Next Article in Journal
Earthworm (Eisenia fetida) Mediated Macropore Network Formation in Black Soil: Decay Straw as a Trigger for Sustainable Tillage
Previous Article in Journal
Decoding Potential Co-Relation Between Endosphere Microbiome Community Composition and Mycotoxin Production in Forage Grasses
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Agriculture
Volume 15
Issue 13
10.3390/agriculture15131396
agriculture-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Genome-Wide Identification and Evolutionary Analysis of the SnRK2 Gene Family in Nicotiana Species

by
Yu Tang
1,
Yangxin Zhang
1,
Zhengrong Hu
2,
Xuebing Yan
1,
Risheng Hu
2 and
Jibiao Fan
1,*
1
College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
2
Hunan Tobacco Research Institute, Changsha 410004, China
*
Author to whom correspondence should be addressed.
Agriculture 2025, 15(13), 1396; https://doi.org/10.3390/agriculture15131396 (registering DOI)
Submission received: 28 April 2025 / Revised: 25 June 2025 / Accepted: 27 June 2025 / Published: 29 June 2025
(This article belongs to the Section Crop Genetics, Genomics and Breeding)
Browse Figures
Versions Notes

Abstract

Soil salinization threatens agriculture by inducing osmotic stress, ion toxicity, and oxidative damage. SnRK2 genes are involved in plant stress responses, but their roles in salt stress response regulation of tobacco remain unclear. Through genome-wide analysis, we identified 54 SnRK2 genes across four Nicotiana species (N. tabacum, N. benthamiana, N. sylvestris, and N. tomentosiformis). Phylogenetic reconstruction clustered these genes into five divergent groups, revealing lineage-specific expansion in diploid progenitors (N. tomentosiformis) versus polyploidy-driven gene loss in N. tabacum. In silico promoter analysis uncovered regulatory networks involving light, hormones, stress, and developmental signals, with prevalent ABA-responsive elements (ABREs) supporting conserved stress-adaptive roles. Structural analysis highlighted functional diversification through variations in intron–exon architecture and conserved kinase motifs. This study provides a genomic atlas of SnRK2 evolution in Nicotiana, offering a foundation for engineering salt-tolerant crops.

1. Introduction

As soil salinization spreads across the world, it endangers agricultural sustainability. According to the FAO, nearly 1.4 billion hectares of land globally (about 10% of the total land area in the world) are affected by salinity, and a further 1 billion hectares are at risk as a result of the climate crisis and human mismanagement [1]. Salt stress is a prevalent abiotic stress that impacts plant growth, development, and productivity [2,3,4]. It induces a range of physiological and biochemical changes in plants, including osmotic stress, ion toxicity, and oxidative damage [5]. Plants have evolved intricate mechanisms to cope with salt stress, including multiple signaling pathways and regulatory networks [6,7]. One of the key components in these networks is the sucrose non-fermenting-1 (SNF1)-related protein kinase 2 (SnRK2) family [8,9]. SnRK2 family members are plant-specific serine/threonine kinases that are ubiquitous in the plant [10]. Since the isolation of the first SnRK2 protein kinase ABA (PKABA1) from wheat (Triticum aestivum) [11], members of the SnRK2 family have been identified in a variety of dicotyledonous and monocotyledonous plants. Studies have shown that SnRK2s genes are involved in both abscisic acid (ABA)-dependent and ABA-independent pathways to regulate plant responses to osmotic stress [12,13]. For example, in pepper (Capsicum annuum), two subclass II SnRK2 genes were found to positively regulate drought stress response, with differential responsiveness to ABA [14]. This report suggested that SnRK2 genes may have diverse functions in different plant species under various stress conditions. A meta-analysis of SnRK2 gene overexpression in plants under drought and salt stress conditions revealed that the overexpression of SnRK2 genes mainly improved plant stress tolerance by reducing osmotic stress and oxidative damage, and improving photosynthesis [15]. Therefore, SnRK2 genes should play a significant role in regulating plant responses to salt stress through multiple mechanisms, including the modulation of ABA signaling, the regulation of downstream target genes, and the interaction with metabolic pathways. Currently, a predominant focus on the roles of SnRK2 genes in ABA signaling pathways has left non-ABA-dependent mechanisms, such as osmotic stress and calcium signaling responses, underexplored [16,17,18]. While interactions between SnRK2 and calcium signaling components, such as CPK kinases, have been identified in Arabidopsis [19], the conservation of such pathways in tobacco and other species remains uncertain, reflecting unresolved functional heterogeneity across organisms. Our analysis of the SnRK2 gene structure and promoter elements (e.g., Ca2+-responsive motifs) may reveal whether calcium signaling crosstalk is evolutionarily conserved in tobacco.
Nicotiana tabacum—an allotetraploid derived from hybridization of N. sylvestris (maternal donor) and N. tomentosiformis (paternal donor) ~200,000 years ago [20]—exhibits polyploidy-driven genome downsizing (4–8% loss) and subfunctionalization [21,22]. Through comparative genomic analysis of four Nicotiana species—the allotetraploid N. tabacum, its diploid progenitors (N. sylvestris and N. tomentosiformis), and the model diploid N. benthamiana—this study aims to identify and characterize the SnRK2 gene family, reconstruct phylogenetic relationships with lineage-specific evolutionary trajectories, decode stress/development-related cis-regulatory elements in promoters, and elucidate structural diversity including conserved motifs and intron–exon architectures, collectively providing a foundation for leveraging SnRK2 genes in stress-resistant crop design.

2. Methods

2.1. Identification and Physicochemical Analysis of SnRK2 Gene Family Members In Silico

Four species were selected based on genomic completeness and evolutionary representation—Nicotiana tabacum (Ntab-TN90, cultivated allotetraploid), Nicotiana benthamiana (NbLab360, model diploid), and its progenitors Nicotiana sylvestris (ASM39365v2) and Nicotiana tomentosiformis (ASM39032v3), downloading from the Sol Genomics Network (https://solgenomics.net/, accessed on 22 November 2024) [23] and NCBI (https://www.ncbi.nlm.nih.gov/, accessed on 6 December 2024). SnRK2 family members were identified using TBtools (v2.310) [24] via BLAST (2.16.0) and domain screening.
Physicochemical properties (amino acid length, molecular weight, isoelectric point, aliphatic index, and grand average of hydropathicity) of SnRK2 proteins were predicted using the ExPASy online tool (https://www.expasy.org/, accessed on 6 December 2024).

2.2. Phylogenetic Tree Construction of SnRK2 Proteins

The SnRK2 protein sequences from tobacco species were aligned using MEGA 11.0 software [25]. A phylogenetic tree was constructed using the neighbor-joining (NJ) method with 1000 bootstrap replicates. The evolutionary distances were computed using the Poisson correction method and are in the units of the number of amino acid substitutions per site.

2.3. Conserved Motif and Gene Structure Analysis of SnRK2 Family

Conserved motifs in SnRK2 proteins were predicted using the MEME Suite (https://meme-suite.org/meme/, accessed on 8 April 2025) [26]. Gene structures (introns/exons) and conserved motifs were visualized using TBtools [24].

2.4. Cis-Acting Element Analysis of SnRK2 Promoters

Promoters (2000 bp upstream of transcription start sites) were extracted, and overlapping genes were excluded and analyzed for cis-acting elements using PlantCARE (https://bioinformatics.psb.ugent.be/webtools/plantcare/html/, accessed on 5 December 2024). The results were visualized with TBtools [24].

3. Results

3.1. Identification and Physicochemical Properties Analysis of SnRK2 Gene Family Members

In the present study, a total of 54 SnRK2 genes were identified in the genomes of four Nicotiana species. Among them, nine, twelve, fifteen, and eighteen SnRK2 gene family members were identified in the genome of Nicotiana tabacum (Ntab-TN90), Nicotiana benthamiana (NbLab360), Nicotiana sylvestris (ASM39365v2), and Nicotiana tomentosiformis (ASM39032v3), respectively. Physicochemical properties are summarized in Table 1. The numbers of amino acids encoded by these genes ranged from 96 to 363 aa; the molecular weight ranged from 10,805.51 to 41,475.91 Da; the isoelectric point ranged between 4.72 and 9.08; the stability index ranged from 34.78 to 59.18; the aliphatic index ranged from 78.69 to 94.10; and the average hydrophobicity ranged from −0.607 to 0.033.

3.2. Phylogenetic Tree Analysis

A phylogenetic tree was constructed for the SnRK2 proteins from Nicotiana benthamiana, Nicotiana sylvestris, Nicotiana tomentosiformis, and Nicotiana tabacum. The results showed that the SnRK2 proteins from the four Nicotiana species were divided into five major groups based on the main branches. Genes on the red branch exhibited a smaller evolutionary distance (0.0159) coupled with a higher bootstrap value (0.98). Those on the blue branch showed a moderate evolutionary distance (0.0293) and a high bootstrap value (1.00). In contrast, genes on the green branch displayed a moderate evolutionary distance (0.0214) but a lower bootstrap value (0.59). Genes residing on the yellow branch, however, had a larger evolutionary distance (0.0966) paired with a higher bootstrap value (0.98). Finally, genes on the purple branch were characterized by a larger evolutionary distance (0.0799) and a lower bootstrap value (0.59) (Figure 1). Among these groups, the largest group contained 18 members, while the smallest group had only 4 members.

3.3. The Conserved Motif and Gene Structure Analysis of the SnRK2 Family

The conserved motif analysis of SnRK2 proteins using TBtools software revealed that different SnRK2 proteins possess varying numbers of conserved motifs (Figure 2). Almost all motifs were conserved in the SnRK2 protein sequence except Motif 7 (Figure 2).
The analysis of eight motifs in the tobacco SnRK2 gene revealed that all motifs exhibited extremely low E-values (Figure 3), indicating high statistical significance. Structurally and functionally, the first four long motifs (width = 50) showed a close alignment between their number of sites (50–52) and width, while the fifth and sixth medium-length motifs (width = 41, sites = 51) displayed higher site density; among the seventh and eighth short motifs, the seventh (width = 29, sites = 29) had a site count equal to its length, and the eighth (width = 15, sites = 51) was notably short in length but exhibited exceptionally dense sites. Gene structure analysis showed that the 54 SnRK2 genes had intron numbers ranging from 0 to 10, with most containing 7 or 8 introns (Figure 4).

3.4. Cis-Acting Element Analysis of the SnRK2 Family

To investigate the regulatory roles of these genes, we performed cis-acting element analysis on the promoter sequences (2000 bp upstream) of the SnRK2 gene family using the online software PlantCARE, thereby predicting the potential biological functions of each gene (Figure 5). These cis-acting elements can be categorized into four groups based on their functional annotations: light-responsive elements, hormone-responsive elements (such as auxin, gibberellin, abscisic acid, and jasmonic acid), stress-responsive elements (including cold-responsive elements, defense and stress response elements, wound-responsive elements, antioxidant response elements, and hypoxia-specific induction elements), and development-related cis-acting elements (such as meristem expression or specific activation elements and MYB binding sites).
As shown in Figure 5, different genes contain various types of cis-acting elements. For example, some genes have light-responsive elements, indicating that their expression may be induced by light. Additionally, some genes contain cold-responsive elements, suggesting that they may function under low-temperature stress. Others have defense and stress response elements, indicating their potential roles in plant defense and stress responses. Furthermore, some genes contain antioxidant response elements, suggesting their involvement in antioxidant processes.

4. Discussion

The analysis of the physicochemical properties of the SnRK2 protein family revealed the molecular basis of its functional diversity and environmental adaptability. The wide variation in amino acid numbers and molecular weights among family members suggested functional differentiation through structural domain variations, such as the retention of the kinase core region or the extension of the C-terminal regulatory domain [27]. The significant range of isoelectric points reflected adaptations to subcellular microenvironments: nuclear-localized proteins with alkaline pI may regulate gene expression via charge interactions, while acidic pI members may participate in cytoplasmic signaling networks [28]. The distribution of stability indices implied that some proteins rely on chaperone molecules or post-translational modifications to maintain functional conformations, consistent with the dynamic regulation of kinase activity. High aliphatic indices and near-neutral average hydrophobicity values further supported their roles as soluble proteins functioning in the cytoplasm or cytoskeleton [18]. Subcellular localization predictions indicated that 31 members were localized to the cytoplasm (dominating signal transduction), 22 were enriched in the cytoskeleton (potentially involved in stress-induced cellular remodeling), and only one resides in the nucleus (likely directly regulating transcription) [28]. This spatial divergence may originate from subfunctionalization following gene duplication events, enabling the SnRK2 family to enhance regulatory plasticity through modular specialization for plant adaptation to complex stresses [27].
The identification of 54 SnRK2 genes across four Nicotiana species (Nicotiana tabacum: 9, Nicotiana benthamiana: 12, Nicotiana sylvestris: 15, and Nicotiana tomentosiformis: 18), combined with phylogenetic analysis of 54 SnRK2 proteins, reveals critical evolutionary and functional patterns. Genomic studies of the allotetraploid tobacco (Nicotiana tabacum) have revealed asymmetric genome remodeling during polyploidization [29]. The T subgenome (derived from N. tomentosiformis) exhibited extensive gene loss due to high elimination of repetitive sequences (e.g., LTR retrotransposons) [20,22] and epigenetic regulation (e.g., CHG methylation pattern changes) [30]. The retention of only nine SnRK2 family members in the tetraploid (far below the theoretical sum of 33 from its diploid progenitors) reflected evolutionary strategies of functional redundancy elimination and subgenome competitive silencing [31,32]. This reduction may be buffered by functional redundancy among retained SnRK2 paralogs, akin to compensatory mechanisms in maize, where duplicated ZmSnRK2 genes maintain stress resilience despite partial losses [17]. Such redundancy could permit subfunctionalization without compromising core kinase activities in N. tabacum. Research indicated that retained SnRK2 genes may adapt to polyploid complexity through subgenome expression bias (e.g., S-subgenome dominance in basal stress responses and T-subgenome specialization in environmental adaptation) [31,33] and neofunctionalization/subfunctionalization [32]. Their reduced copy number also implied artificial selection pressures—during domestication, stress-responsive genes less associated with agronomic traits (e.g., leaf width [34], metabolic regulation [35]) were likely pruned due to “trade-off” costs, while polygenic coordination of minor-effect alleles (e.g., interaction with Arf9 [34]) emerged as the mainstream phenotypic regulatory mechanism [36,37]. Phylogenetic clustering into five groups—with extreme size variation (largest group: 18 members; smallest: 4)—suggests distinct evolutionary trajectories: expanded clades may reflect adaptive gene duplication for broad stress responses (e.g., drought/osmotic signaling) [38], while minimal groups represent conserved, functionally specialized modules [39]. Species-specific gene counts correlate with ecological adaptation [40], such as the high gene number (18) of Nicotiana tomentosiformis, potentially linked to its native Andean highland habitat, whereas laboratory-adapted Nicotiana benthamiana (12 genes) showed accelerated redundancy loss under artificial selection. Technical limitations (e.g., incomplete annotation of Nicotiana tabacum complex genome) may partially explain observed disparities. Collectively, these findings illustrate how polyploidy-driven genome remodeling, ecological pressures, and functional diversification shape SnRK2 family dynamics, providing insights into the evolutionary optimization of plant stress–response networks.
The SnRK2 gene family maintains its core functions through highly conserved motifs (e.g., Motif 3 and Motif 4), which likely participate in critical processes such as kinase activity, ATP binding, or substrate recognition [17]. Gene structure analysis reveals that the significant variation in intron numbers (0–10) may reflect regulatory complexity: genes with more introns might generate diverse transcripts through alternative splicing to adapt to environmental changes, while intronless genes could rapidly respond to stress via immediate transcription [41]. The distribution of UTR regions (particularly the absence of 5′ UTR in some genes) further highlights their importance in regulating mRNA stability or translation efficiency. Cis-acting element analysis uncovers a multidimensional regulatory network of SnRK2 genes [27]: the coexistence of hormone-responsive elements (e.g., ABA and JA) indicates their ability to integrate multiple signaling pathways to coordinate plant responses to biotic and abiotic stresses [42]; elements related to low temperature, antioxidant defense, and pathogen resistance point to their critical roles in cold acclimation, ROS scavenging, and disease resistance; and light-responsive and development-associated elements (e.g., G-box and MYB binding sites) suggest that SnRK2 may balance growth and stress adaptation through crosstalk between photoperiod signaling and developmental regulation. However, these predictions require experimental validation (e.g., promoter activity assays or protein interaction studies). Future work should target metabolites in SnRK2-linked pathways: osmoprotectants (proline/glycine betaine), antioxidant pools (glutathione–ascorbate), and ion transporters (SOS1 and NHX) to elucidate the adaptive evolutionary mechanisms of the SnRK2 family and its potential applications in crop stress-resistance breeding [43].

5. Conclusions

In this study, the genome-wide identification of 54 SnRK2 genes across four Nicotiana species revealed significant evolutionary divergence. Phylogenetic clustering into five groups demonstrated asymmetric gene retention in the allotetraploid N. tabacum (nine genes), reflecting polyploidy-driven subgenome silencing and functional specialization. In silico analysis of promoters uncovered enrichment of stress/hormone-responsive cis-elements (e.g., ABRE, MYB, and antioxidant motifs), implicating SnRK2s in integrated stress signaling. Structural diversity—including variable intron numbers (0–10) and conserved kinase domains—suggested mechanisms for functional plasticity. These findings provide a genomic framework for understanding SnRK2-mediated stress adaptation in Nicotiana. Future work should prioritize functional validation of candidate genes (e.g., cytoskeleton-localized members) and cross-species transfer of stress-resilient alleles to crops.

Author Contributions

Conceptualization, Y.T. and J.F.; formal analysis, Y.T. and Y.Z.; resources, J.F. and Z.H.; writing—original draft preparation, Y.T.; writing—review and editing, X.Y., Z.H., and R.H.; supervision, J.F.; validation, R.H. All authors have read and agreed to the published version of the manuscript.

Funding

This work was funded by the Jiangsu Students’ Platform for Innovation and Entrepreneurship Training Program (202411117138Y).

Institutional Review Board Statement

Not applicable.

Data Availability Statement

The data are contained within the article.

Acknowledgments

We are grateful to the Hunan Tobacco Research Institute for providing plant materials.

Conflicts of Interest

The authors declare no conflicts of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

References

  1. FAO. Global Status of Salt-Affected Soils—Main Report; FAO: Rome, Italy, 2024. [Google Scholar] [CrossRef]
  2. Acosta-Motos, J.R.; Ortuño, M.F.; Bernal-Vicente, A.; Diaz-Vivancos, P.; Sanchez-Blanco, M.J.; Hernandez, J.A. Plant Responses to Salt Stress: Adaptive Mechanisms. Agronomy 2017, 7, 38. [Google Scholar] [CrossRef]
  3. Munns, R.; Tester, M. Mechanisms of salinity tolerance. Annu. Rev. Plant Biol. 2008, 59, 651–681. [Google Scholar] [CrossRef]
  4. Tunçturk, M.; Tunçturk, R.; Yasar, F. Changes in micronutrients, dry weight and plant growth of soybean (Glycine max L. Merrill) cultivars under salt stress. Afr. J. Biotechnol. 2008, 7, 1650–1654. [Google Scholar]
  5. Boopal, J.; Sathee, L.; Ramasamy, R.; Pandey, R.; Chinnusamy, V. Influence of Incremental Short Term Salt Stress at the Seedling Stage on Root Plasticity, Shoot Thermal Profile and Ion Homeostasis in Contrasting Wheat Genotypes. Agriculture 2023, 13, 20. [Google Scholar] [CrossRef]
  6. Duarte, B.; Sleimi, N.; Cacador, I. Biophysical and biochemical constraints imposed by salt stress: Learning from halophytes. Front. Plant Sci. 2014, 5, 746. [Google Scholar] [CrossRef]
  7. Zhao, C.Z.; Zhang, H.; Song, C.P.; Zhu, J.K.; Shabala, S. Mechanisms of Plant Responses and Adaptation to Soil Salinity. Innovation 2020, 1, 41. [Google Scholar] [CrossRef]
  8. Fujii, H.; Verslues, P.E.; Zhu, J.-K. Arabidopsis decuple mutant reveals the importance of SnRK2 kinases in osmotic stress responses in vivo. Proc. Natl. Acad. Sci. USA 2011, 108, 1717–1722. [Google Scholar] [CrossRef]
  9. Kulik, A.; Wawer, I.; Krzywinska, E.; Bucholc, M.; Dobrowolska, G. SnRK2 Protein Kinases-Key Regulators of Plant Response to Abiotic Stresses. Omics 2011, 15, 859–872. [Google Scholar] [CrossRef]
  10. Hrabak, E.M.; Chan, C.W.M.; Gribskov, M.; Harper, J.F.; Choi, J.H.; Halford, N.; Kudla, J.; Luan, S.; Nimmo, H.G.; Sussman, M.R.; et al. The Arabidopsis CDPK-SnRK Superfamily of Protein Kinases. Plant Physiol. 2003, 132, 666–680. [Google Scholar] [CrossRef]
  11. Anderberg, R.J.; Walker-Simmons, M.K. Isolation of a wheat cDNA clone for an abscisic acid-inducible transcript with homology to protein kinases. Proc. Natl. Acad. Sci. USA 1992, 89, 10183–10187. [Google Scholar] [CrossRef]
  12. Yoshida, T.; Mogami, J.; Yamaguchi-Shinozaki, K. ABA-dependent and ABA-independent signaling in response to osmotic stress in plants. Curr. Opin. Plant Biol. 2014, 21, 133–139. [Google Scholar] [CrossRef] [PubMed]
  13. Boudsocq, M.; Barbier-Brygoo, H.; Laurière, C. Identification of nine sucrose nonfermenting 1-related protein kinases 2 activated by hyperosmotic and saline stresses in Arabidopsis thaliana. J. Biol. Chem. 2004, 279, 41758–41766. [Google Scholar] [CrossRef]
  14. Lim, C.W.; Baek, W.; Lee, S.C. Two pepper subclass II SnRK2 genes positively regulate drought stress response, with differential responsiveness to abscisic acid. Plant Physiol. Biochem. 2025, 220, 109477. [Google Scholar] [CrossRef] [PubMed]
  15. Liu, H.; Wang, X.; Zhu, X.; Zhang, D.; Wang, Y.; Wang, T.; Chen, L.; Wang, B.; Wei, X. Meta-analysis of SnRK2 gene overexpression in response to drought and salt stress. Physiol. Plant. 2024, 176, e14578. [Google Scholar] [CrossRef] [PubMed]
  16. Hasan, M.M.; Liu, X.-D.; Waseem, M.; Guang-Qian, Y.; Alabdallah, N.M.; Jahan, M.S.; Fang, X.-W. ABA activated SnRK2 kinases: An emerging role in plant growth and physiology. Plant Signal. Behav. 2022, 17, 2071024. [Google Scholar] [CrossRef]
  17. Long, T.; Xu, B.; Hu, Y.; Wang, Y.; Mao, C.; Wang, Y.; Zhang, J.; Liu, H.; Huang, H.; Liu, Y.; et al. Genome-wide identification of ZmSnRK2 genes and functional analysis of ZmSnRK2.10 in ABA signaling pathway in maize (Zea mays L). BMC Plant Biol. 2021, 21, 309. [Google Scholar] [CrossRef]
  18. Yin, S.; Ma, H.; Ye, Q.; Lu, H.; Wang, K.; Kong, S.; Hou, D.; Li, X.; Lin, X. Identification of SnRK2 family and functional study of PeSnRK2.2A and PeSnRK2.2B for drought resistance in Phyllostachys edulis. Ind. Crops Prod. 2024, 219, 119087. [Google Scholar] [CrossRef]
  19. Li, Q.; Hu, T.; Lu, T.; Yu, B.; Zhao, Y. Calcium-dependent protein kinases CPK3/4/6/11 and 27 respond to osmotic stress and activate SnRK2s in Arabidopsis. Dev. Cell 2025, 60, 1423–1438. [Google Scholar] [CrossRef]
  20. Sierro, N.; Battey, J.N.D.; Ouadi, S.; Bakaher, N.; Bovet, L.; Willig, A.; Goepfert, S.; Peitsch, M.C.; Ivanov, N.V. The tobacco genome sequence and its comparison with those of tomato and potato. Nat. Commun. 2014, 5, 3833. [Google Scholar] [CrossRef]
  21. Leitch, I.J.; Hanson, L.; Lim, K.Y.; Kovarik, A.; Chase, M.W.; Clarkson, J.J.; Leitch, A.R. The Ups and Downs of Genome Size Evolution in Polyploid Species of Nicotiana (Solanaceae). Ann. Bot. 2008, 101, 805–814. [Google Scholar] [CrossRef]
  22. Renny-Byfield, S.; Chester, M.; Kovařík, A.; Le Comber, S.C.; Grandbastien, M.-A.; Deloger, M.; Nichols, R.A.; Macas, J.; Novák, P.; Chase, M.W.; et al. Next Generation Sequencing Reveals Genome Downsizing in Allotetraploid Nicotiana tabacum, Predominantly through the Elimination of Paternally Derived Repetitive DNAs. Mol. Biol. Evol. 2011, 28, 2843–2854. [Google Scholar] [CrossRef] [PubMed]
  23. Fernandez-Pozo, N.; Menda, N.; Edwards, J.D.; Saha, S.; Tecle, I.Y.; Strickler, S.R.; Bombarely, A.; Fisher-York, T.; Pujar, A.; Foerster, H.; et al. The Sol Genomics Network (SGN)—From genotype to phenotype to breeding. Nucleic Acids Res. 2014, 43, D1036–D1041. [Google Scholar] [CrossRef] [PubMed]
  24. Chen, C.; Wu, Y.; Li, J.; Wang, X.; Zeng, Z.; Xu, J.; Liu, Y.; Feng, J.; Chen, H.; He, Y.; et al. TBtools-II: A “one for all, all for one” bioinformatics platform for biological big-data mining. Mol. Plant 2023, 16, 1733–1742. [Google Scholar] [CrossRef] [PubMed]
  25. Tamura, K.; Stecher, G.; Kumar, S. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol. Biol. Evol. 2021, 38, 3022–3027. [Google Scholar] [CrossRef]
  26. Bailey, T.L.; Johnson, J.; Grant, C.E.; Noble, W.S. The MEME Suite. Nucleic Acids Res. 2015, 43, W39–W49. [Google Scholar] [CrossRef]
  27. Ahmed, B.; Hasan, F.; Tabassum, A.; Ahmed, R.; Hassan, R.; Amin, M.R.; Alam, M. Genome-wide investigation of SnRK2 gene family in two jute species: Corchorus olitorius and Corchorus capsularis. J. Genet. Eng. Biotechnol. 2023, 21, 5. [Google Scholar] [CrossRef]
  28. Mathura, S.R.; Sutton, F.; Bowrin, V. Characterization and expression analysis of SnRK2, PYL, and ABF/ AREB/ ABI5 gene families in sweet potato. PLoS ONE 2023, 18, e0288481. [Google Scholar] [CrossRef]
  29. Zan, Y.; Chen, S.; Ren, M.; Liu, G.; Liu, Y.; Han, Y.; Dong, Y.; Zhang, Y.; Si, H.; Liu, Z.; et al. The genome and GeneBank genomics of allotetraploid Nicotiana tabacum provide insights into genome evolution and complex trait regulation. Nat. Genet. 2025, 57, 986–996. [Google Scholar] [CrossRef]
  30. Li, N.; Xu, C.; Zhang, A.; Lv, R.; Meng, X.; Lin, X.; Gong, L.; Wendel, J.F.; Liu, B. DNA methylation repatterning accompanying hybridization, whole genome doubling and homoeolog exchange in nascent segmental rice allotetraploids. New Phytol. 2019, 223, 979–992. [Google Scholar] [CrossRef]
  31. Edger, P.P.; Smith, R.; McKain, M.R.; Cooley, A.M.; Vallejo-Marin, M.; Yuan, Y.; Bewick, A.J.; Ji, L.; Platts, A.E.; Bowman, M.J.; et al. Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower. Plant Cell 2017, 29, 2150–2167. [Google Scholar] [CrossRef]
  32. Bird, K.A.; Niederhuth, C.E.; Ou, S.; Gehan, M.; Pires, J.C.; Xiong, Z.; VanBuren, R.; Edger, P.P. Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus. New Phytol. 2021, 230, 354–371. [Google Scholar] [CrossRef] [PubMed]
  33. Burns, R.; Mandáková, T.; Gunis, J.; Soto-Jiménez, L.M.; Liu, C.; Lysak, M.A.; Novikova, P.Y.; Nordborg, M. Gradual evolution of allopolyploidy in Arabidopsis suecica. Nat. Ecol. Evol. 2021, 5, 1367–1381. [Google Scholar] [CrossRef] [PubMed]
  34. Shi, R.; Jin, J.; Nifong, J.M.; Shew, D.; Lewis, R.S. Homoeologous chromosome exchange explains the creation of a QTL affecting soil-borne pathogen resistance in tobacco. Plant Biotechnol. J. 2022, 20, 47–58. [Google Scholar] [CrossRef] [PubMed]
  35. Yuan, G.; Sun, K.; Yu, W.; Jiang, Z.; Jiang, C.; Liu, D.; Wen, L.; Si, H.; Wu, F.; Meng, H.; et al. Development of a MAGIC population and high-resolution quantitative trait mapping for nicotine content in tobacco. Front. Plant Sci. 2022, 13, 1086950. [Google Scholar] [CrossRef]
  36. Schulthess, A.W.; Kale, S.M.; Liu, F.; Zhao, Y.; Philipp, N.; Rembe, M.; Jiang, Y.; Beukert, U.; Serfling, A.; Himmelbach, A.; et al. Genomics-informed prebreeding unlocks the diversity in genebanks for wheat improvement. Nat. Genet. 2022, 54, 1544–1552. [Google Scholar] [CrossRef]
  37. Milner, S.G.; Jost, M.; Taketa, S.; Mazón, E.R.; Himmelbach, A.; Oppermann, M.; Weise, S.; Knüpffer, H.; Basterrechea, M.; König, P.; et al. Genebank genomics highlights the diversity of a global barley collection. Nat. Genet. 2019, 51, 319–326. [Google Scholar] [CrossRef]
  38. Du, L.; Ma, Z.; Mao, H. Duplicate Genes Contribute to Variability in Abiotic Stress Resistance in Allopolyploid Wheat. Plants 2023, 12, 2465. [Google Scholar] [CrossRef]
  39. Lin, Z.; Li, Y.; Wang, Y.; Liu, X.; Ma, L.; Zhang, Z.; Mu, C.; Zhang, Y.; Peng, L.; Xie, S.; et al. Initiation and amplification of SnRK2 activation in abscisic acid signaling. Nat. Commun. 2021, 12, 2456. [Google Scholar] [CrossRef]
  40. Suryawanshi, V.; Talke, I.N.; Weber, M.; Eils, R.; Brors, B.; Clemens, S.; Krämer, U. Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri. BMC Genom. 2016, 17, 1034. [Google Scholar] [CrossRef]
  41. Liu, Z.; Ge, X.; Yang, Z.; Zhang, C.; Zhao, G.; Chen, E.; Liu, J.; Zhang, X.; Li, F. Genome-wide identification and characterization of SnRK2 gene family in cotton (Gossypium hirsutum L.). BMC Genet. 2017, 18, 54. [Google Scholar] [CrossRef]
  42. Chen, G.; Wang, J.; Qiao, X.; Jin, C.; Duan, W.; Sun, X.; Wu, J. Genome-wide survey of sucrose non-fermenting 1-related protein kinase 2 in Rosaceae and expression analysis of PbrSnRK2 in response to ABA stress. BMC Genom. 2020, 21, 781. [Google Scholar] [CrossRef] [PubMed]
  43. Wan, Z.; Luo, S.; Zhang, Z.; Liu, Z.; Qiao, Y.; Gao, X.; Yu, J.; Zhang, G. Identification and expression profile analysis of the SnRK2 gene family in cucumber. PeerJ 2022, 10, e13994. [Google Scholar] [CrossRef] [PubMed]
Agriculture 15 01396 g001
Figure 1. Phylogenetic analysis of SnRK2 proteins from Nicotiana benthamiana, Nicotiana sylvestris, Nicotiana tomentosiformis, and Nicotiana tabacum. The MEGA 11.0 program was used to generate the unrooted phylogenetic tree using the neighbor-joining method with 1000 bootstrap replicates. The evolutionary distances were computed using the Poisson correction method.
Figure 1. Phylogenetic analysis of SnRK2 proteins from Nicotiana benthamiana, Nicotiana sylvestris, Nicotiana tomentosiformis, and Nicotiana tabacum. The MEGA 11.0 program was used to generate the unrooted phylogenetic tree using the neighbor-joining method with 1000 bootstrap replicates. The evolutionary distances were computed using the Poisson correction method.
Agriculture 15 01396 g001
Agriculture 15 01396 g002
Figure 2. Phylogenetic tree, motif analysis, and domain of SnRK2s: (a) phylogenetic analysis of SnRK2s using the neighbor-joining method; (b) SnRK2 protein motifs were analyzed using TBtools. The order of the motifs corresponds to their position in the protein sequence. Conserved motifs are shown in different colored boxes; (c) domain of SnRK2 genes.
Figure 2. Phylogenetic tree, motif analysis, and domain of SnRK2s: (a) phylogenetic analysis of SnRK2s using the neighbor-joining method; (b) SnRK2 protein motifs were analyzed using TBtools. The order of the motifs corresponds to their position in the protein sequence. Conserved motifs are shown in different colored boxes; (c) domain of SnRK2 genes.
Agriculture 15 01396 g002
Agriculture 15 01396 g003
Figure 3. Detailed information on conserved motifs owned by deduced SnRK2 family proteins in tobacco. The numbers on the left side represent 8 different motifs, which correspond to Motif 1 to Motif 8 in Figure 2. The letters with different sizes and colors imply the types of amino acid residues and predicted reliability in the logo of each conserved motif.
Figure 3. Detailed information on conserved motifs owned by deduced SnRK2 family proteins in tobacco. The numbers on the left side represent 8 different motifs, which correspond to Motif 1 to Motif 8 in Figure 2. The letters with different sizes and colors imply the types of amino acid residues and predicted reliability in the logo of each conserved motif.
Agriculture 15 01396 g003
Agriculture 15 01396 g004
Figure 4. The gene structure of SnRK2s. CDS and UTR are represented by yellow rectangles and green rectangles, respectively. Introns are shown with black lines.
Figure 4. The gene structure of SnRK2s. CDS and UTR are represented by yellow rectangles and green rectangles, respectively. Introns are shown with black lines.
Agriculture 15 01396 g004
Agriculture 15 01396 g005
Figure 5. Cis-acting regulatory elements in the promoters of SnRK2 family genes. Different colors represent various types of regulatory elements and their positions in the promoter regions.
Figure 5. Cis-acting regulatory elements in the promoters of SnRK2 family genes. Different colors represent various types of regulatory elements and their positions in the promoter regions.
Agriculture 15 01396 g005
Table 1. The computed physicochemical parameters of identified SnRK2 proteins in tobacco species.
Table 1. The computed physicochemical parameters of identified SnRK2 proteins in tobacco species.
Sequence IDTobacco SpeciesNumber of Amino AcidsMolecular WeightTheoretical pIInstability IndexAliphatic IndexGrand Average of HydropathicitySubcellular Localization
NbL01g02360.1N. benthamiana36341,310.024.8838.2689.42−0.3cyto
NbL01g13690.1N. benthamiana35540,881.365.7953.2879.38−0.578cysk
NbL05g01010.1N. benthamiana35340,709.335.7848.3982.04−0.488cysk
NbL06g14250.1N. benthamiana17019,773.529.0843.0581.94−0.46cyto
NbL07g02500.1N. benthamiana35440,337.964.7242.4688.64−0.331cysk
NbL07g15210.1N. benthamiana36241,001.654.9434.7887.54−0.284cyto
NbL11g09710.1N. benthamiana36341,3334.9341.1788.35−0.333cyto
NbL11g11750.1N. benthamiana35941,475.915.4558.2478.77−0.607cysk
NbL15g05780.1N. benthamiana35440,856.515.7152.1382.06−0.511cysk
XP_009591903.1N. tomentosiformis35440,346.974.7641.9188.64−0.33cysk
XP_009601198.1N. tomentosiformis36341,303.034.9240.6788.62−0.305cyto
XP_009601199.1N. tomentosiformis36341,303.034.9240.6788.62−0.305cyto
XP_009601200.1N. tomentosiformis36341,303.034.9240.6788.62−0.305cyto
XP_009601202.1N. tomentosiformis36341,303.034.9240.6788.62−0.305cyto
XP_009601520.1N. tomentosiformis36241,060.554.8635.7589.14−0.318cyto
XP_009601521.1N. tomentosiformis36241,060.554.8635.7589.14−0.318cyto
XP_009601522.1N. tomentosiformis36241,060.554.8635.7589.14−0.318cyto
XP_009602813.1N. tomentosiformis35540,839.365.7952.3979.38−0.575cysk
XP_009621087.1N. tomentosiformis35340,775.395.7851.3481.47−0.508cysk
XP_018632104.1N. tomentosiformis35340,775.395.7851.3481.47−0.508cysk
XP_033508174.1N. tomentosiformis9610,805.518.5149.1493.440.033nucl
XP_033512100.1N. tomentosiformis35240,243.774.9241.9788.89−0.339cysk
XP_033512101.1N. tomentosiformis35240,243.774.9241.9788.89−0.339cysk
XP_033516221.1N. tomentosiformis28232,332.885.1536.1189.54−0.307cyto
XP_009774098.1N. sylvestris36341,302.914.9341.1788.35−0.34cyto
XP_009774100.1N. sylvestris36341,302.914.9341.1788.35−0.34cyto
XP_009774101.1N. sylvestris36341,302.914.9341.1788.35−0.34cyto
XP_009774102.1N. sylvestris36341,302.914.9341.1788.35−0.34cyto
XP_009774903.1N. sylvestris21324,636.795.0459.1878.69−0.57cyto
XP_009776074.1N. sylvestris35641,082.545.6456.1279.16−0.595cysk
XP_009777005.1N. sylvestris35440,337.964.7242.4688.64−0.331cysk
XP_009786561.1N. sylvestris36240,964.524.8635.0388.34−0.295cyto
XP_009786562.1N. sylvestris36240,964.524.8635.0388.34−0.295cyto
XP_009786563.1N. sylvestris36240,964.524.8635.0388.34−0.295cyto
XP_009804586.1N. sylvestris35440,890.525.751.4581.24−0.515cysk
XP_009804587.1N. sylvestris35440,890.525.751.4581.24−0.515cysk
XP_016440803.1N. tabacum35340,789.425.7851.8981.47−0.508cysk
XP_016443905.1N. tabacum36341,302.914.9341.1788.35−0.34cyto
XP_016443906.1N. tabacum36341,302.914.9341.1788.35−0.34cyto
XP_016443907.1N. tabacum36341,302.914.9341.1788.35−0.34cyto
XP_016443908.1N. tabacum36341,302.914.9341.1788.35−0.34cyto
XP_016468367.1N. tabacum34439,333.794.9241.1290.12−0.315cysk
XP_016468369.1N. tabacum31535,951.044.8546.8994.1−0.225cyto
XP_016469069.1N. tabacum35641,082.545.6456.1279.16−0.595cysk
XP_016469733.1N. tabacum35440,337.964.7242.4688.64−0.331cysk
XP_016487598.1N. tabacum36241,060.554.8635.7589.14−0.318cyto
XP_016487599.1N. tabacum29132,941.695.8736.4289.42−0.234cyto
XP_016490562.1N. tabacum33638,722.135.7552.6781.85−0.49cysk
XP_016499197.1N. tabacum35540,839.365.7952.3979.38−0.575cysk
XP_016501298.1N. tabacum28232,366.895.1535.2588.51−0.312cyto
XP_016506694.1N. tabacum36240,964.524.8635.0388.34−0.295cyto
XP_016506695.1N. tabacum36240,964.524.8635.0388.34−0.295cyto
XP_016506696.1N. tabacum36240,964.524.8635.0388.34−0.295cyto
XP_016510127.1N. tabacum35440,337.964.7242.4688.64−0.331cysk
Note: Cyto: cytoplasm; Cysk: cytoskeleton; Nucl: nucleus.
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

MDPI and ACS Style

Tang, Y.; Zhang, Y.; Hu, Z.; Yan, X.; Hu, R.; Fan, J. Genome-Wide Identification and Evolutionary Analysis of the SnRK2 Gene Family in Nicotiana Species. Agriculture 2025, 15, 1396. https://doi.org/10.3390/agriculture15131396

AMA Style

Tang Y, Zhang Y, Hu Z, Yan X, Hu R, Fan J. Genome-Wide Identification and Evolutionary Analysis of the SnRK2 Gene Family in Nicotiana Species. Agriculture. 2025; 15(13):1396. https://doi.org/10.3390/agriculture15131396

Chicago/Turabian Style

Tang, Yu, Yangxin Zhang, Zhengrong Hu, Xuebing Yan, Risheng Hu, and Jibiao Fan. 2025. "Genome-Wide Identification and Evolutionary Analysis of the SnRK2 Gene Family in Nicotiana Species" Agriculture 15, no. 13: 1396. https://doi.org/10.3390/agriculture15131396

APA Style

Tang, Y., Zhang, Y., Hu, Z., Yan, X., Hu, R., & Fan, J. (2025). Genome-Wide Identification and Evolutionary Analysis of the SnRK2 Gene Family in Nicotiana Species. Agriculture, 15(13), 1396. https://doi.org/10.3390/agriculture15131396

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop