Genome-wide identification and expression analysis of carotenoid cleavage oxygenase genes in Litchi (Litchi chinensis Sonn.)

Abstract

Background: Carotenoid cleavage oxygenases (CCOs) include the carotenoid cleavage dioxygenase (CCD) and 9-cis-epoxycarotenoid (NCED), which can catalize carotenoid to form various apocarotenoids and their derivatives, has been found that play important role in the plant world. But little information of CCO gene family has been reported in litchi (Litchi chinensis Sonn.) till date.

Results: In this study, a total of 15 LcCCO genes in litchi were identified based on genome wide lever. Phylogeny analysis showed that LcCCO genes could be classified into six subfamilies (CCD1, CCD4, CCD7, CCD8, CCD-like, and NCED), which gene structure, domain and motifs exhibited similar distribution patterns in the same subfamilies. MiRNA target site prediction found that there were 32 miRNA target sites in 13 (86.7%) LcCCO genes. Cis-elements analysis showed that the largest groups of elements were light response related, following was plant hormones, stress and plant development related. Expression pattern analysis revealed that LcCCD4, LcNCED1, and LcNCED2 might be involving with peel coloration, LcCCDlike-b might be an important factor deciding fruit flavor, LcNCED2 and LcNCED3 might be related to flower control, LcNCED1 and LcNCED2 might function in fruitlet abscission, LcCCD4a1, LcCCD4a2, LcCCD1, LcCCD4, LcNCED1, and LcNCED2 might participate in postharvest storage of litchi.

Conclusion: Herein, Genome-wide analysis of the LcCCO genes was conducted in litchi to investigate their structure features and potential functions. These valuable and expectable information of LcCCO genes supplying in this study will offer further more possibility to promote quality improvement and breeding of litchi and further function investigation of this gene family in plant.

Keywords: CCO genes; Expression analysis; Flower control; Fruit development and maturation; Litchi; Postharvest storage.

Fig. 1

Phylogenetic tree was constructed by ML method. Red character represented CCO proteins from Litchi chinensis Sonn., black character represented CCO proteins from Arabidopsis thaliana, Solanum lycopersicum, Malus × domestica

Fig. 2

Gene structure, conserved domain and motif of LcCCO genes. A Phylogenetic tree of LcCCO genes. B The distribution of gene structure and conserved domain. C The distribution of conserved motif, D motif elements. E Chromosomal distribution of LcCCO genes

Fig. 3

Cis-regulatory element analysis of LcCCO genes in litchi. A The distribution of cis regulatory elements on the LcCCO gene promoter. B and C The statistics of cis regulatory elements of each LcCCO genes.

Fig. 4

Prediction of three-dimensional domain of LcCCO proteins (purple, blue, green, yellow, orange, red, N-terminal to C-terminal)

Fig. 5

The GO enrichment analysis and expression pattern analysis of LcCCO genes by RNA-seq data. A The GO enrichment analysis of LcCCO genes in litchi. B The expression of LcCCO genes during peel coloring of ‘Feizixiao’ litchi treated by exogenous CPPU, CK: control group, T: CPPU treatment group. CK1 and T1: Green stage (the peel just completely wraps the pulp, 35d after anthesis), CK2 and T2: The best edible stage of fruit (57d after anthesis). C The expression of LcCCO genes of ‘Feizixiao’ litchi on the 0, 1, 3 and 7 days after bags removed. 0d: completely green; 1d, only the stipe was colored, 3d: The peel was half colored, 7d: fully colored. D The expression of LcCCO genes of ‘Nuomici’ Litchi during three different development stages of fruit. Green: the peel is completely green; Yellow: peel yellow; Red: peel red. E The expression of LcCCO genes of the entire inflorescences samples of ‘Feizixiao’ litchi on 28 days after the uniconazole treatment. CK: control group; T: treatment group. F The expression of LcCCO genes of fruit samples of ‘Wuye’ litchi after 2, 4 and 7 days treated by girdling plus defoliation. CK: control group, GPD: girdling plus defoliation. G The expression of LcCCO genes of abscission zone samples of ‘Feizixiao’ litchi after 0, 1, 2, 3 days treated by exogenous ethephon. CK: control group, ETH: exogenous ethephon treatment. H The expression of LcCCO genes of the peel samples on 0d and 4d after stored at room temperature and 0 h, 24 h and 48 h stored at room temperature after precooling for 14 days

Fig. 6

The expression of LcCCO genes identified by by qPCR. A The expression of LcCCO genes of the peel tissues during fruit maturation of ‘Feizixiao’ litchi treated by exogenous CPPU after anthesis. 35d: Green stage (the peel just completely wraps the pulp), corresponding to the CK1 and T1, 57d: The best edible stage of fruit, corresponding to the CK2 and T2 in Fig. 5A. B The expression of LcCCO genes of the peel tissues during fruit natural maturation of ‘Nuomici’ litchi. C The expression of LcCCO genes of fruitlet during the fruitlet abscission of ‘Feizixiao’ litchi treated by girdling plus defoliation treatment. D The expression of LcCCO genes of abscission zone tissues during the fruitlet abscission of ‘Feizixiao’ litchi treated by exogenous ethephon