Plastid DNA is a major source of nuclear genome complexity and of RNA genes in the orphan crop moringa

Abstract

Abstract Background: Unlike Transposable Elements (TEs) and gene/genome duplication, the role of the so-called nuclear plastid DNA sequences (NUPTs) in shaping the evolution of genome architecture and function remains poorly studied. We investigate here the functional and evolutionary fate of NUPTs in the orphan crop Moringa oleifera (moringa), featured by the highest fraction of plastid DNA found so far in any plant genome, focusing on i) any potential biases in their distribution in relation to specific nuclear genomic features, ii) their contribution to the emergence of new genes and gene regions, and iii) their impact on the expression of target nuclear genes. Results: In agreement with their potential mutagenic effect, NUPTs are underrepresented among structural genes, although their transcription levels and broadness were only lower when involving exonic regions; the occurrence of plastid DNA did not generally result in a broader expression, except among those affected in introns by older NUPTs. In contrast, we found a strong enrichment of NUPTs among several classes of RNA genes, especially those involved in the protein biosynthetic machinery (i.e., rRNA and tRNA genes) and specific classes of regulatory RNAs; a significant fraction of these is functionally expressed, thus potentially contributing to the nuclear pool. Conclusions: Our results complete our view of the molecular factors driving the evolution of nuclear genome architecture and function, and support plastid DNA in moringa as a major source of i) genome complexity and, ii) the nuclear pool of RNA genes.