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Genome-Wide Identification, Evolution, and Expression Analysis of RING Finger Gene Family in Solanum lycopersicum.
Int J Mol Sci. 2019 Sep 30; 20(19)IJ

Abstract

RING domain proteins generally have E3 ubiquitin ligase activity and are involved in degrading their substrate proteins. The roles of these proteins in growth, development, and responses to different abiotic stresses have been described well in various plant species, but little is available on tomatoes. Here, we identified 474 RING domains in 469 potential proteins encoded in the tomato genome. These RING genes were found to be located in 12 chromosomes and could be divided into 51 and 11 groups according to the conserved motifs outside the RING domain and phylogenetic analysis, respectively. Segmental duplication could be the major driver in the expansion of the tomato RING gene family. Further comparative syntenic analysis suggested that there have been functional divergences of RING genes during plant evolution and most of the RING genes in various species are under negative selection. Expression profiles derived from a transcriptomic analysis showed that most tomato RING genes exhibited tissue-specific expression patterning. Further RT-qPCR validation showed that almost all genes were upregulated by salt treatment, which was consistent with the microarray results. This study provides the first comprehensive understanding of the RING gene family in the tomato genome. Our results pave the way for further investigation of the classification, evolution, and potential functions of the RING domain genes in tomato.

Authors+Show Affiliations

Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China. yangliang0911@gmail.com. Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement in Southwest Regions, Ministry of Agriculture, Chengdu 610066, China. yangliang0911@gmail.com. Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China. yangliang0911@gmail.com.Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China. miaomingjun11@126.com. Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement in Southwest Regions, Ministry of Agriculture, Chengdu 610066, China. miaomingjun11@126.com.Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China. hongjunlv2008@126.com. Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Shandong Province Key Laboratory for Biology of Greenhouse Vegetables, Shandong Branch of National Improvement Center for Vegetables, Jinan 250100, China. hongjunlv2008@126.com.College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China. xsunshine11@163.com.Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China. dandelionlj@126.com. Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement in Southwest Regions, Ministry of Agriculture, Chengdu 610066, China. dandelionlj@126.com.Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China. yuejian_li@163.com.Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China. lz20031977@126.com. Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement in Southwest Regions, Ministry of Agriculture, Chengdu 610066, China. lz20031977@126.com.Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China. changwei972@126.com. Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement in Southwest Regions, Ministry of Agriculture, Chengdu 610066, China. changwei972@126.com.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31574992

Citation

Yang, Liang, et al. "Genome-Wide Identification, Evolution, and Expression Analysis of RING Finger Gene Family in Solanum Lycopersicum." International Journal of Molecular Sciences, vol. 20, no. 19, 2019.
Yang L, Miao M, Lyu H, et al. Genome-Wide Identification, Evolution, and Expression Analysis of RING Finger Gene Family in Solanum lycopersicum. Int J Mol Sci. 2019;20(19).
Yang, L., Miao, M., Lyu, H., Cao, X., Li, J., Li, Y., Li, Z., & Chang, W. (2019). Genome-Wide Identification, Evolution, and Expression Analysis of RING Finger Gene Family in Solanum lycopersicum. International Journal of Molecular Sciences, 20(19). https://doi.org/10.3390/ijms20194864
Yang L, et al. Genome-Wide Identification, Evolution, and Expression Analysis of RING Finger Gene Family in Solanum Lycopersicum. Int J Mol Sci. 2019 Sep 30;20(19) PubMed PMID: 31574992.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-Wide Identification, Evolution, and Expression Analysis of RING Finger Gene Family in Solanum lycopersicum. AU - Yang,Liang, AU - Miao,Mingjun, AU - Lyu,Hongjun, AU - Cao,Xue, AU - Li,Ju, AU - Li,Yuejian, AU - Li,Zhi, AU - Chang,Wei, Y1 - 2019/09/30/ PY - 2019/08/04/received PY - 2019/09/27/revised PY - 2019/09/29/accepted PY - 2019/10/3/entrez PY - 2019/10/3/pubmed PY - 2020/2/11/medline KW - RING E3 ligases KW - Solanum lycopersicum KW - abiotic stress KW - collinearity KW - expression patterns KW - phylogenetic analysis JF - International journal of molecular sciences JO - Int J Mol Sci VL - 20 IS - 19 N2 - RING domain proteins generally have E3 ubiquitin ligase activity and are involved in degrading their substrate proteins. The roles of these proteins in growth, development, and responses to different abiotic stresses have been described well in various plant species, but little is available on tomatoes. Here, we identified 474 RING domains in 469 potential proteins encoded in the tomato genome. These RING genes were found to be located in 12 chromosomes and could be divided into 51 and 11 groups according to the conserved motifs outside the RING domain and phylogenetic analysis, respectively. Segmental duplication could be the major driver in the expansion of the tomato RING gene family. Further comparative syntenic analysis suggested that there have been functional divergences of RING genes during plant evolution and most of the RING genes in various species are under negative selection. Expression profiles derived from a transcriptomic analysis showed that most tomato RING genes exhibited tissue-specific expression patterning. Further RT-qPCR validation showed that almost all genes were upregulated by salt treatment, which was consistent with the microarray results. This study provides the first comprehensive understanding of the RING gene family in the tomato genome. Our results pave the way for further investigation of the classification, evolution, and potential functions of the RING domain genes in tomato. SN - 1422-0067 UR - https://www.unboundmedicine.com/medline/citation/31574992/Genome_Wide_Identification_Evolution_and_Expression_Analysis_of_RING_Finger_Gene_Family_in_Solanum_lycopersicum_ L2 - https://www.mdpi.com/resolver?pii=ijms20194864 DB - PRIME DP - Unbound Medicine ER -