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Zhu J, Tang G, Xu P, Li G, Ma C, Li P, Jiang C, Shan L, Wan S. Genome-wide identification of xyloglucan endotransglucosylase/hydrolase gene family members in peanut and their expression profiles during seed germination. PeerJ 2022; 10:e13428. [PMID: 35602895 PMCID: PMC9121870 DOI: 10.7717/peerj.13428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/21/2022] [Indexed: 01/14/2023] Open
Abstract
Seed germination marks the beginning of a new plant life cycle. Improving the germination rate of seeds and the consistency of seedling emergence in the field could improve crop yields. Many genes are involved in the regulation of seed germination. Our previous study found that some peanut XTHs (xyloglucan endotransglucosylases/hydrolases) were expressed at higher levels at the newly germinated stage. However, studies of the XTH gene family in peanut have not been reported. In this study, a total of 58 AhXTH genes were identified in the peanut genome. Phylogenetic analysis showed that these AhXTHs, along with 33 AtXTHs from Arabidopsis and 61 GmXTHs from soybean, were classified into three subgroups: the I/II, IIIA and IIIB subclades. All AhXTH genes were unevenly distributed on the 18 peanut chromosomes, with the exception of chr. 07 and 17, and they had relatively conserved exon-intron patterns, most with three to four introns. Through chromosomal distribution pattern and synteny analysis, it was found that the AhXTH family experienced many replication events, including 42 pairs of segmental duplications and 23 pairs of tandem duplications, during genome evolution. Conserved motif analysis indicated that their encoded proteins contained the conserved ExDxE domain and N-linked glycosylation sites and displayed the conserved secondary structural loops 1-3 in members of the same group. Expression profile analysis of freshly harvested seeds, dried seeds, and newly germinated seeds using transcriptome data revealed that 26 AhXTH genes, which account for 45% of the gene family, had relatively higher expression levels at the seed germination stage, implying the important roles of AhXTHs in regulating seed germination. The results of quantitative real-time PCR also confirmed that some AhXTHs were upregulated during seed germination. The results of GUS histochemical staining showed that AhXTH4 was mainly expressed in germinated seeds and etiolated seedlings and had higher expression levels in elongated hypocotyls. AhXTH4 was also verified to play a crucial role in the cell elongation of hypocotyls during seed germination.
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Affiliation(s)
- Jieqiong Zhu
- College of Life Science, Shandong Normal University, Jinan, China,Bio-Tech Research Center, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Crop Genetic Improvement, Jinan, China
| | - Guiying Tang
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Crop Genetic Improvement, Jinan, China
| | - Pingli Xu
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Crop Genetic Improvement, Jinan, China
| | - Guowei Li
- College of Life Science, Shandong Normal University, Jinan, China,Bio-Tech Research Center, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Crop Genetic Improvement, Jinan, China
| | - Changle Ma
- College of Life Science, Shandong Normal University, Jinan, China
| | - Pengxiang Li
- College of Life Science, Shandong Normal University, Jinan, China,Bio-Tech Research Center, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Crop Genetic Improvement, Jinan, China
| | - Chunyu Jiang
- College of Life Science, Shandong Normal University, Jinan, China,Bio-Tech Research Center, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Crop Genetic Improvement, Jinan, China
| | - Lei Shan
- College of Life Science, Shandong Normal University, Jinan, China,Bio-Tech Research Center, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Crop Genetic Improvement, Jinan, China
| | - Shubo Wan
- College of Life Science, Shandong Normal University, Jinan, China,Bio-Tech Research Center, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Crop Genetic Improvement, Jinan, China
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Opazo MC, Lizana R, Stappung Y, Davis TM, Herrera R, Moya-León MA. XTHs from Fragaria vesca: genomic structure and transcriptomic analysis in ripening fruit and other tissues. BMC Genomics 2017; 18:852. [PMID: 29115918 PMCID: PMC5678779 DOI: 10.1186/s12864-017-4255-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 11/01/2017] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Fragaria vesca or 'woodland strawberry' has emerged as an attractive model for the study of ripening of non-climacteric fruit. It has several advantages, such as its small genome and its diploidy. The recent availability of the complete sequence of its genome opens the possibility for further analysis and its use as a reference species. Fruit softening is a physiological event and involves many biochemical changes that take place at the final stages of fruit development; among them, the remodeling of cell walls by the action of a set of enzymes. Xyloglucan endotransglycosylase/hydrolase (XTH) is a cell wall-associated enzyme, which is encoded by a multigene family. Its action modifies the structure of xyloglucans, a diverse group of polysaccharides that crosslink with cellulose microfibrills, affecting therefore the functional structure of the cell wall. The aim of this work is to identify the XTH-encoding genes present in F. vesca and to determine its transcription level in ripening fruit. RESULTS The search resulted in identification of 26 XTH-encoding genes named as FvXTHs. Genetic structure and phylogenetic analyses were performed allowing the classification of FvXTH genes into three phylogenetic groups: 17 in group I/II, 2 in group IIIA and 4 in group IIIB. Two sequences were included into the ancestral group. Through a comparative analysis, characteristic structural protein domains were found in FvXTH protein sequences. In complement, expression analyses of FvXTHs by qPCR were performed in fruit at different developmental and ripening stages, as well as, in other tissues. The results showed a diverse expression pattern of FvXTHs in several tissues, although most of them are highly expressed in roots. Their expression patterns are not related to their respective phylogenetic groups. In addition, most FvXTHs are expressed in ripe fruit, and interestingly, some of them (FvXTH 18 and 20, belonging to phylogenic group I/II, and FvXTH 25 and 26 to group IIIB) display an increasing expression pattern as the fruit ripens. CONCLUSION A discrete group of FvXTHs (18, 20, 25 and 26) increases their expression during softening of F. vesca fruit, and could take part in cell wall remodeling required for softening in collaboration with other cell wall degrading enzymes.
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Affiliation(s)
- María Cecilia Opazo
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile.,Present address: Laboratorio de Biología Celular y Farmacología, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Rodrigo Lizana
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Yazmina Stappung
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Thomas M Davis
- Department of Biological Sciences, University of New Hampshire, Durham, NH, USA
| | - Raúl Herrera
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - María Alejandra Moya-León
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile.
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