Do plants have junk DNA?

Current Opinion in Plant Biology has a special edition devoted to Genome studies and molecular genetics 2024. The only paper (so far) that discusses plant genomes is one devoted to RNAs. Here's the abstract ...

Anyatama, A., Datta, T., Dwivedi, S. and Trivedi, P.K. (2024) Transcriptional junk: Waste or a key regulator in diverse biological processes? Current Opinion in Plant Biology 82:102639. [doi: 10.1016/j.pbi.2024.102639]

Plant genomes, through their evolutionary journey, have developed a complex composition that includes not only protein-coding sequences but also a significant amount of non-coding DNA, repetitive sequences, and transposable elements, traditionally labeled as “junk DNA”. RNA molecules from these regions, labeled as “transcriptional junk,” include non-coding RNAs, alternatively spliced transcripts, untranslated regions (UTRs), and short open reading frames (sORFs). However, recent research shows that this genetic material plays crucial roles in gene regulation, affecting plant growth, development, hormonal balance, and responses to stresses. Additionally, some of these regulatory regions encode small proteins, such as miRNA-encoded peptides (miPEPs) and microProteins (miPs), which interact with DNA or nuclear proteins, leading to chromatin remodeling and modulation of gene expression. This review aims to consolidate our understanding of the diverse roles that these so-called “transcriptional junk” regions play in regulating various physiological processes in plants.

As you can see from the abstract, the issue of functional transcripts is framed as a controversy about junk DNA. This perspective is repeated in the introduction but the rest of the article is simply a list of all the known transcripts that have a function. This includes several examples of lncRNAs, circular RNAs, siRNAs, and miRNAs. The only other mention of "junk" is in the legend of Figure 1 (below), which has the following title: "Key players of transcriptional junk regulating plant homeostasis and stress responses in Ababidopsis thaliana."

There's very little doubt that most of the genomes of flowering plants is junk and very little doubt that most of the transcripts from these genomes are junk RNA. It's also a fact that, contrary to the first sentence of the abstract, no knowledgeable scientist ever labeled all non-coding DNA as junk. Thus, the first sentence is extemely misleading.

Here's what I don't understand. There's nothing wrong with a review that summarizes the data for some functional RNAs but why do the authors feel it necessary to insert false rhetoric about junk DNA? Why not just say that most of the genome is junk and most of the transcripts are junk but, nevertheless, there are some important regulatory RNAs whose abundance and function we are just beginning to appreciate?

Do the authors not believe what I just wrote? Do they think that most of the DNA in plant genomes is actually functional? Have they ever examined the evidence for junk DNA? Have they ever heard of the Onion Test?

I have sent an email message to the corresponding author, Prabodh Kumar Trivedi, and invited them to respond to my criticism.

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