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Onion test

The onion test is a way of assessing the validity of an argument for a functional role for junk DNA. It relates to the paradox that would emerge if the majority of eukaryotic non-coding DNA were assumed to be functional and the difficulty of reconciling that assumption with the diversity in genome sizes among species.[1] The term "onion test" was originally proposed[2] informally in a blog post by T. Ryan Gregory in order to help clarify the debate about junk DNA. The term has been mentioned in newspapers and online media,[3][4] scientific journal articles,[5][6][7][8] and a textbook.[9] The test is defined as:

The onion test is a simple reality check for anyone who thinks they have come up with a universal function for junk DNA. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?

Onions and their relatives vary dramatically in their genome sizes,[10] without changing their ploidy, and this gives an exceptionally valuable window on the genomic expansion junk DNA. Since the onion (Allium cepa) is a diploid organism having a haploid genome size of 15.9 Gb,[10] it has 4.9x as much DNA as does a human genome (3.2 Gb). Other species in the genus Allium vary hugely in DNA content without changing their ploidy. Allium schoenoprasum (chives) for example has a haploid genome size of 7.5 Gb, less than half that of onions, yet Allium ursinum (wild garlic) has a haploid genome size of 30.9 Gb, nearly twice (1.94x) that of onion and over four times (4.1x) that of chives. This extreme size variation between closely related species in the genus Allium is also part of the extended onion test rationale as originally defined:[2]

Further, if you think perhaps onions are somehow special, consider that members of the genus Allium range in genome size from 7 pg to 31.5 pg. So why can A. altyncolicum make do with one fifth as much regulation, structural maintenance, protection against mutagens, or [insert preferred universal function] as A. ursinum?

  1. ^ Palazzo, Alexander F.; Gregory, T. Ryan (8 May 2014). Akey, Joshua M. (ed.). "The Case for Junk DNA". PLOS Genetics. 10 (5): e1004351. doi:10.1371/journal.pgen.1004351. ISSN 1553-7404. PMC 4014423. PMID 24809441. In summary, the notion that the majority of eukaryotic noncoding DNA is functional is very difficult to reconcile with the massive diversity in genome size observed among species, including among some closely related taxa. The onion test is merely a restatement of this issue, which has been well known to genome biologists for many decades.
  2. ^ a b "The onion test. « Genomicron". www.genomicron.evolverzone.com. 25 April 2007. Retrieved 13 February 2019.
  3. ^ Moran, Laurence A. (12 October 2011). "Sandwalk: A Twofer". Sandwalk. Retrieved 13 February 2019.
  4. ^ Zimmer, Carl (8 March 2015). "Is most of our DNA garbage?". The New York Times Magazine.
  5. ^ Palazzo, Alexander F.; Gregory, T. Ryan (8 May 2014). Akey, Joshua M. (ed.). "The Case for Junk DNA". PLOS Genetics. 10 (5): e1004351. doi:10.1371/journal.pgen.1004351. ISSN 1553-7404. PMC 4014423. PMID 24809441.
  6. ^ Freeling, Michael; Xu, Jie; Woodhouse, Margaret; Lisch, Damon (2015). "A Solution to the C-Value Paradox and the Function of Junk DNA: The Genome Balance Hypothesis". Molecular Plant. 8 (6): 899–910. doi:10.1016/j.molp.2015.02.009. PMID 25743198.
  7. ^ Germain, Pierre-Luc; Ratti, Emanuele; Boem, Federico (2014). "Junk or functional DNA? ENCODE and the function controversy". Biology & Philosophy. 29 (6): 807–831. doi:10.1007/s10539-014-9441-3. ISSN 0169-3867. S2CID 84480632.
  8. ^ Graur, D.; Zheng, Y.; Price, N.; Azevedo, R. B. R.; Zufall, R. A.; Elhaik, E. (26 March 2013). "On the Immortality of Television Sets: "Function" in the Human Genome According to the Evolution-Free Gospel of ENCODE". Genome Biology and Evolution. 5 (3): 578–590. doi:10.1093/gbe/evt028. ISSN 1759-6653. PMC 3622293. PMID 23431001.
  9. ^ Graur, Dan (2016). Molecular and genome evolution. Sunderland, Massachusetts: Oxford University Press. ISBN 9781605354699. OCLC 951474209.
  10. ^ a b Ricroch, A; Yockteng, R; Brown, S C; Nadot, S (2005). "Evolution of genome size across some cultivated Allium species". Genome. 48 (3): 511–520. doi:10.1139/g05-017. ISSN 0831-2796. PMID 16121247.

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