Genome-Wide Identification and Transcriptome Analysis of P450 Superfamily Genes in Flax (Linum usitatissimum L.)

Abstract

Flax (Linum usitatissimum L.) seed is rich in α-linolenic acid, lignans, and fiber, which have potential health benefits. However, the potential toxicity of its cyanogenic glycosides limits its widespread use. The cytochrome P450 gene family is one of the largest gene families in plants and is involved in synthesizing phytohormones, secondary metabolites, and various defense compounds. Two P450 genes have been found to be important enzymes for the biosynthesis of cyanogenic glycosides in common sorghum (Sorghum bicolor (L.) Moench). However, the P450 gene family and its involvement in cyanogenic glycoside synthesis have been less studied in flax. In previous studies, we assembled a high-quality flax genome. In this study, a total of 412 P450 genes were identified in the flax genome, with molecular weights in the range of 7.42 kDa to 154.5 kDa and encoding amino acid lengths between 67 and 1378. These genes belonged to 48 families under eight clans and were distributed across 15 chromosomes. The number of introns varied from 0 to 14. Thirty-nine cis-acting elements were identified within 1500 bp upstream of the promoter, mainly related to the light response. There were 147 segmental duplications and 53 tandem duplication events among these P450 genes. Eleven genes potentially related to cyanogenic glycoside synthesis were identified by transcriptome analysis, and the RT-qPCR results verified the reliability of the transcriptome analysis. This study lays the foundation for the classification and functional study of the flax P450 gene family. The results will be useful for breeding new low-cyanogenic-glycoside flax varieties by genetic engineering.

Keywords: RNA-seq; cyanogenic glycosides; cytochrome; flax genome; gene family.

Figure 1

Distribution of LuP450 on flax chromosomes.

Figure 2

Phylogenetic tree of LuP450 genes.

Figure 3

Cis-acting element distribution of the LuP450 genes.

Figure 4

Intragenomic covariance analysis of the LuP450 genes. The gray lines in the background indicate other gene collinear blocks of flax, and the red lines indicate the syntenic P450 gene pairs.

Figure 5

Synteny analysis of P450 genes among three genomes. The gray lines in the background indicate other gene collinear blocks of flax, and the red lines indicate the syntenic P450 gene pairs.

Figure 6

LuP450 differentially expressed gene volcano plot. (A) A15S vs. A224S. (B) A15M vs. A224M. (C) A15L vs. A224L. Each dot represents a differentially expressed gene, and genes with -log(padj) > 10 while abs(log2FoldChange) > 3 were labeled.

Figure 7

Venn diagram of LuP450 differentially expressed genes at three developmental periods.

Figure 8

The relative expression of nine genes was analyzed by RT-qPCR, and the dotted line plots are drawn jointly with the FPKM value.

Figure 9

LuP450 protein interactions network map. Red dots represent flax P450 genes and green diamonds represent other genes. (A) All LuP450 protein interactions network map. (B) Core network map calculated by the MCODE plugin.