Genome-Wide Identification and Comparative Analysis of the 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase (HMGR) Gene Family in Gossypium

Abstract

Terpenes are the largest and most diverse class of secondary metabolites in plants and play a very important role in plant adaptation to environment. 3-Hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) is a rate-limiting enzyme in the process of terpene biosynthesis in the cytosol. Previous study found the HMGR genes underwent gene expansion in Gossypium raimondii, but the characteristics and evolution of the HMGR gene family in Gossypium genus are unclear. In this study, genome-wide identification and comparative study of HMGR gene family were carried out in three Gossypium species with genome sequences, i.e., G. raimondii, Gossypium arboreum, and Gossypium hirsutum. In total, nine, nine and 18 HMGR genes were identified in G. raimondii, G. arboreum, and G. hirsutum, respectively. The results indicated that the HMGR genes underwent gene expansion and a unique gene cluster containing four HMGR genes was found in all the three Gossypium species. The phylogenetic analysis suggested that the expansion of HMGR genes had occurred in their common ancestor. There was a pseudogene that had a 10-bp deletion resulting in a frameshift mutation and could not be translated into functional proteins in G. arboreum and the A-subgenome of G. hirsutum. The expression profiles of the two pseudogenes showed that they had tissue-specific expression. Additionally, the expression pattern of the pseudogene in the A-subgenome of G. hirsutum was similar to its paralogous gene in the D-subgenome of G. hirsutum. Our results provide useful information for understanding cytosolic terpene biosynthesis in Gossypium species.

Keywords: Gossypium; HMGR; gene expansion; pseudogene; terpene biosynthesis.

Figure 1

Phylogenetic relationship of HMGS, MK, PMK, MVD and HMGR proteins from G. raimondii, G. arboreum and G. hirsutum. (a) HMGS; (b) MK; (c) PMK; (d) MVD; (e) HMGR. Numbers at the nodes represent bootstrap support values (1000 replicates). The bars in (a–e) indicate 0.5%, 5%, 0.2%, 0.1% and 5% sequence divergence, respectively.

Figure 2

Locations and homologous relationships of the MVA pathway genes in G. raimondii and G. arboreum, and in the A-subgenome and D-subgenome of G. hirsutum. (a) Locations and orthologous relationships of the MVA pathway genes in G. raimondii and G. arboreum; (b) Locations and paralogous relationships of the MVA pathway genes in the D-subgenome and the A-subgenome of G. hirsutum. The chromosomes of G. raimondii, G. arboreum, G. hirsutum D-subgenome, and G. hirsutum A-subgenome are shown with different colors and labeled as Gr, Ga, Gh_Dt and Gh_At, respectively. The putative homologous gene pairs belonging to the HMGS, HMGR, MK, PMK and MVD gene families are connected by orange, purple, blue, yellow and grey lines, respectively. Several genes are located on the scaffolds that do not determine the exact locations and are placed next to the corresponding chromosomes.

Figure 3

The HMGR gene clusters in G. raimondii, G. arboreum and G. hirsutum. The putative homologous gene pairs are displayed by arrows of the same color and connected by lines of the same color. The direction of arrows indicates the direction of transcriptions.

Figure 4

Phylogenetic relationship, gene structure, and conserved motifs of HMGR genes from G. raimondii, G. arboreum and G. hirsutum. Exons are represented by green boxes and introns by black lines. The two HMG-CoA binding motifs (EMPVGYVQIP and TTEGCLVA) and two NADP(H) binding motifs (DAMGMNM and GTVGGGT) are represented by red, light blue, yellow and dark blue boxes, respectively.

Figure 5

The HMGR pseudogenes in G. arboreum and G. hirsutum. (a) The gene structure of GaHMGR1, GhHMGR1A, GrHMGR1 and GhHMGR1D. Exons are represented by green boxes and introns by black lines. The red boxes in the first exons of GrHMGR1 and GhHMGR1D indicate the 10-bp deletion at the 169-bp position in GaHMGR1 and GhHMGR1A; (b) The alignment of predicted coding sequence of GaHMGR1 and GhHMGR1A, and corresponding sequence of GrHMGR1 and GhHMGR1D. The red outlined box indicates the 10-bp deletion of GaHMGR1 and GhHMGR1A. The three red stars indicate the premature stop codon (TGA) at the 367-bp position of GaHMGR1 and GhHMGR1A.

Figure 6

Expression patterns of GaHMGR1, GhHMGR1A and GhHMGR1D in different tissues. (a) GaHMGR1; (b) GhHMGR1A; (c) GhHMGR1D.