Genomic insights into lineage-specific evolution of the oleosin family in Euphorbiaceae

Abstract

Background Lipid droplets (LDs) present in land plants serve as an essential energy and carbon reserve for seed germination and seedling development. Oleosins, the most abundant structural proteins of LDs, comprise a small family involved in LD formation, stabilization and degradation. Despite their importance, our knowledge on oleosins is still poor in Euphorbiaceae, a large plant family that contains several important oil-bearing species. Results To uncover lineage-specific evolution of oleosin genes in Euphorbiaceae, in this study, we performed a genome-wide identification and comprehensive comparison of the oleosin family in Euphorbiaceae species with available genome sequences, i.e. castor bean (Ricinus communis), physic nut (Jatropha curcas), tung tree (Vernicia fordii), Mercurialis annua, cassava (Manihot esculenta) and rubber tree (Hevea brasiliensis), and a number of five, five, five, five, eight and eight members were found, respectively. Synteny analysis revealed one-to-one collinear relationship of oleosin genes between the former four (i.e. castor bean, physic nut, tung tree and M. annua) as well as latter two species (i.e. cassava and rubber tree), whereas one-to-one and one-to-two collinear relationships were observed between physic nut and cassava, reflecting the occurrence of one recent whole-genome duplication (WGD) in the last common ancestor of cassava and rubber tree. The presence of five ortholog groups representing three previously defined clades (i.e. U, SL and SH) dates back at least to the Malpighiales ancestor, because they are also conserved in poplar (Populus trichocarpa), a tree having experienced one Salicaceae-specific recent WGD. As observed in poplar, WGD was shown to be the main driver for the family expansion in both cassava and rubber tree. Nevertheless, same retention patterns of WGD-derived duplicates observed in cassava and rubber tree are somewhat different from that of poplar, though certain homologous fragments are still present in rubber tree. Further transcriptional profiling revealed an apparent seed-predominant expression pattern of oleosin genes in physic nut, castor bean and rubber tree. Moreover, structure and expression divergence of paralogous pairs were also observed in both cassava and rubber tree. Conclusion Comparative genomics analysis of oleosin genes reported in this study improved our knowledge on lineage-specific family evolution in Euphorbiaceae, which also provides valuable information for further functional analysis and utilization of key members and their promoters.

Integrated Transcriptome and Proteome Analysis Provides Insight into the Ribosome Inactivating Proteins in Plukenetia volubilis Seeds

“…Transcripts encoding 2S albumin-like (Unigene0003223, Unigene0049069, Unigene0046600, Unigene0011183, and Unigene0048736), legumin-like (Unigene0048787, Unigene0010858, and Unigene0010856) and vicilin-like proteins (Unigene0049803 and Unigene0044374) were also abundant; these proteins are specifically synthesized during seed maturation. Other abundant transcripts of the Oleosin genes (Unigene0044871, Unigene0028565, and Unigene0050906) are highly abundant in land plants and could positively regulate total seed oil accumulation [ 24 , 25 ].…”

Integrative Analysis of Oleosin Genes Provides Insights into Lineage-Specific Family Evolution in Brassicales

“…In the present study, we used Brassicales, an economically important order of flowering plants that harbors the lineage-specific T clade [ 3 , 8 , 17 ], as an example to address evolution patterns of the oleosin gene family. In addition to 34 members reported in Arabidopsis, cassava, and poplar ([ 12 ], this study), a number of 64 oleosin family genes were identified from ten species representing eight plant families, i.e., Amborellaceae ( A. trichopoda ), Lauraceae (avocado), Ranunculaceae ( A. coerulea ), Caricaceae (papaya), Moringaceae (horseradish), Akaniaceae ( B. sinensis ), Capparaceae (caperbush), and Cleomaceae ( C. violacea , acaya, and spider flower), while gene numbers of the family vary from three to ten. Interestingly, the family amounts are usually higher in species that experienced recent WGDs.…”

“…Correspondingly, compared with five members present in both A. trichopoda and A. coerulea , one more was identified in papaya, horseradish, and C. violacea . By contrast, more than seven members were identified in B. sinensis , acaya, and spider flower, which are comparative to eight and nine reported in cassava and poplar, respectively [ 12 ].…”

“…Oleosins are a class of highly abundant structural proteins of lipid droplets (LDs), which represent a major carbon reserve and are widely present in various plant organs such as seeds, pollen, flowers, fruits, and certain tubers [ 1 , 2 , 3 , 4 , 5 ]. Oleosins are typical for their small molecular weight (MW) of 14–30 kDa [ 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 ]. Nevertheless, all of them share a conserved central hydrophobic portion of approximately 72 residues, which could form a hairpin penetrating the surface phospholipid monolayer of an LD into the matrix.…”

“…By contrast, Clades M and T were reported to be lineage-specific, which are confined to Lauraceae and Brassicaceae, respectively [ 4 , 8 ]. Comparative genomics analyses indicated that, for most clades, gene expansion was mainly contributed by whole-genome duplications (WGDs) especially those lineage-specific recent WGDs, e.g., the Brassicaceae-specific α WGD and the ρ WGD shared by cassava ( Manihot esculenta ) and rubber tree ( Hevea brasiliensis ) in Euphorbiaceae [ 5 , 6 , 12 ], in stark contrast to a key role of tandem duplication for Clade T in Brassicaceae [ 3 , 8 , 16 ].…”