Genomic analysis of Nypa fruticans elucidates its intertidal adaptations and early palm evolution

Insights into membrane-bound fatty acid desaturase genes in tigernut (Cyperus esculentus L.), an oil-rich tuber plant in Cyperaceae

BACKGROUND

Tigernut (Cyperus esculentus L.), an oil-rich tuber plant of the Cyperaceae family, is typical for the naturally high content of oleic acid. However, to date, genes contributing to oil composition have not been well characterized.

RESULTS

In this study, the first genome-wide analysis of tigernut genes encoding membrane-bound fatty acid desaturases (FADs), the key contributors to oil composition, is presented. According to phylogenetic analysis, ten members identified from the tigernut genome were assigned into seven out of eight evolutionary groups as defined in Arabidopsis thaliana, i.e., FAD2 (3), FAD6 (1), FAD3 (1), FAD7 (1), FAD4 (1), DES (1), and SLD (2). In contrast to the absence of an FAD5 homolog, FAD2 and SLD in tigernut were shown to have expanded via tandem and dispersed duplications, respectively. Comparison of 285 members from 29 representative plant species resulted in 11 orthogroups, where FAD2a, FAD6, FAD7, FAD3, FAD4, FAD5, DES, and SLD1 were shown to have already appeared in the ancestor of seed plants. Significantly, orthologous and syntenic analyses revealed that loss of FAD5 and expansion of SLD in tigernut are lineage-specific, occurred sometime before the radiation of core monocots, in contrast to species-specific expansion of FAD2. Moreover, though no syntenic relationship was observed between CeFAD genes, our comparative genomics analyses indicated that FAD3 and -7 are more likely to arise from segmental duplication. Structural variation and expression divergence of CeFAD genes were also observed. Gain of introns in CeFAD4, CeSLD1, and CeSLD2 was shown to be lineage-specific, occurred sometime before Cyperaceae-Juncaceae split. Tissue-specific expression analysis revealed that CeFAD2-1, CeFAD6, and CeFAD7 were constitutively expressed, whereas others were tissue-specific. Among five paralogs identified, CeFAD2-1 and CeSLD1 have evolved to be two dominant members. Putative roles of CeFAD2-1 in oil accumulation are supported by 1) exhibited an expression pattern positively associated with oil accumulation during tuber development; 2) were expressed more in tubers than their orthologs in C. rotundus. Additionally, in contrast to high expression of CrFAD3, transcript levels of CeFAD3 in tubers were fairly low, which may explain the distinct α-linolenic acid content between these two close species.

CONCLUSIONS

Our findings provide a global view of CeFAD genes, which not only highlights lineage-specific evolution of the family, but also provides valuable information for further functional analysis and genetic improvement in tigernut.