1.

Fig. 1
figure 1

Confirmation of DIR domains in all the S. lycopersicum retrieved sequences

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Gene structural characterization, conserved motif analysis, and phylogenetic tree construction

The amino acid contents and stoichiometries of molecules in the S. lycopersicum DIR genes family are diverse, and the amount of compound proteins varies greatly among subclasses. The amino acid lengths of the S. lycopersicum DIR genes ranged from 60 (SlDIR23) to 399 (SlDIR11), with an average of 189 base pairs. The lowest molecular weight is 6302.19 kDa, and the maximum is 41413.18 kDa, with an average weight of 20715.22 kDa. The mean isoelectric point (pI) is 7.75, with scores ranging from 4.47 (SlDIR11) to 9.88 (SlDIR11) (SlDIR3). The pI is greater than 7 in 58% of the S. lycopersicum DIR gene family members, while it is less than 7 in the remaining genes. As a direct consequence of these findings, there are more basic DIR proteins than acid proteins. The presence of N-glycosylation (Asn) in each DIR sequence and other physiochemical properties can be seen in Table 1.

The genomic and protein coding sequence (CDS) of the S. lycopersicum were studied, and the genetic makeup of their intron and exon structures were examined to determine how they work. According to the findings of the GSDS 2.0 software program (http://gsds.gao-lab.org/), only six of the 31 DIR genes (16%) had only one intron. Notably, 25 of the 31 proteins did not have introns. The genetic structure of all the genes is shown in Fig. 2. The WoLF PSORT results of subcellular localization were predicted using a heatmap from TBtool software. The highest probability values are highlighted in red, and the lowest probability values are highlighted in light blue color as shown in Fig. 3.

Members of the S. lycopersicum DIR genes family from the same subfamily have comparable motif types and quantities; however, there are variations in motif configurations across subfamily members. The precision of the phylogenetic analysis was improved by discovering comparable gene architectures and preserved domains within the same subfamily. Structural variations across subfamilies, on the other hand, imply that the DIR gene family in S. lycopersicum has functional variability. The genes and their respective motifs can be visualized in Fig. 4 which shows that each gene has its functionality depending upon the number of motifs present.

ClustalW was employed to evaluate the amino acid patterns of 31 S. lycopersicum DIR genes against 26 Arabidopsis thaliana DIR genes in addition to assessing the DIR gene family in model plants and S. lycopersicum from an evolutionary perspective and to investigate the unique features of the S. lycopersicum DIR genes. MEGA X, minimal evolution, and neighbor-joining (NJ) methods were used to study the phylogenetic relation. The S. lycopersicum DIR and Arabidopsis thaliana DIR genes were clustered together, suggesting that the S. lycopersicum DIR genes that can be categorized from Arabidopsis thaliana sequences are part of the same grouping. The DIR group of all these sequences may be categorized into seven subclasses (indicated by different colors) based on their similarity to DIR sequences in Arabidopsis thaliana, as shown in Fig. 5.

Table 1 Physiochemical properties of all the DIR genes in S. lycopersicum
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Fig. 2
figure 2

The intron-exon structure of DIR genes, the exons are shown in light yellow, and the black curve line indicates an intronic region with a blue color indicating the upstream/downstream region

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Fig. 3
figure 3

Heatmap interpretation of the subcellular localization of S. lycopersicum DIR genes

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Fig. 4
figure 4

Phylogenetic analysis and conserved motif analysis of S. lycopersicum DIR genes (A) Phylogeny of DIR genes via MEGA X with neighbor-joining methodology. (B) Different colors represent the various conserved motif domains of DIR genes in all S. lycopersicum DIR genes

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Fig. 5
figure 5

Phylogenetic relationship of S. lycopersicum and Arabidopsis thaliana DIR genes

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DIR genes promoter analysis

To advance the study of the putative biological responses of S. lycopersicum DIR genes during signaling, development, and endurance to abiotic and biotic stress feedback, PlantCARE [26] was utilized to evaluate cis-acting regions within the 2 kb upstream sequence and 200 base pairs upstream from each transcription start site of the S. lycopersicum DIR genes. Upon further investigation of the responsive parts of each gene, it was found that, as also shown in Fig. 6a (2 kb base pairs) and Fig. 6b (200 base pairs), each gene seems to have a diverse range of activities in response to environmental stress as well as plant development, growth, and control.

Fig. 6
figure 6

(a) A comprehensive analysis of all S. lycopersicum DIR gene promoter analysis (up to 2 kb upstream). (b) A comprehensive analysis of all S. lycopersicum DIR gene promoter analysis (up to 200 bases upstream region)

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Chromosomal location and gene duplication analysis

The Phytozome dataset v13 provided the chromosomal locations of all S. lycopersicum DIR genes. All DIR genes were physically allocated to their appropriate chromosomes by using the phenogram tool, as shown in Fig. 7. The 31 DIR genes were highly heterogeneous and dispersed throughout the S. lycopersicum genome on all the 12 chromosomes, excluding chromosome number 03, indicating that biological variability evolved during evolution. Nine genes were found on chromosome 10 (chr10). On the other hand, chromosomes 5, 8, 9, 11, and 12 contained the fewest DIR genes, with only one. Two DIR genes were found on three chromosomes (chromosome number 04, chromosome number 06, and chromosome number 07). Furthermore, chromosomes 2 and 8 contain 3 DIR genes.

The (synonymous rate) Ks, (non-synonymous rate) Ka, and Ka/Ks for these iterations were calculated, and the values were used to predict duplication divergence time. Throughout the genome, there is a wide variety of duplications. The ratio of Ka/Ks indicated that all of the values were less than one, implying that they were purified.

Ka/Ks = 1 indicates neutrality in the process of selection, while Ka/Ks > 1 indicates positive selection, and Ka/Ks < 1 indicates purifying selection. A Ka/Ks < 1 was found for all duplicated DIR gene pairs, indicating purifying selection throughout evolution, except for the SlDIR2 and SlDIR3 gene pairs, which indicate positive selection and are highly conserved throughout evolution. In addition, duplication events of duplicated gene pairs were predicted to have happened somewhere between 3.75 and 74.36 million years ago (Table 2).

Fig. 7
figure 7

Allocation of DIR genes across the S. lycopersicum genome

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Table 2 Ka, Ks, and Ka/Ks calculations and divergence times of the duplicated S. Lycopersicum DIR gene pairs
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Protein-protein linkage association, signal peptide prediction, and coexpression analysis

To determine the importance of S. lycopersicum DIR proteins, data relating to proteins were obtained, and coexpression studies of these proteins with linked taxa were performed. The String Browser revealed significant associations among proteins at different stages. A preliminary shell of contact is observed throughout the intersection, as indicated by all the bright clusters. Figure 8b depicts the evolution, preservation, and coexpression of the differentially expressed proteins in a set of related taxa. It can be visualized from Fig. 8b that DIR sequences are preserved throughout the related taxa, black color indicates high preservation while light color indicates low. Figure 8a depicts the anticipated relationship of 31 S. lycopersicum DIR proteins that shows the established linkage among them. SignalP 6.0 was used to predict peptide signals, and the results are shown in Table 3. All the proteins were predicted to have signal peptides, except for nine proteins, SlDIR1, SlDIR2, SlDIR4, SlDIR10, SlDIR12, SlDIR22, SlDIR23, SlDIR28, and SlDIR30. The values of the cleavage site position and marginal probabilities for the signal peptide regions are also given in Table 3.

Fig. 8
figure 8

(a) String database prediction of S. lycopersicum DIR genes. (b) STRING database depicts DIR genes co-expression in related taxa. Black color shows the highest expression in the S. lycopersicum genome vs. light color at a different scale

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Table 3 Signal peptide prediction, cleavage site position, and marginal probabilities for the signal peptide regions of S. Lycopersicum DIR genes
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Synteny analysis and tertiary structure prediction

DIR proteins were analyzed to find orthologous pairs between S. lycopersicum and Arabidopsis thaliana to further deduce the evolutionary connection. According to synteny analysis, S. lycopersicum DIR genes and Arabidopsis thaliana DIR genes have collinear gene pairs. A Circos plot [31] was constructed to predict that S. lycopersicum DIR genes possess a high degree of evolutionary homology with Arabidopsis thaliana, indicating that they could have similar biological activities (Fig. 9). Within the circle, ribbons in four semitransparent colors—blue, green, orange, and red—show the local alignments generated by the BLAST approach. These colors correspond to the four quartiles up to the maximum score; that is, a local alignment scoring 80% of the maximum score is red, while one scoring 20% of the maximum score is blue.For the prediction of protein tertiary structure, the Phyre2 online tool was used, the results of which are shown in Fig. 10. (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index)

Fig. 9
figure 9

Synteny map of all the identified S. lycopersicum DIR and Arabidopsis thaliana DIR genes

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Fig. 10
figure 10

Tertiary prediction of all S. lycopersicum DIR proteins

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Transmembrane potential and sequence identity and similarity analysis

To test whether the potential transmembrane outcome is active for all of the studied sequences, TMHMM, an online tool, was used to search for all of the S. lycopersicum DIR genes. 15 DIR genes out of the 31 S. lycopersicum DIR genes were found to be involved in the essential functions of the cellular membrane. The SIAS assessment was used to determine the sequence distinctiveness, coherence, and global similarity. Table 4 presents common findings in a tabular arrangement. The resemblance and identification ability of S. lycopersicum DIR genes were greater than those of the global similarities based on the data (Table 4).

Table 4 Sequence analysis of S. lycopersicum DIR genes
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Discussion

Plants are constantly exposed to adverse environmental factors such as salt, drought, and cold, which have significant influences on geographical distribution, proliferation, growth, and plant production. Plants respond to external stresses through a complex set of resistance strategies that are activated and incorporated by the expression of thousands of genes [32]. Such stresses induce the expression of genes that were discovered to be important for plant stress resistance. These gene products act as regulatory proteins, increasing stress tolerance in plants and boosting plant immunity.

The study of transcriptional regulators is a diverse issue in the genetic sciences. Transcription factors influence a range of activities, including physical, biochemical, and evolutionary activities, as well as the activation routes of downstream genes. Numerous transcription factors that control dehydration, high salt, and other environmental variables have been identified in recent years. In addition, genomic data may be utilized to develop an interpretative layout for gene transformation technology that can be employed to generate highly resistant transgenic organisms.

DIR molecules are a multigene family in plants that respond to pathogen resistance [29, 33, 34]. They serve an essential function in improving stress tolerance in many crops [35]. The DIR genes are vital disease resistance-responsive genes that play a pivotal function in improving stress resistance across numerous plant species. The primary function of DIR, which are often higher oligomers or dimmers, is to protect plant tissues, particularly those involved in seed and heartwood production [34]. DIR and its homologs have been found in all vascular plants [36], and they are thought to play a role in lignin and lignan production [4]. Different plant species have different numbers of DIR genes. There have already been reports of 25 DIR genes in Arabidopsis thaliana, 19 DIR genes in Isatis indigotica, 54 DIR genes in rice, 35 DIR genes in Picea glauca, and 29 DIR genes in Brassica rapa [29, 35, 37, 38]. There has never been a genome-wide identification or characterization of the DIR gene family in S. lycopersicum.

In this study, we identified and explored via bioinformatics tools, a total of 31 DIR genes in the S. lycopersicum genome. Five well-conserved motifs were identified in the amino acid sequence alignments of all 31 S. lycopersicum DIR genes that show they have functional variability. Only 16% (6 out of 31) of the DIR had one intron and the rest of the S. lycopersicum DIR genes (25 out of 31) contained no intronic regions, according to the gene structural analysis. Like the previously examined DIR genes of Arabidopsis thaliana and poplar, the structure of the DIR genes, which contain minimal introns, was also assessed in this study [13]. Nevertheless, 1–5 introns are found in one-third of the rice genome [34]. This implies that after divergence, rice, S. lycopersicum, poplar, and Arabidopsis thaliana may have divergent paths. The amino acid (aa) sequences varied from 60 aa (smallest) (SlDIR23) to 399 aa (largest) (SlDIR11), having an average of 189 base pairs. The lowest molecular weight is 6302.19 kDa, and the maximum is 41413.18 kDa, with an average weight of 20715.22 kDa. The mean isoelectric point (pI) is 7.75, with scores ranging from 4.47 (SlDIR11) to 9.88 (SlDIR11) (SlDIR3). The pI is greater than 7 in 58% of the S. lycopersicum DIR gene family members, while it is less than 7 in the rest of the genes, which shows that they are more basic.

Phylogenetic analysis revealed that the S. lycopersicum DIR genes and Arabidopsis thaliana DIR sequences are likely part of the same group since they were grouped together. Upon examining the proximity of these sequences to DIR sequences in Arabidopsis thaliana, it becomes apparent that there are seven distinct subclasses, each characterized by a unique color as shown in Fig. 5. According to findings via promoter analysis, it revealed that every gene seems to have a unique role in plant development, growth, regulation, and response to environmental stresses. This study supports previous research on cis-elements [15], with elements linked to stress and light being discovered in the upstream region, demonstrating that environmental stress and light may have a regulatory function in DIR genes. Furthermore, components sensitive to salicylic acid and methyl jasmonate have been found upstream of many S. lycopersicum DIR genes. Gibberellin-responsive domains were also found in the majority of the studied genes and are good signs of plant defense responses. Taken together, these findings suggest that the rhythms of the hormone responses of S. lycopersicum DIR genes are extremely complicated. Distinct DIR genes are considered to have multiple functions in a diverse range at various times; nevertheless, they still need to be examined further in the laboratory to demonstrate their functionality.

All S. lycopersicum DIR genes were physically allocated on their chromosomes. On all 12 S. lycopersicum chromosomes except chromosome 03, the 31 DIR genes were very diverse and scattered, showing biological diversity arose over evolution. Chromosome 10 had nine genes, and chromosomes 5, 8, 9, 11, and 12 have the fewest DIR genes, one. Three chromosomes 04, 06, and 07 had two DIR genes. Furthermore, chromosomes 2 and 8 have 3 DIR genes. The duplication divergence time is predicted using the ka/ks ratio, which shows duplications are widespread throughout the genome. The Ka/Ks ratio showed that all values were smaller than one, indicating purification. Every duplicated DIR gene pair has a Ka/Ks < 1, showing purifying selection, except for the SlDIR2 and SlDIR3 gene pairs, which show positive selection and are highly conserved. Additionally, gene pair duplication events were anticipated to have occurred between 3.75 and 74.36 million years ago.

Based on synteny research, it has been shown that there are collinear gene pairings between S. lycopersicum genes and Arabidopsis thaliana. A Circos plot predicted that S. lycopersicum DIR genes have a significant level of evolutionary similarity with Arabidopsis thaliana, suggesting that they may have comparable biological functions. Our finding also shows the cooccurrence of the S. lycopersicum DIR genes family in different related taxa which shows their divergence. The Phyre2 tool was used to establish the prediction of protein tertiary structure. The String Browser revealed substantial correlations across proteins at various stages. An initial framework for interaction is seen at the junction. The presence of all these sequences indicates the conservation, preservation, and simultaneous expression of the differentially expressed proteins in a group of closely related organisms. In addition to shedding light on how these S. lycopersicum DIR genes carry out their roles, this work paves the way for future investigations into gene functional analysis.

Conclusion

It is possible to study plant species genomes using data analysis and evolutionary approaches. The environmental selection did not displace most of the S. lycopersicum DIR genes in the S. lycopersicum genome, but they did exhibit remarkable conservation throughout the evolutionary process. Future studies on members of the S. lycopersicum DIR gene family involved in the intricate network of plant growth and development will provide a useful reference for further functional analysis of the DIR gene family in S. lycopersicum.

Data availability

Various databases are used that are cited separately.

Abbreviations

DIR:

Dirigent

S. lycopersicum :

Solanum lycopersicum

CDS protein:

coding sequence

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Funding

This work was supported by the National Key R&D Program of China (2023YFE0199400), Central Public-interest Scientific Institution Basal Research Fund (No. Y2024QC33), Sichuan Science and Technology Program (2023YFQ0100), the Science and Technology Innovation Project of the Chinese Academy of Agricultural Sciences (No. 34-IUA-02).

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Authors and Affiliations

  1. Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu National Agricultural2Science and Technology Center, Chengdu, 610213, China

    Muhammad Abu Bakar Saddique, Ge Guan, Beibei Hu, Zahid Hussain, Xiumei Luo & Maozhi Ren

  2. School of Agricultural Science, Zhengzhou University, Zhengzhou, 450001, China

    Ge Guan, Beibei Hu, Xiumei Luo & Maozhi Ren

  3. Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, 20122, Milan, Italy

    Mudassir khan

  4. Department of Medical, Oral and Biotechnological Sciences, Università degli Studi ’G. d’Annunzio’ Chieti - Pescara, Chieti, Italy

    Muhammad Dawood Amjad

  5. Department of Mathematics & Statistics, Pir Mehr Ali Shah Arid Agriculture University - PMAS AAUR, Rawalpindi, Pakistan

    Sana Abbas

  6. Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan

    Muhammad Faizan Khurram Maqsood

  7. Department of Plant Biotechnology, National University of Sciences and Technology, Islamabad, Pakistan

    Muhammad Abu Bakar Saddique

Authors
  1. Muhammad Abu Bakar Saddique
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  2. Ge Guan
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  9. Xiumei Luo
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Contributions

Conception and design: M.A.B.S, X.L, R.M. Development of methodology: M.A.B.S, M.K, M.D.A, Z.H, B.H, M.F.K.M. Analysis and interpretation of data: M.A.B.S, M.F.K.M, S.A, M.D.A, M.K. Writing of the manuscript: M.A.B.S, M.K, S.A, M.D.A, B.H, G.G. Figure preparation: M.A.B.S, M.F.K.M, S.A, Z.H. Study supervision: X.L, R.M.

Corresponding authors

Correspondence to Xiumei Luo or Maozhi Ren.

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Saddique, M.A.B., Guan, G., Hu, B. et al. Genome-wide computational analysis of the dirigent gene family in Solanum lycopersicum. Proteome Sci 22, 10 (2024). https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s12953-024-00233-0

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Keywords

Proteome Science

ISSN: 1477-5956