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A Comprehensive Analysis of Carotenoid Cleavage Dioxygenases Genes in Solanum Lycopersicum

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Abstract

Carotenoid cleavage dioxygenases (CCDs) in plant species is one of the most important enzymes in the carotenoid metabolism. In this study, we performed a comprehensive analysis for the CCDs family in Solanum lycopersicum based on the whole tomato genome sequences and explored their expression pattern. At least seven CCD genes were discovered in the tomato genome sequence. Two pairs of them were arranged in tandem. The tandem duplication events could be dating to approximately 14 and 21 Mya, and the tandem duplication genes experienced a purifying selection during the course of evolution after diversification. Additionally, subcellular localization revealed that four members were predicted to be cytoplasm-localized and the three remaining members plastids-localized. Subsequently, a number of cis-regulatory elements, which were involved in light responsiveness, hormone regulation, and abiotic and biotic stresses, were identified in the promoter sequences of SlCCD genes. Phylogenetic tree revealed that the CCDs from Solanaceae crops have a closer genetic relationship. The difference in abundance and distinct expression patterns during the vegetative and reproductive development suggests different functions for these seven SlCCDs. Our findings suggest that SlCCDs family play important roles throughout the whole life course and will lay the foundation for further elaborating the regulatory mechanism of each member in tomato.

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Acknowledgments

This study was partially supported by the State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control (No. 2010DS700124-KF1518), the Young Talent Training Program of Zhejiang Academy of Agricultural Sciences (2015R23R08E09), the Zhejiang Provincial Natural Science Foundation of China (LQ12C150020), General Program from the National Natural Science Foundation of China (31301774, 31272156, and 31071800), Public Agricultural Technology Application Research Project for Zhejiang Province (2013C32G4010256), Breeding of Vegetable Varieties in Zhejiang Province (2009C02006-1), Technological System of Ordinary Vegetable Industry (CARS-25-G-16), Zhejiang Provincial Vegetable Industry Innovation Team (2009R50026), Zhejiang Provincial major Agricultural Science and Technology Projects of New Varieties Breeding (2012C12903), and Molecular Breeding of Major Vegetable and Functional Genomics Research (2012AA1001).

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  1. State key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China

    Yanping Wei, Hongjian Wan, Rongqing Wang, Meiying Ruan, Qingjing Ye, Zhimiao Li, Guozhi Zhou, Zhuping Yao & Yuejian Yang

  2. Institute of Economic Crop, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, China

    Zhiming Wu

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  1. Yanping Wei
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  2. Hongjian Wan
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Correspondence to Hongjian Wan.

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Wei, Y., Wan, H., Wu, Z. et al. A Comprehensive Analysis of Carotenoid Cleavage Dioxygenases Genes in Solanum Lycopersicum . Plant Mol Biol Rep 34, 512–523 (2016). https://doi.org/10.1007/s11105-015-0943-1

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