Posts Tagged ‘genome’
“Judge me by my size, do you?”*…
A tiny variety of the fork fern seems altogether unremarkable– but has a genome that dwarfs the human genome in size. Max Kozlov explains what that might teach us…
A small, unassuming fern-like plant has something massive lurking within: the largest genome ever discovered, outstripping the human genome by more than 50 times.
The plant (Tmesipteris oblanceolata) contains a whopping 160 billion base pairs, the units that make up a strand of DNA. That’s 11 billion more than the previous record holder, the flowering plant Paris japonica, and 30 billion more than the marbled lungfish (Protopterus aethiopicus), which has the largest animal genome. The findings were published [on May 31] in iScience…
The world’s genomic champion, which is native to New Caledonia and neighbouring archipelagos in the South Pacific, is a species of plant called a fork fern. Its colossal number of base pairs raises questions as to how the plant manages its genetic material. Only a small proportion of DNA is made of protein-coding genes, leading study co-author Ilia Leitch, an evolutionary biologist at London’s Royal Botanic Gardens, Kew, to wonder how the plant’s cellular machinery accesses those bits of the genome “amongst this huge morass of DNA. It’s like trying to find a few books with the instructions for how to survive in a library of millions of books — it’s just ridiculous.”
There’s also the question of how and why an organism evolved to have so many base pairs. Generally, having more base pairs leads to higher demand for the minerals that comprise DNA and for energy to duplicate the genome with every cell division, Leitch says. But if the organism lives in a relatively stable environment with little competition, a gargantuan genome might not come with a high cost, she adds.
That could help to provide an explanation — although a rather boring one — for the fork fern’s large genome: it might be neither detrimental nor particularly helpful for the plant’s ability to survive and reproduce, so the fork fern has gone on accumulating base pairs over time, says Julie Blommaert, a genomicist at the New Zealand Institute for Plant and Food Research in Nelson.
For now, researchers can only speculate on answers to these questions. The largest genome to be sequenced and assembled belongs to the European mistletoe (Viscum album), with about 90 billion base pairs. Modern techniques might not be sufficient to do the same for the fork fern’s genome: even if it’s sequenced, there’s still the computational challenge of taking the data and “sticking them together in a way that biologically reflects what’s going on”, Leitch says.
Finding ways to analyse enormous genomes could yield crucial insights into how genome size influences where organisms can grow, how they are able to flourish in their environments and their resilience to climate change, independent of their specific DNA sequence, she adds. Pellicer says it’s remarkable that a tiny, non-flowering plant that most people “wouldn’t bother to stop and look at” could offer such important lessons. “The beauty of the plant is inside.”
“Biggest genome ever found belongs to this odd little plant,” from @maxdkozlov in @Nature.
* Yoda, “The Empire Strikes Back”
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As we rescope scale, we might send insightful birthday greetings to Phillip Allen Sharp; he was born on this date in 1944. A geneticist and molecular biologist, he co-discovered RNA splicing— for which he shared the 1993 Nobel Prize in Physiology or Medicine (with Richard J. Roberts). His work has spurred new research in evolutionary biology, and has contributed to the development of both treatments and vaccines for infectious diseases, cancer and other ailments.
“History repeats itself, in part because the genome repeats itself. And the genome repeats itself, in part because history does.”*…
The original Human Genome Project map of the human genome was largely based on the DNA of one mixed-race man from Buffalo, with inputs from a few dozen other individuals, mostly of European descent. Now, researchers have released draft results from an ongoing effort to capture the entirety of human genetic variation…
More than 20 years after the first draft genome from the landmark Human Genome Project was released, researchers have published a draft human ‘pangenome’ — a snapshot of what is poised to become a new reference for genetic research that captures more of human diversity than has been previously available. Geneticists have welcomed the milestone, while also highlighting key ethical considerations surrounding the effort to make genome research more inclusive…
The draft genome, published in Nature on 10 May, was produced by the Human Pangenome Reference Consortium. Launched in 2019, the international project aims to map the entirety of human genetic variation, to create a comprehensive reference against which geneticists will be able to compare other sequences. Such a reference would aid studies investigating potential links between genes and disease.
The draft pangenome follows the 2022 publication of the first complete sequence of the human genome, which filled gaps that had been left by the original Human Genome Project. But unlike the original draft human genome and its successor, both of which were derived mostly from the DNA of just one person, the draft pangenome represents a collection of sequences from a diverse selection of 47 people from around the globe, including individuals from Africa, the Americas, Asia and Europe…
More at “First human ‘pangenome’ aims to catalogue genetic diversity,” in @Nature.
See the paper on the Pangenome Project here; and for more background, “This new genome map tries to capture all human genetic variation.”
* Siddhartha Mukherjee, The Gene: An Intimate History
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As we go wide on genetics, we might send microscopic birthday greetings to Christian Anfinsen; he was born on this date in 1916. A biochemist, he won the 1972 Nobel Prize for Chemistry for his research on the shape and primary structure of ribonuclease (the enzyme that hydrolyses RNA), in whihc he found that found that its shape and consequently its enzymatic power could be restored– leading him to conclude that ribonuclease must retain all of the information about its configuration within its amino acids.
“LOCK-AND-KEY, n. The distinguishing device of civilization and enlightenment”*…
The pursuit of lock picking is as old as the lock, which is itself as old as civilization. But in the entire history of the world, there was only one brief moment, lasting about 70 years, where you could put something under lock and key—a chest, a safe, your home—and have complete, unwavering certainty that no intruder could get to it.
This is a feeling that event security guard service experts call “perfect security.”
Since we lost perfect security in the 1850s, it has has remained elusive. Despite tremendous leaps forward in security technology, we have never been able to get perfect security back…
Joseph Bramah’s challenge lock: “The artist who can make an instrument that will pick or open this lock shall receive 200 Guineas the moment it is produced.” 200 Guineas in 1777 would be about £20,000 today. The challenge held until 1851.
From the late 1770s until the mid-19th century, two British locks– the Bramah and the Chubb– offered their users unpickable security. Then, at A. C. Hobbs, an American locksmith, attended The Great Exhibition—the first international exhibition of manufactured products– and destroyed that sense of security forever…
The “unpickable” Chubb Detector Lock
Read the remarkable Roman Mars’ account of security (and the loss thereof) in “In 1851, A Man Picked Two Unpickable Locks and Changed Security Forever“; hear it on his wonderful podcast, 99% Invisible.
* Ambrose Bierce, The Devil’s Dictionary
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As we reach for our keys, we might recall that it was on this date in 1953 that a different kind of lock was picked: Nature published a one-page article by James Watson and Francis Crick outlining the structure of DNA– te work for which the pair won a Nobel Prize in 1962. (Their paper ran immediately ahead of one co-authored by Maurice Wilkins, who shared the Nobel award, in the same issue.)
source (and larger, legible version)
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