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.
5 comments :
As a student in the 70s I learned that, especially in plants, polyploidy is widespread: triploidy, tetraploidy, pentaploidy, etc up to tetratetracontaploid (= 44 x haploid set of chromosomes). At that time already an Atlas existed with all chromosome numbers of plants known. It was obvious that polyploidy occurred in all families. Polyploidy means redundant sets of chromosomes! It is easy to understand that mutations accumulate, making many genes nonfunctional... a source of junk DNA.
Since Arabidopsis has an unusually small genome, it presumably has a lower proportion of junk than most plants. So why is it being used as a model for all plants? And if it turned out that the entire Arabidopsis genome was functional, wouldn't the onion test, applied to the rest of the plants, be an even more powerful argument for the prevalence of junk?
PS. for those interested: the 'Chromosome Atlas Of Cultivated plants' by C. D. Darlington Frs was published in 1945. A that time it was already noted: "Related forms usually arrange themselves in polyploid series with chromosome numbers that are multiples of a common basic number, x: diploid 2x, tetraploid 4x, hexaploid 6x and so on."
There is a free full text online copy at:
https://archive.org/details/lbg.633.03.dar.0811/page/30/mode/2up
In 1945 the first edition of 'Chromosome atlas of flowering plants' was published also by Darlington.
(mostly @gert korthof)
I did some work (starting in 2011, Gothenburg)) on the phylogenetics of allopolyploids (hybrid polyploids) and although I'm a mathematician, not biologist, I learned some things about polyploids. Colleagues had a lot of (~1000bp) DNA sequences from a bunch of plant species, but didn't know the ploidy levels. I said "I thought you'd just look down a microscope and count chromosomes" but it is a specialised skill, only one old professor in the department had the skills and she was too busy. It is odd to be able to read a book without being able to count the chapters. The current world record for genome size is the New Caledonian fork fern at 160B bp. The paper says "we believe with relatively high confidence, that the individual analyzed in this study is also octoploid".
When polyploids form, the cell size generally increases in proportion to ploidy level, so its not obvious that the
extra gene copies are redundant. (I guess many are in high ploidy plants, but you can't just assume it.)
(mostly @John Harshman)
I think Arabidopsis became a model plant /because/ it has an unusually small genome so was easy to sequence. It can go through a complete lifecycle in 6 weeks which I imagine is also handy. As for it being a model for all plants, perhaps there's too much money going into the dark matter of 'the' genome and not enough into botany?
The New Caledonian fork fern paper says the range of genome sizes known for eukaryotes is over 61,000-fold, and about 2,500-fold among plants.
"I thought you'd just look down a microscope and count chromosomes":
the problem here is that with high number of chromosomes (even 46 human chromosomes!) it gets pretty crowded in a cell. In a two-dimensional microscopic preparation, chromosomes are overlapping (on top of each other) and that makes it difficult or impossible to count. The higher the number of chromosomes in a cell the higher the probability chromosomes lie on top of each other. Its time-consuming to find a cell in which all chromosomes are neatly separated. Automated image recognition by computer can assist in finding those rare cells.
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