This is not a big deal and the authors of the paper don't even mention junk DNA.
The paper was reviewed by Peter M. Waterhouse and Roger P. Hellens in the same issue (Waterhouse and Hellens, 2015). They think it's a big deal. Here's what they say,
In the 1970s, as it started to become clear that the genomic regions that encode proteins (the genes) swim in a sea of non-protein-coding sequences, the idea of meaningless, or 'junk', DNA became a hot topic of discussion. Biologists are now well aware of introns, the sequences within genes that separate the coding regions (exons) and which are spliced out at the messenger-RNA level, as well as their notable regulatory roles. However, the term junk DNA has survived and is used loosely to describe genomic sequences between genes, giving them an implied lack of importance.There's a lot of confusion here. First, not all genes encode proteins so right off the bat the paragraph begins to sound uninformed. Second, there's lots of function in "non-protein-coding sequences," including lots of genes, so they seem to combining multiple misconceptions. Third, the concept of junk DNA was supported by far more knowledge that the authors are aware of. Fourth, introns are junk DNA (mostly). Fourthly, no knowledgeable scientist thinks that all of the DNA between genes is junk. (And many of them think that most of the DNA of eukaryotic genes (introns) is junk.)
The debate about the usefulness of non-protein-coding DNA sequences continues to rage3, 4References 3 and 4 are the original ENCODE summary paper and the backtracking PNAS paper published 18 months later. There is no debate among knowledgeable scientists about the usefulness of some noncoding sequences. It would be helpful to explain that the debate is about whether 90% of our genome is junk of whether most of it is functional.
However, within these intergenic regions of a genome are the sequences that produce most plant and many animal pri-miRs. Clearly, these sequences are not useless.If there are regions of the genome that specify functional small RNAs then the proper word for those regions is "genes." You can't have genes "within" intergenic regions. This is very confusing.
The rest of the review is also confusing. If the small RNAs are functional then they aren't junk. If they encode small functional peptides then they aren't junk. The Lauressergues et al. paper doesn't seem to have anything to do with junk DNA, so why all the fuss in the review?
If all the suspected small RNAs were actually functional in plants then how much of the genome does this cover? I suspect it's about 1% or less. That's just background noise in the junk DNA debate.
Lauressergues, D., Couzigou, J-M., San Clemente, S., Martinez, Y., Dunand, C., Bécard, G., and Combier, J-P. (2015) Primary transcripts of microRNAs encode regulatory peptides. Nature Published online March 25, 2015. [doi:10.1038/nature14346]
Waterhouse, P.M. and Hellens, R.P. (2015) Plant biology: Coding in non-coding RNAs. Nature Published online March 25, 2015. [doi: 10.1038/nature14378]