Integrative Analysis Provides Insights into Genes Encoding LEA_5 Domain-Containing Proteins in Tigernut (Cyperus esculentus L.)
Abstract
1. Introduction
2. Results
2.1. Characterization of Four LEA_5 Family Genes in Tigernut
2.2. Characterization of LEA_5 Genes from Representative Plant Species and Insights into Lineage-Specific Family Evolution
2.3. CeLEA5 Genes Have Evolved to Be Preferentially Expressed in Tigernut Tubers
2.4. CeLEA5 Genes Were Expressed More than Their Orthologs in C. rotundus
2.5. Transcripts of Most CeLEA5 Genes Were Gradually Upregulated During Tuber Development
3. Discussion
3.1. The Tigernut Genome Encodes a High Number of Four LEA_5 Genes, and the Family Expansion Was Contributed by Dispersed Duplication
3.2. Comparative Genomics Analysis Reveals the Monogenic Origin and Lineage-Specific Evolution of the LEA_5 Family in Poales
3.3. CeLEA5 Genes Underwent Apparent Expression and Functional Divergence
4. Conclusions
5. Materials and Methods
5.1. Identification of LEA_5 Family Genes from Datasets
5.2. Phylogenetic and Conserved Motif Analyses
5.3. Synteny Analysis and Definition of Orthogroups
5.4. Plant Materials
5.5. Gene Expression Analysis Based on RNA-Seq
5.6. Gene Expression Analysis Based on qRT-PCR
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Mistry, J.; Chuguransky, S.; Williams, L.; Qureshi, M.; Salazar, G.A.; Sonnhammer, E.L.L.; Tosatto, S.C.E.; Paladin, L.; Raj, S.; Richardson, L.J.; et al. Pfam: The protein families database in 2021. Nucleic Acids Res. 2021, 49, D412–D419. [Google Scholar] [CrossRef] [PubMed]
- Cuming, A.C.; Lane, B.G. Protein synthesis in imbibing wheat embryos. Eur. J. Biochem. 1979, 99, 217–224. [Google Scholar] [CrossRef] [PubMed]
- Baker, J.; Van Dennsteele, C.; Dure, L., III. Sequence and characterization of 6 Lea proteins and their genes from cotton. Plant Mol. Biol. 1988, 11, 277–291. [Google Scholar] [CrossRef] [PubMed]
- Campos, F.; Cuevas-Velazquez, C.; Fares, M.A.; Reyes, J.L.; Covarrubias, A.A. Group 1 LEA proteins, an ancestral plant protein group, are also present in other eukaryotes, and in the archeae and bacteria domains. Mol. Genet. Genomics 2013, 288, 503–517. [Google Scholar] [CrossRef]
- Artur, M.A.S.; Zhao, T.; Ligterink, W.; Schranz, E.; Hilhorst, H.W. Dissecting the genomic diversification of late embryogenesis abundant (LEA) protein gene families in plants. Genome Biol. Evol. 2019, 11, 459–471. [Google Scholar] [CrossRef]
- McCubbin, W.D.; Kay, C.M.; Lane, B.G. Hydrodynamic and optical properties of the wheat-germ Em protein. Can. J. Biochem. Cell Biol. 1985, 63, 803–811. [Google Scholar] [CrossRef]
- Russouw, P.S.; Farrant, J.; Brandt, W.; Lindsey, G.G. The most prevalent protein in a heat-treated extract of pea (Pisum sativum) embryos is an LEA group I protein; its conformation is not affected by exposure to high temperature. Seed Sci. Res. 1997, 7, 117–123. [Google Scholar] [CrossRef]
- Soulages, J.L.; Kim, K.; Walters, C.; Cushman, J.C. Temperature-induced extended helix/random coil transitions in a group 1 late embryogenesis-abundant protein from soybean. Plant Physiol. 2002, 128, 822–832. [Google Scholar] [CrossRef]
- Williams, M.E.; Tsang, A. A maize gene expressed during embryogenesis is abscisic acid-inducible and highly conserved. Plant Mol. Biol. 1991, 16, 919–923. [Google Scholar] [CrossRef]
- Gaubier, P.; Raynal, M.; Hull, G.; Huestis, G.M.; Grellet, F.; Arenas, C.; Pages, C.; Delseny, M. Two different Em-like genes are expressed in Arabidopsis thaliana seeds during maturation. Mol. Gen. Genet. 1993, 238, 409–418. [Google Scholar] [CrossRef]
- Stacy, R.A.; Espelund, M.; Saebøe-Larssen, S.; Hollung, K.; Helliesen, E.; Jakobsen, K.S. Evolution of the Group 1 late embryogenesis abundant (Lea) genes: Analysis of the Lea B19 gene family in barley. Plant Mol. Biol. 1995, 28, 1039–1054. [Google Scholar] [CrossRef] [PubMed]
- Wang, X.S.; Zhu, H.B.; Jin, G.L.; Liu, H.L.; Wu, W.R.; Zhu, J. Genome-scale identification and analysis of LEA genes in rice (Oryza sativa L.). Plant. Sci. 2007, 172, 414–420. [Google Scholar] [CrossRef]
- Zou, Z.; Huang, Q.X.; An, F. Genome-wide identification, classification and phylogenetic analysis of LEA gene family in castor bean (Ricinus communis L.). Chin. J. Oil Crop. Sci. 2013, 35, 637–643. [Google Scholar]
- Zou, Z.; Guo, J.Y.; Zheng, Y.J.; Xiao, Y.H.; Guo, A.P. Genomic analysis of LEA genes in Carica papaya and insight into lineage-specific family evolution in Brassicales. Life 2022, 12, 1453. [Google Scholar] [CrossRef]
- Wu, C.; Hu, W.; Yan, Y.; Tie, W.; Ding, Z.; Guo, J.; He, G. The late embryogenesis abundant protein family in cassava (Manihot esculenta Crantz): Genome-wide characterization and expression during abiotic stress. Molecules 2018, 23, 1196. [Google Scholar] [CrossRef]
- Morris, P.C.; Kumar, A.; Bowles, D.J.; Cuming, A.C. Osmotic stress and abscisic acid induce expression of the wheat Em genes. Eur. J. Biochem. 1990, 190, 625–630. [Google Scholar] [CrossRef]
- Espelund, M.; Saebøe-Larssen, S.; Hughes, D.W.; Galau, G.A.; Larsen, F.; Jakobsen, K.S. Late embryogenesis-abundant genes encoding proteins with different numbers of hydrophilic repeats are regulated differentially by abscisic acid and osmotic stress. Plant J. 1992, 2, 241–252. [Google Scholar] [CrossRef]
- Miyoshi, K.; Kagaya, Y.; Ogawa, Y.; Nagato, Y.; Hattori, T. Temporal and spatial expression pattern of the OSVP1 and OSEM genes during seed development in rice. Plant Cell Physiol. 2002, 43, 307–313. [Google Scholar] [CrossRef]
- Manfre, A.J.; Lanni, L.M.; Marcotte, W.R. The Arabidopsis group 1 LATE EMBRYOGENESIS ABUNDANT protein ATEM6 is required for normal seed development. Plant Physiol. 2006, 140, 140–149. [Google Scholar] [CrossRef]
- Manfre, A.J.; LaHatte, G.A.; Climer, C.R.; Marcotte, W.R. Seed dehydration and the establishment of desiccation tolerance during seed maturation is altered in the Arabidopsis thaliana mutant atem6-1. Plant Cell Physiol. 2009, 50, 243–253. [Google Scholar] [CrossRef]
- Vicient, C.M.; Hull, G.; Guilleminot, J.; Devic, M.; Delseny, M. Differential expression of the Arabidopsis genes coding for Em-like proteins. J. Exp. Bot. 2000, 51, 1211–1220. [Google Scholar] [CrossRef] [PubMed]
- Hundertmark, M.; Hincha, D.K. LEA (late embryogenesis abundant) proteins and their encoding genes in Arabidopsis thaliana. BMC Genom. 2008, 9, 118. [Google Scholar] [CrossRef] [PubMed]
- McCarty, D.R.; Hattori, T.; Carson, C.B.; Vasil, V.; Lazar, M.; Vasil, I.K. The Viviparous-1 developmental gene of maize encodes a novel transcriptional activator. Cell 1991, 66, 895–905. [Google Scholar] [CrossRef]
- Giraudat, J.; Hauge, B.M.; Valon, C.; Smalle, J.; Parcy, F.; Goodman, H.M. Isolation of the Arabidopsis ABI3 gene by positional cloning. Plant Cell 1992, 4, 1251–1261. [Google Scholar] [CrossRef]
- Hattori, T.; Terada, T.; Hamasuna, S. Regulation of the Osem gene by abscisic acid and the transcriptional activator VP1: Analysis of cis-acting promoter elements required for regulation by abscisic acid and VP1. Plant J. 1995, 7, 913–925. [Google Scholar] [CrossRef]
- Zou, Z.; Xiao, Y.; Zhang, L.; Zhao, Y. Analysis of Lhc family genes reveals development regulation and diurnal fluctuation expression patterns in Cyperus esculentus, a Cyperaceae plant. Planta 2023, 257, 59. [Google Scholar] [CrossRef]
- Zou, Z.; Zheng, Y.J.; Xiao, Y.H.; Liu, H.Y.; Huang, J.Q.; Zhao, Y.G. Molecular insights into PIP aquaporins in tigernut (Cyperus esculentus L.), a Cyperaceae tuber plant. Tropical Plants 2024, 3, e027. [Google Scholar] [CrossRef]
- Zou, Z.; Fu, X.; Li, C.; Yi, X.; Huang, J.; Zhao, Y. Insights into the stearoyl-acyl carrier protein desaturase (SAD) family in tigernut (Cyperus esculentus L.), an oil-bearing tuber plant. Plants 2025, 14, 584. [Google Scholar] [CrossRef]
- Makareviciene, V.; Gumbytea, M.; Yunik, A. Opportunities for the use of chufa sedge in biodiesel production. Ind. Crop. Prod. 2013, 50, 633–637. [Google Scholar] [CrossRef]
- Codina-Torrella, I.; Guamis, B.; Trujillo, A.J. Characterization and comparison of tiger nuts (Cyperus esculentus L.) from different geographical origin. Ind. Crop. Prod. 2015, 65, 406–414. [Google Scholar] [CrossRef]
- Yang, X.; Niu, L.; Zhang, Y.; Ren, W.; Yang, C.; Yang, J.; Xing, G.; Zhong, X.; Zhang, J.; Slaski, J.; et al. Morpho-agronomic and biochemical characterization of accessions of tiger nut (Cyperus esculentus) grown in the north temperate zone of China. Plants 2022, 11, 923. [Google Scholar] [CrossRef] [PubMed]
- Yu, Y.; Lu, X.; Zhang, T.; Zhao, C.; Guan, S.; Pu, Y.; Gao, F. Tiger nut (Cyperus esculentus L): Nutrition, processing, function and applications. Foods 2022, 11, 601. [Google Scholar] [CrossRef]
- Turesson, H.; Marttila, S.; Gustavsson, K.E.; Hofvander, P.; Olsson, M.E.; Bülow, L.; Stymne, S.; Carlsson, A.S. Characterization of oil and starch accumulation in tubers of Cyperus esculentus var. sativus (Cyperaceae): A novel model system to study oil reserves in nonseed tissues. Am. J. Bot. 2010, 97, 1884–1893. [Google Scholar] [CrossRef]
- Niemeyer, P.W.; Irisarri, I.; Scholz, P.; Schmitt, K.; Valerius, O.; Braus, G.H.; Herrfurth, C.; Feussner, I.; Sharma, S.; Carlsson, A.S.; et al. A seed-like proteome in oil-rich tubers. Plant J. 2022, 112, 518–534. [Google Scholar] [CrossRef]
- Zou, Z.; Zhao, Y.; Zhang, L.; Xiao, Y.; Guo, A. Analysis of Cyperus esculentus SMP family genes reveals lineage-specific evolution and seed desiccation-like transcript accumulation during tuber maturation. Ind. Crop. Prod. 2022, 187, 115382. [Google Scholar] [CrossRef]
- Zou, Z.; Zheng, Y.J.; Zhang, Z.T.; Xiao, Y.H.; Xie, Z.N.; Chang, L.L.; Zhang, L.; Zhao, Y.G. Molecular characterization oleosin genes in Cyperus esculentus, a Cyperaceae plant producing oil in underground tubers. Plant Cell Rep. 2023, 42, 1791–1808. [Google Scholar] [CrossRef]
- Zou, Z.; Fu, X.W.; Huang, J.Q.; Zhao, Y.G. Molecular characterization of CeOLE6, a diverged SH oleosin gene, preferentially expressed in Cyperus esculentus tubers. Planta 2024, 260, 122. [Google Scholar] [CrossRef]
- Zhao, Y.; Fu, X.; Zou, Z. Insights into genes encoding LEA_1 domain-containing proteins in Cyperus esculentus, a desiccation-tolerant tuber plant. Plants 2024, 13, 2933. [Google Scholar] [CrossRef]
- Zou, Z.; Zhao, Y.G.; Zhang, L.; Kong, H.; Guo, Y.L.; Guo, A.P. Single-molecule real-time (SMRT)-based full-length transcriptome analysis of tigernut (Cyperus esculentus L.). Chin. J. Oil Crop Sci. 2021, 43, 229–235. [Google Scholar] [CrossRef]
- Wang, W.; Haberer, G.; Gundlach, H.; Gläßer, C.; Nussbaumer, T.; Luo, M.C.; Lomsadze, A.; Borodovsky, M.; Kerstetter, R.A.; Shanklin, J.; et al. The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle. Nat. Commun. 2014, 5, 3311. [Google Scholar] [CrossRef]
- Olsen, J.L.; Rouzé, P.; Verhelst, B.; Lin, Y.C.; Bayer, T.; Collen, J.; Dattolo, E.; De Paoli, E.; Dittami, S.; Maumus, F.; et al. The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea. Nature 2016, 530, 331–335. [Google Scholar] [CrossRef] [PubMed]
- Bredeson, J.V.; Lyons, J.B.; Oniyinde, I.O.; Okereke, N.R.; Kolade, O.; Nnabue, I.; Nwadili, C.O.; Hřibová, E.; Parker, M.; Nwogha, J.; et al. Chromosome evolution and the genetic basis of agronomically important traits in greater yam. Nat. Commun. 2022, 13, 2001. [Google Scholar] [CrossRef] [PubMed]
- Emms, D.M.; Kelly, S. OrthoFinder: Phylogenetic orthology inference for comparative genomics. Genome Biol. 2019, 20, 238. [Google Scholar] [CrossRef] [PubMed]
- Jiao, Y.; Li, J.; Tang, H.; Paterson, A.H. Integrated syntenic and phylogenomic analyses reveal an ancient genome duplication in monocots. Plant Cell 2014, 26, 2792–2802. [Google Scholar] [CrossRef]
- Zou, Y.; Wei, Z.; Xiao, K.; Wu, Z.; Xu, X. Genomic analysis of the emergent aquatic plant Sparganium stoloniferum provides insights into its clonality, local adaptation and demographic history. Mol. Ecol. Resour. 2023, 23, 1868–1879. [Google Scholar] [CrossRef]
- Schnable, P.S.; Ware, D.; Fulton, R.S.; Stein, J.C.; Wei, F.; Pasternak, S.; Liang, C.; Zhang, J.; Fulton, L.; Graves, T.A.; et al. The B73 maize genome: Complexity, diversity, and dynamics. Science 2009, 326, 1112–1115. [Google Scholar] [CrossRef]
- Oliver, M.J.; Farrant, J.M.; Hilhorst, H.W.M.; Mundree, S.; Williams, B.; Bewley, J.D. Desiccation tolerance: Avoiding cellular damage during drying and rehydration. Annu. Rev. Plant Biol. 2020, 71, 435–460. [Google Scholar] [CrossRef]
- Verdier, J.; Lalanne, D.; Pelletier, S.; Torres-Jerez, I.; Righetti, K.; Bandyopadhyay, K.; Leprince, O.; Chatelain, E.; Vu, B.L.; Gouzy, J.; et al. A regulatory network-based approach dissects late maturation processes related to the acquisition of desiccation tolerance and longevity of Medicago truncatula seeds. Plant Physiol. 2013, 163, 757–774. [Google Scholar] [CrossRef]
- Zou, Z.; Zheng, Y.J.; Chang, L.L.; Zou, L.P.; Zhang, L.; Min, Y.; Zhao, Y.G. TIP aquaporins in Cyperus esculentus: Genome-wide identification, expression profiles, subcellular localizations, and interaction patterns. BMC Plant Biol. 2024, 24, 298. [Google Scholar] [CrossRef]
- Jiao, Y.; Leebens-Mack, J.; Ayyampalayam, S.; Bowers, J.E.; McKain, M.R.; McNeal, J.; Rolf, M.; Ruzicka, D.R.; Wafula, E.; Wickett, N.J.; et al. A genome triplication associated with early diversification of the core eudicots. Genome Biol. 2012, 13, R3. [Google Scholar] [CrossRef]
- Singh, R.; Ong-Abdullah, M.; Low, E.T.L.; Manaf, M.A.A.; Rosli, R.; Nookiah, R.; Ooi, L.C.-L.; Ooi, S.E.; Chan, K.L.; Azizi, N.; et al. Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds. Nature 2013, 500, 335–339. [Google Scholar] [CrossRef] [PubMed]
- Can, M.; Wei, W.; Zi, H.; Bai, M.; Liu, Y.; Gao, D.; Tu, D.; Bao, Y.; Wang, L.; Chen, S.; et al. Genome sequence of Kobresia littledalei, the first chromosome-level genome in the family Cyperaceae. Sci. Data 2020, 7, 175. [Google Scholar] [CrossRef] [PubMed]
- Walters, C.; Ried, J.L.; Walker-Simmons, M.K. Heat soluble proteins extracted from wheat embryos have tightly bound sugars and unusual hydration properties. Seed Sci. Res. 1997, 7, 125–134. [Google Scholar] [CrossRef]
- Delahaie, J.; Hundertmark, M.; Bove, J.; Leprince, O.; Rogniaux, H.; Buitink, J. LEA polypeptide profiling of recalcitrant and orthodox legume seeds reveals ABI3-regulated LEA protein abundance linked to desiccation tolerance. J. Exp. Bot. 2013, 64, 4559–4573. [Google Scholar] [CrossRef]
- Hu, B.; Jin, J.; Guo, A.Y.; Zhang, H.; Luo, J.; Gao, G. GSDS 2.0: An upgraded gene feature visualization server. Bioinformatics. 2015, 31, 1296–1297. [Google Scholar] [CrossRef]
- Edgar, R.C. MUSCLE v5 Enables Improved Estimates of Phylogenetic Tree Confidence by Ensemble Bootstrapping; Cold Spring Harbor Laboratory: Cold Spring Harbor, NY, USA, 2021. [Google Scholar] [CrossRef]
- Zou, Z.; Yang, J.H. Genomic analysis of Dof transcription factors in Hevea brasiliensis, a rubber-producing tree. Ind. Crops Prod. 2019, 134, 271–283. [Google Scholar] [CrossRef]
- Qiao, X.; Li, Q.; Yin, H.; Qi, K.; Li, L.; Wang, R.; Zhang, S.; Paterson, A.H. Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants. Genome Biol. 2019, 20, 38. [Google Scholar] [CrossRef]
- Mortazavi, A.; Williams, B.A.; McCue, K.; Schaeffer, L.; Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat. Methods 2008, 5, 621–628. [Google Scholar] [CrossRef]
- Zou, Z.; Gong, J.; An, F.; Xie, G.S.; Wang, J.K.; Mo, Y.Y.; Yang, L.F. Genome-wide identification of rubber tree (Hevea brasiliensis Muell. Arg.) aquaporin genes and their response to ethephon stimulation in the laticifer, a rubber-producing tissue. BMC Genom. 2015, 16, 1001. [Google Scholar] [CrossRef]
Gene Name | Locus ID | Position | AA | MW (kDa) | pI | GRAVY | LEA_5 Location | Duplicate | Mode |
---|---|---|---|---|---|---|---|---|---|
CeLEA5-1 | CESC_21264 | Scf50:743435..744190(−) | 84 | 8.88 | 5.43 | −1.398 | 2..67 | - | |
CeLEA5-2 | CESC_23041 | Scf10:593714..594313(−) | 112 | 12.34 | 5.61 | −1.388 | 16..58, 57..105 | CeLEA5-1 | Dispersed |
CeLEA5-3 | CESC_08006 | Scf17:1581661..1582217(+) | 154 | 16.92 | 6.02 | −1.582 | 2..84, 82..148 | CeLEA5-1 | Dispersed |
CeLEA5-4 | CESC_16081 | Scf34:1210271..1210837(−) | 83 | 8.96 | 5.22 | −1.313 | 9..49, 47..70 | CeLEA5-3 | Dispersed |
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Zou, Z.; Fu, X.; Yi, X.; Li, C.; Huang, J.; Zhao, Y. Integrative Analysis Provides Insights into Genes Encoding LEA_5 Domain-Containing Proteins in Tigernut (Cyperus esculentus L.). Plants 2025, 14, 762. https://doi.org/10.3390/plants14050762
Zou Z, Fu X, Yi X, Li C, Huang J, Zhao Y. Integrative Analysis Provides Insights into Genes Encoding LEA_5 Domain-Containing Proteins in Tigernut (Cyperus esculentus L.). Plants. 2025; 14(5):762. https://doi.org/10.3390/plants14050762
Chicago/Turabian StyleZou, Zhi, Xiaowen Fu, Xiaoping Yi, Chunqiang Li, Jiaquan Huang, and Yongguo Zhao. 2025. "Integrative Analysis Provides Insights into Genes Encoding LEA_5 Domain-Containing Proteins in Tigernut (Cyperus esculentus L.)" Plants 14, no. 5: 762. https://doi.org/10.3390/plants14050762
APA StyleZou, Z., Fu, X., Yi, X., Li, C., Huang, J., & Zhao, Y. (2025). Integrative Analysis Provides Insights into Genes Encoding LEA_5 Domain-Containing Proteins in Tigernut (Cyperus esculentus L.). Plants, 14(5), 762. https://doi.org/10.3390/plants14050762