Exploring selection signatures in the divergence and evolution of lipid droplet (LD) associated genes in major oilseed crops

Abstract

Background: Oil bodies or lipid droplets (LDs) in the cytosol are the subcellular storage compartments of seeds and the sites of lipid metabolism providing energy to the germinating seeds. Major LD-associated proteins are lipoxygenases, phospholipaseD, oleosins, TAG-lipases, steroleosins, caleosins and SEIPINs; involved in facilitating germination and enhancing peroxidation resulting in off-flavours. However, how natural selection is balancing contradictory processes in lipid-rich seeds remains evasive. The present study was aimed at the prediction of selection signatures among orthologous clades in major oilseeds and the correlation of selection effect with gene expression.

Results: The LD-associated genes from the major oil-bearing crops were analyzed to predict natural selection signatures in phylogenetically close-knit ortholog clusters to understand adaptive evolution. Positive selection was the major force driving the evolution and diversification of orthologs in a lineage-specific manner. Significant positive selection effects were found in 94 genes particularly in oleosin and TAG-lipases, purifying with excess of non-synonymous substitution in 44 genes while 35 genes were neutral to selection effects. No significant selection impact was noticed in Brassicaceae as against LOX genes of oil palm. A heavy load of deleterious mutations affecting selection signatures was detected in T-lineage oleosins and LOX genes of Arachis hypogaea. The T-lineage oleosin genes were involved in mainly anther, tapetum and anther wall morphogenesis. In Ricinus communis and Sesamum indicum > 85% of PLD genes were under selection whereas selection pressures were low in Brassica juncea and Helianthus annuus. Steroleosin, caleosin and SEIPINs with large roles in lipid droplet organization expressed mostly in seeds and were under considerable positive selection pressures. Expression divergence was evident among paralogs and homeologs with one gene attaining functional superiority compared to the other. The LOX gene Glyma.13g347500 associated with off-flavor was not expressed during germination, rather its paralog Glyma.13g347600 showed expression in Glycine max. PLD-α genes were expressed on all the tissues except the seed,δ genes in seed and meristem while β and γ genes expressed in the leaf.

Conclusions: The genes involved in seed germination and lipid metabolism were under strong positive selection, although species differences were discernable. The present study identifies suitable candidate genes enhancing seed oil content and germination wherein directional selection can become more fruitful.

Keywords: Germination; Lipid droplet; Lipoxygenase; Natural selection; Oleosin; Phospholipase D; Rancidity; TAG lipase.

Fig. 1

Violin plot representing the relationship between exon numbers and species with interquartile range distribution for gene families studied including lipoxygenases (A), phospholipase D (B), oleosin (C) and TAG-lipases (D)

Fig. 2

The effect of natural selection on the genes studied as indicated by Tajima’s D test (A) in all the species studied for lipoxygenases, phospholipase D, oleosin and TAG-lipases included in the study. The relationship between McDonald and Kreitman analysis (MK test) and the highly expressed genes of all the 4 gene families in cotton (G. hirsutum) (B) and sesame (S. indicum) (C)

Fig. 3

The expression of lipoxygenase genes in ball, flower bud, leaf, meristem, stem and seed in cotton (G. hirsutum) (A); seed, husk, flower, stem, leaf and apical meristem in sesame (S. indicum) (B); and the germinating cotyledons of soybean (G. max) (C). The red arrow indicates the higher expression of 13S-LOX gene, Glyma. 13G030300 in soybean germinating cotyledons

Fig. 4

The expression of phospholipase-D genes in ball, flower bud, leaf, meristem, stem and seed in cotton (G. hirsutum) (A) and seed, husk, flower, stem, leaf and apical meristem in sesame (S. indicum) (B)

Fig. 5

The expression of oleosin genes in ball, flower bud, leaf, meristem, stem and seed in cotton (G. hirsutum) (A) and seed, husk, flower, stem, leaf and apical meristem in sesame (S. indicum) (B) and the tapetum cells of A. thaliana (C)

Fig. 6

Synteny among the genomes of A. thaliana Vs H. annuus (A), A.thaliana Vs S. indicum (B), G. hirsutum Vs S. indicum (C), G.max Vs S. indicum (D), G.max Vs H. annuus (E), A. hypogaea Vs G. max (F), O. sativa Vs S. indicum (G) and R. communis Vs O. sativa (H)

Fig. 7

Duplication, Cis-element distribution and protein-protein interactions in the species studied. Duplication status among the genomes (A), divergence of paralogs as expression difference among different tissues in G. hirsutum (B), divergence of homeologs and altered expression among different tissues in G. hirsutum (C) functional divergence of cis-elements as pie-chart (D) Cis-element distribution in G. hirsutum, A. thaliana, O. sativa and R. communis. (E) and string diagram representing protein-protein interactions (F)