Genome-wide identification and gene expression pattern analysis of the carotenoid cleavage oxygenase gene family in Fagopyrum tataricum

Abstract

Background: Carotenoid cleavage oxygenases (CCOs) convert carotenoids into volatile aromatic compounds implicated in plant growth and development. They affect the synthesis of hormones, including abscisic acid (ABA) and strigolactone (SL). However, the CCO family in Tartary buckwheat remains unelucidated.

Results: We identified the FtCCO gene family based on Tartary buckwheat genomic data and analyzed the biological function of the FtCCO genes using bioinformatics methods and the expression pattern of the gene using fluorescence quantitative PCR. Three pairs of fragment duplication genes were found in FtCCOs, and the motifs were highly conserved within the same subfamily. FtCCO genes are closely related to the dicotyledonous Arabidopsis thaliana, which has the highest number of co-linear genes. The qRT-PCR showed that among the tissue-specific expression patterns of Tartary buckwheat CCO genes, the expression of the FtCCOs was higher in the leaves. In Tartary buckwheat grain development, the relative expression of most FtCCOs was higher at the later stage. The relative expression of many genes was higher in the stems under cold, dark, NaCl, and abiotic stress conditions. However, under the hormone and plant growth regulator treatments, the expression of the nine FtCCOs was relatively low in the stems. Notably, the relative expression of FtNCED4 was extremely high under abiotic stress and hormone induction, indicating that FtNCED4 may be involved in the growth and development of Tartary buckwheat. In this study, the FtCCO family genes of Tartary buckwheat were identified at the genome-wide level, and the gene expression pattern of the FtCCO gene family in different tissues or treatments was determined. This study provides a theoretical basis for further analysis of the functions of theFtCCO family, which is of great significance for the mining of resistance genes and trait improvement.

Keywords: CCO gene family; Fagopyrum tataricum; Evolution analysis; Expression patterns; Genome-wide analysis.

Fig. 1

Subcellular localization of the FtCCO family members. Blue bars indicate a lower confidence in the prediction results, whereas red indicates a higher confidence. Chlo indicates chloroplast, mito is mitochondria, cyto is cytoplasm, pero is peroxisome, plas is plasma membrane, nul is nucleus, cysk is cytoskeleton, vacu is vacuole, golg is Golgi apparatus

Fig. 2

Phylogenetic tree of CCO proteins in F. tataricum, O. sativa, and A. thaliana. FtCCO proteins are red font, and different subgroups correspond to different regional colors

Fig. 3

Phylogenetic relationships, gene structure, and motif distribution of CCO genes in F. tataricum. A Phylogenetic tree of FtCCO protein with 1000 replicates per node. B Genetic structure diagram of the FtCCO gene, respectively UTR (untranslated), CDS (coding sequence), structural domain (RPE65), and introns (black lines). C Amino acid conserved Motif 1–10 in FtCCO proteins, with different color blocks corresponding to different conserved motifs, and the black lines indicate the relative length of corresponding proteins

Fig. 4

Chromosomal distribution and interchromosomal relationships of the F. tataricum CCO genes. A Vertical bars represent the chromosomes of F. tataricum; each chromosome is labeled with a chromosome number on the left side of the chromosome; the scale on the left represents chromosome length. B Colored lines indicate all homologous blocks in the F. tataricum genome; chromosome numbers are labeled at the bottom of each chromosome

Fig. 5

Cis-acting elements of promoters in FtCCO family gene

Fig. 6

Collinearity analysis of F. tataricum and six plants (A. thaliana, B. napus, C. annuum, O. sativa, Z. mays and S. bicolor). Gray lines indicate collinear blocks in the genomes of F. tataricum and other plants. Red lines highlight syntenic F. tataricum CCO gene pairs

Fig. 7

Phylogenetic tree for F. tataricum and six plants (A. thaliana, B. napus, C. annuum, O. sativa, Z. mays and S. bicolor) and conserved motif composition of CCO protein. FtCCO is marked in red, and different module colors represent different conserved motif

Fig. 8

Tissue-specific expression levels and correlation analysis of FtCCO family members. A Expression levels of FtCCO at the mid-grain filling stage in roots, stems, young leaf, mature leaf, flower, grain, and husk. Values of the column chart are expressed as mean ± SD, the lowercase letters represent significant differences (p < 0.05, Duncan). B Correlation hierarchical cluster analysis between their expression in different tissues. Positive number indicates a positive correlation and negative number indicates a negative correlation

Fig. 9

Grain development expression levels and correlation analysis of FtCCOs. A Expression levels of FtCCOs of grain and husk in the early, middle, and late stages of grain filling. Values of the column chart are expressed as mean ± SD, the lowercase letters represent significant differences (p < 0.05, Duncan). B Correlation hierarchical cluster analysis between their expression in different tissues. Positive number indicates positive correlation and negative number indicates negative correlation

Fig. 10

Spatiotemporal expression levels and correlation analysis of FtCCOs under six abiotic stresses (cold, dark, flooding, heat, NaCl, and PEG) at the seedling stage. A Expression level of FtCCOs at 3 h, 12 h, and 24 h in root, stem, and leaf. Values of the column chart are expressed as mean ± SD, lowercase letters represent significant differences (p < 0.05, Duncan). B Correlation hierarchical cluster analysis between their expression in different tissues. Positive number indicates a positive correlation, and negative number indicates a negative correlation

Fig. 11

Spatiotemporal expression levels and correlation analysis of FtCCOs under four hormonal treatments (ABA, GA₃, MeJA, and SA) at the seedling stage. A Expression levels of FtCCOs at 3 h, 12 h, and 24 h in root, stem, and leaf. Values of the column chart are expressed as mean ± SD, the lowercase letters represent significant differences (p < 0.05, Duncan). B Correlation hierarchical cluster analysis between their expression in different tissues. Positive number indicates a positive correlation, and negative number indicates a negative correlation