If you’re looking for good advice on how to live a long and healthy life, you might ask someone who’s been around the block a few times. Or, in this case, a few centuries.
Meet Jonathan the Aldabra giant tortoise, who was basking on South Atlantic beaches decades before the Civil War. Or the Greenland shark, silently cruising the deep while Napoleon was still on the throne. And Goethe’s Palm, a monumental Mediterranean plant that was photosynthesizing long before Newton encountered his first falling apple. These living legends have not just survived history, they are history.
Scientists are just beginning to unravel their genomic secrets to longevity. Equipped with HiFi long-read sequencing technology that can tackle these complex genomes, researchers can finally peek inside the remarkable biology of these living fossils with exceptional clarity. With the power of accurate long reads, scientists are resolving genomic regions that were once too complex or too repetitive to decode. As you’ll see, HiFi sequencing is helping uncover the secrets behind long lives, resilient biology, and maybe even the future of our own health.
Here are three recent studies that use HiFi sequencing to unlock the genomes of some of Earth’s oldest living organisms and examine how the latest advances in sequencing technology are making this work possible.
The long life (and long reads) of Jonathan the tortoise
With an estimated birth date in 1832, Jonathan the Aldabra giant tortoise not only holds the Guiness World Record for the oldest living land animal, but may also harbor the secret to his old age deep in his genome. With this recent paper, researchers from Myriad Genetics, Igenbio, Vanderbilt University, and Kallel Labs set out to uncover this gentle giant’s secrets by sequencing his genome for the first time.
Due to Jonathan’s protected status, the researchers swapped traditional blood sampling with cheek swabbing to collect DNA. (Though non-invasive, using this method was no small feat: the manuscript details Jonathan’s resistance to being swabbed on par with his hatred for kale!) As a way to highlight Jonathan’s enduring genetics, the authors compared his genome with Tank’s, a 36-year-old giant tortoise. With this high-quality HiFi reference genome, the researchers could pinpoint what exactly makes Jonathan so exceptional.
Jonathan’s genome did not disappoint. This side-by-side comparison uncovered major differences in DNA methylation, highlighting genomic markers of aging. Jonathan’s genome retained gene variants tied to DNA repair and telomere regulation, two systems key to longevity. These findings support a new model of aging that ties DNA methylation to efficient energy production.
Performing HiFi sequencing on precious and protected samples like these is only becoming more possible with the Ampli-Fi protocol, which allows researchers to generate high-quality HiFi libraries from as little as 1 ng of DNA. This is a game-changer for working with rare or limited samples and making studies of life’s most fascinating secrets more accessible than ever.
Piecing together the puzzle of a massive shark genome
Few animals capture the imagination quite like the elusive Greenland shark. Living in the frigid depths of the North Atlantic and Arctic Oceans, these massive predators can grow to 6 meters long and live for over 400 years. In a new study, researchers from the University of Tokyo produced the first chromosome-level genome assembly of this long-lived species.
The shark’s genome clocks in at a staggering 5.9 Gb and is over 80% repetitive, an intimidating prospect for any sequencing technology. But HiFi sequencing, with its unique combination of long read lengths and extraordinary accuracy, was up to the task. These long, accurate reads are essential for resolving complex repeat regions in massive genomes like this one.
Similar to Jonathan’s, the shark’s genome revealed expansions in gene families tied to DNA repair and chromosomal stability, particularly genes involved in the NF-κB pathway when compared to short-lived shark species. Several genes associated with cancer suppression were also under positive selection, providing potential explanations for the shark’s low cancer risk despite its longevity and size. The study also uncovered adaptations for deep-sea living, including changes in rhodopsin genes that enhance dim-light vision.
Ultimately, the ability of HiFi sequencing to traverse vast stretches of repetitive sequences and accurately anchor those reads across the genome was crucial to this project. In short: to unlock the secrets of a massive, repeat-rich genome, you need long, faithful reads. That’s where HiFi shines.
A palm tree older than the Constitution meets long-read sequencing
Far from the depths of the Arctic is the sun-drenched Goethe’s Palm, planted in 1585 and still thriving in the Botanical Garden of the University of Padua in Italy. As the oldest cultivated palm in the world, this Mediterranean marvel is now also the proud subject of the most contiguous and complete palm genome ever assembled.
Researchers from the University of Padua used HiFi sequencing to generate a chromosome-level assembly with nearly all telomeres and centromeres for a total of 4.41 Gbp. And here’s where it gets wild: 88% of the palm genome is made up of repeats, mostly long terminal repeat (LTR) elements.
Not only did HiFi sequencing easily uncover a recent burst of LTR activity, likely related to environmental stress adaptation, it also marked the first identification in palms of a unique microRNA involved in nutrient regulation, a potential key to its evolutionary and ecological success. These findings not only point to specific mechanisms that contribute to the Goethe’s Palm enduring legacy, but they also provide valuable information in the conservation of its species and biodiversity at large.
This study beautifully demonstrates how HiFi sequencing can handle the toughest genomic challenges, opening doors not only for evolutionary insights but also for conservation strategies aimed at preserving endangered flora.
The power of long-read sequencing to unlock the biology of longevity
It’s not every day you get to peek inside the genomes of organisms that are outliving empires. But with the accuracy and read lengths of HiFi sequencing, we’re not just preserving these species, we’re learning from them.
HiFi technology is enabling researchers to unlock the secrets of longevity, resilience, and adaptation hidden deep within the genomes of Earth’s oldest living species. Whether it’s unlocking the secrets of DNA repair mechanisms, maintaining chromosomal stability, or navigating an extreme repeat landscape, HiFi long reads are up for the challenge.
So what’s the final verdict in the secret to a long life? Scientists are still consulting with Jonathan the tortoise, the Greenland shark, and Goethe’s Palm. But with HiFi sequencing, we’re starting to decode their story, one base at a time.
No matter what species in the tree of life you’re working on, check out our Plant + Animal brochure to learn where to get started.