Abstract
Carotenoid cleavage dioxygenases (CCDs) are a group of enzymes that catalyze the selective oxidative cleavage steps from carotenoids to apocarotenoids, which are essential for the synthesis of biologically important molecules such as retinoids, and the phytohormones abscisic acid (ABA) and strigolactones. In addition, CCDs play important roles in plant biotic and abiotic stress responses. Till now, a comprehensive characterization of the CCD gene family in the economically important crop cotton (Gossypium spp.) is still missing. Here, we performed a genome-wide analysis and identified 33, 31, 16 and 15 CCD genes from two allotetraploid Gossypium species, G. hirsutum and G. barbadense, and two diploid Gossypium species, G. arboreum and G. raimondii, respectively. According to the phylogenetic tree analysis, cotton CCDs are classified as six subgroups including CCD1, CCD4, CCD7, CCD8, nine-cis-epoxycarotenoid dioxygenase (NCED) and zaxinone synthase (ZAS) sub-families. Evolutionary analysis shows that purifying selection dominated the evolution of these genes in G. hirsutum and G. barbadense. Predicted cis-acting elements in 2 kb promoters of CCDs in G. hirsutum are mainly involved in light, stress and hormone responses. The transcriptomic analysis of GhCCDs showed that different GhCCDs displayed diverse expression patterns and were ubiquitously expressed in most tissues; moreover, GhCCDs displayed specific inductions by different abiotic stresses. Quantitative reverse-transcriptional PCR (qRT-PCR) confirmed the induction of GhCCDs by heat stress, salinity, polyethylene glycol (PEG) and ABA application. In summary, the bioinformatics and expression analysis of CCD gene family provide evidence for the involvement in regulating abiotic stresses and useful information for in-depth studies of their biological functions in G. hirsutum.
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Nine Arabidopsis and 13 rice CCD proteins downloaded from (https://phytozome.jgi.doe.gov/pz/portal.html). All raw RNA-seq data were downloaded from the NCBI Sequence Read Archive (SRA: PRJNA490626).
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Acknowledgement
We thank Dr. Salim Al-Babili and Dr. Xiongjie Zheng for valuable discussions and critical reading for the manuscript. We thank Dr. Dingding Zhu for technical support.
Funding
This work was funded by the National Natural Science Foundation of China (Grant No. 31900245 and 31770300), the key research and promotion projects (202102110002), Open Fund of State Key Laboratory of Cotton Biology (CB2019A19) and 111 project of China.
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KJ, YM and SZ designed the research. KJ and YG did the qRT-PCR experiments. KJ, YM, SZ, YG, YZ, JG, KL, WF, ZJ and WL analyzed the data with the input of L-SPT. KJ and SZ wrote the manuscript. YM, L-SPT and WL revised the manuscript.
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Zhang, S., Guo, Y., Zhang, Y. et al. Genome-wide identification, characterization and expression profiles of the CCD gene family in Gossypium species. 3 Biotech 11, 249 (2021). https://doi.org/10.1007/s13205-021-02805-9
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DOI: https://doi.org/10.1007/s13205-021-02805-9