Genome-wide identification and expression analysis of lipoxygenase genes in Tartary buckwheat

Figures & data

Table 1. Overview of the LOX gene family in the F. tataricum genome.

Gene ID	Transcript ID	Gene location	Gene name	CDS (bp)
FtPinG0002952800.01	FtPinG0002952800.01.T01	Ft1:44390330-44395670(+)	FtLOX1	2205
FtPinG0009495000.01	FtPinG0009495000.01.T01	Ft1:59529412-59538032(+)	FtLOX2	2199
FtPinG0009494800.01	FtPinG0009494800.01.T01	Ft1:59558438-59561582(+)	FtLOX3	2214
FtPinG0008408200.01	FtPinG0008408200.01.T01	Ft1:62637301-62641536(+)	FtLOX4a	2583
FtPinG0008408200.01	FtPinG0008408200.01.T02	Ft1:62637301-62641536(+)	FtLOX4b	2565
FtPinG0000487200.01	FtPinG0000487200.01.T01	Ft5:769694-773404(-)	FtLOX5	2658
FtPinG0006513900.01	FtPinG0006513900.01.T01	Ft6:281041-285035(+)	FtLOX6a	2607
FtPinG0006513900.01	FtPinG0006513900.01.T02	Ft6:281041-285035(+)	FtLOX6b	2604
FtPinG0006513900.01	FtPinG0006513900.01.T03	Ft6:281041-285035(+)	FtLOX6c	2637
FtPinG0007379300.01	FtPinG0007379300.01.T01	Ft7:17575420-17579241(-)	FtLOX7	2580
FtPinG0003282300.01	FtPinG0003282300.01.T01	Ft8:9456863-9461537(+)	FtLOX8	2568

Figure 1. Multiple alignment of LOX amino acid sequences from F. tataricum and other plants (A–C). Note: Black dots represent the characteristic amino acids of 9-LOXs.

Figure 2. Phylogenetic analysis of LOX members from 14 species. Note: Evolutionary relationships were inferred using the neighbor-joining method (with 1,000 bootstrap replicates). Branches corresponding to partitions that were reproduced in less than 50% of the bootstrap replicates were collapsed.

Figure 3. FtLOX gene features. (A) Chromosomal locations of FtLOX members. The length of each chromosome is shown. (B) Gene structure of FtLOX genes. (C) Codon usage patterns in FtLOX genes.

Figure 4. Analysis of FtLOXs. (A) Analysis of functional domains of FtLOXs. The motif analysis was performed using TBtools. LOX proteins are listed on the left. Squares in different colors represent different motifs in each LOX sequence. (B) Distribution of cis-elements in the promoter regions (−2,000 bp) of the eight FtLOX genes. Different colors represent different elements.

Table 2. Physical and chemical properties of Tartary buckwheat LOX proteins.

Gene name	Molecular weight (kDa)	Amino acid length	Theoretical (pI)	Instability index	GRAVY	Plant-mPLoc
FtLOX1	83.3	734	5.94	44.3	−0.402	Chloroplast
FtLOX2	83.09	732	5.83	44.07	−0.381	Cytoplasm
FtLOX3	83.86	737	5.79	49.92	−0.433	Chloroplast, Cytoplasm
FtLOX4a	98.27	860	6.21	39.15	−0.427	Cytoplasm
FtLOX4b	97.63	854	6.21	39.46	−0.438	Cytoplasm
FtLOX5	100.28	885	6.83	50.4	−0.462	Cytoplasm, Chloroplast
FtLOX6a	99.4	868	7.12	36.11	−0.418	Cytoplasm
FtLOX6b	99.33	867	7.12	36.21	−0.42	Cytoplasm
FtLOX6c	100.41	878	7.12	36.72	−0.404	Cytoplasm
FtLOX7	97.81	859	5.99	36.39	−0.39	Cytoplasm
FtLOX8	97.21	855	5.55	35.19	−0.409	Cytoplasm

Figure 5. Expression profiles and enrichment analysis of FtLOX genes. The scale bar represents log₂ FPKM values. (A) Heatmap of LOX gene expression in various buckwheat tissues. BT18F1: flower; BT18L1: leaf; BT18R: root; BT18ST1: stem; BT18S1: seed at the cell division stage; BT18S3: seed at the cell enlargement stage; BT18S5: seed at the reserve deposition stage; BT18S7: seed at the maturation stage; BT18S9: seed at the desiccation stage. (B) Heatmap of FtLOX gene expression with various light treatments. B: blue; D: dark; FR: far red; R: red. (C–J) qRT-PCR analysis of LOX gene expression in Tartary buckwheat exposed to different light wavelengths. Vertical bars indicate standard deviation. Asterisks indicate significantly up- or downregulated genes compared with their expression in the untreated control (*p < 0.05, **p < 0.01; Student’s t-test). (K–P) Co-expression network of FtLOX genes, obtained using Cytoscape v3.7.0. (Q) GO enrichment analysis of co-expressed genes. (R) KEGG enrichment analysis of co-expressed genes.