The oldest living organism in New York City is said to be a tulip tree (Liriodendron tulipifera) – although exactly which tulip tree is still up for debate – and this majestic tree now has a new claim for extraordinary agedness. A recent study published in BMC Biology from Aaron Richardson and colleagues, and reported by the BBC, reveals that the mutation rate of the tulip tree mitochondrial genome is so low that it appears to have changed very little over the last tens of millions of years. This led the authors to refer to the tree’s mitochondrial genome as a molecular ‘fossil’.
In much the same way as animal conservation efforts often focus disproportionately on the charismatic mammalian groups, sequencing of plant genomes and mitochondrial genomes has tended to focus on a group called the monocotyledons – or ‘monocots’ colloquially, named for a distinguishing feature of the seeds – because it contains many major crop plants. The tulip tree is of particular interest because it comes from the Magnoliid clade, an early-branching group that split from the rest of the flowering plants early in their evolutionary history. The surprisingly low mutation rate makes it now even more interesting than one would otherwise expect.
Mutation rate is usually measured as the rate of ‘silent site’ nucleotide substitutions – those which do not cause a change in amino acids in the associated proteins. For L. tulipifera mitochondria, this rate is 0.035 substitutions per site per billion years: to put that into perspective, it’s around 2,000 times slower than the human mitochondrial mutation rate. Quite how it maintains such a low mutation rate isn’t clear but it may have something to do with the tree’s long lifespan, as discussed by Ian Small in an accompanying commentary. Long-lived organisms tend to have proactive genome protection systems – antioxidants and the like – to guard against ageing, and these will naturally reduce the mutation rate. Alternatively, the low mutation rate may be a result of the high levels of reactive genome protection often found in plant mitochondria, which have a highly-active DNA repair system.
Other genome characteristics also point towards the ancient nature of the L. tulipifera mitochondrial genome. It shows extensive RNA editing – whereby specific RNA nucleotides are altered after transcription – concurring with an existing theory that levels of RNA editing were high in ancient mitochondria and have since declined. It also shares transfer RNA genes with species across the flowering plant clade, suggesting an even earlier origin for some of these genes than previously thought.
The L. tulipifera mitochondrial genome is the first from the Magnoliid clade to be fully sequenced and the sequencing of further Magnoliid species will offer further insight. One should, of course, be cautious about drawing too many general conclusions from a single species. But the signs are good that this clade will offer a unique insight into the evolution and ancestry of flowering plant mitochondria.
The “fossilized” mitochondrial genome of
Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate
BMC Biology 2013, 11:29 (15/04/2013)
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