Abstract
It is necessary to identify suitable alternative crops to ensure the nutritional demands of a growing global population. The genome of Moringa oleifera, a fast-growing drought-tolerant orphan crop with highly valuable agronomical, nutritional and pharmaceutical properties, has recently been reported. We model here gene family evolution in Moringa as compared with ten other flowering plant species. Despite the reduced number of genes in the compact Moringa genome, 101 gene families, grouping 957 genes, were found as significantly expanded. Expanded families were highly enriched for chloroplastidic and photosynthetic functions. Indeed, almost half of the genes belonging to Moringa expanded families grouped with their Arabidopsis thaliana plastid encoded orthologs. Microsynteny analysis together with modeling the distribution of synonymous substitutions rates, supported most plastid duplicated genes originated recently through a burst of simultaneous insertions of large regions of plastid DNA into the nuclear genome. These, together with abundant short insertions of plastid DNA, contributed to the occurrence of massive amounts of plastid DNA in the Moringa nuclear genome, representing 4.71%, the largest reported so far. Our study provides key genetic resources for future breeding programs and highlights the potential of plastid DNA to impact the structure and function of nuclear genes and genomes.
Highlights
It is necessary to identify suitable alternative crops to ensure the nutritional demands of a growing global population
Using a classification of orthogroups in the Moringa genome and 10 other plant species representing the main flowering plant lineages, we modelled gene family turnover using the Maximum Likelihood (ML) framework implemented in Badirate[26]
We found many orthogroups clustering with Arabidopsis plastid encoded genes, including, OG0000125, annotated as ribulose1,5-bisphosphate carboxylase/oxygenase (RuBisCO) large subunit (RBCL), OG0000374, encoding for the CP47 subunit of the photosystem II reaction center, OG0003080, corresponding to the plastidic NADH dehydrogenase enzymatic activity, OG0000842, annotated as encoding for the beta subunit of the plastidic acetyl-CoA carboxylase carboxyltransferase, OG0000207, conforming the RNA polymerase beta’ subunit-2 involved in plastid transcription machinery, or OG0003554, annotated as RF1/YCF1, a group of proteins highly variable both in length and number of transmembrane regions which play a key role in the plastid protein import m achinery[35] and has 11 members in Moringa, zero in most species and five in Arabidopsis (Supplementary Table S4)
Summary
It is necessary to identify suitable alternative crops to ensure the nutritional demands of a growing global population. Of the 5436 different GO terms found in the Moringa genome, 81 were found as differentially represented among expanded gene families, including 68 overrepresented (Supplementary Table S4).
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