Genome-wide identification, characterization and expression profiles of the CCD gene family in Gossypium species

Shulin Zhang; Yutao Guo; Yanqi Zhang; Jinggong Guo; Kun Li; Weiwei Fu; Zhenzhen Jia; Weiqiang Li; Lam-Son Phan Tran; Kun-Peng Jia; Yuchen Miao

doi:10.1007/s13205-021-02805-9

Genome-wide identification, characterization and expression profiles of the CCD gene family in Gossypium species

3 Biotech. 2021 May;11(5):249. doi: 10.1007/s13205-021-02805-9. Epub 2021 May 1.

Authors

Shulin Zhang^#^{1

2}, Yutao Guo^#¹, Yanqi Zhang¹, Jinggong Guo¹, Kun Li¹, Weiwei Fu¹, Zhenzhen Jia³, Weiqiang Li¹, Lam-Son Phan Tran^{4

5}, Kun-Peng Jia¹, Yuchen Miao¹

Affiliations

¹ State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China.
² College of Biology and Food Engineering, Innovation and Practice Base for Postdoctors, Anyang Institute of Technology, Anyang, China.
³ Agricultural Research Center, Pingdingshan Academy of Agricultural Sciences, Pingdingshan, China.
⁴ Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock,, TX USA.
⁵ Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045 Japan.

^# Contributed equally.

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.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-021-02805-9.

Keywords: Abiotic stresses; CCD genes; Cotton; Expression analysis; Genome-wide analysis; Phylogenetic tree.