The study sheds light on the “black holes” in th

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image: Todd Michael
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Credit: Institut Salk

LA JOLLA – (November 11, 2021) Salk scientists, together with researchers at Cambridge University and Johns Hopkins University, have sequenced the genome of the world’s most widely used model plant species, Arabidopsis thaliana, at a level of detail never seen before. The study, published in Science on November 12, 2021, reveals the secrets of Arabidopsis chromosomal regions called centromeres. The results shed light on the evolution of the centromere and provide insight into the genomic equivalent of black holes.

“A little over 20 years ago, the Arabidopsis genome has been published, and it has been the benchmark plant genome since it has given rise to amazing advances, from models to cultures, ”says Todd Michael, research professor at the Plant Molecular and Cellular Biology Laboratory. “Our new assembly resolves the last missing pieces of the genome, paving the way for exciting research into the architecture and evolution of chromosomes, which will be critical to our efforts to design plants to combat climate change in the United States. to come up.”

Arabidopsis thaliana was adopted as a model plant due to its short generation time, small size, ease of growth, and prolific seed production by self-pollination. Its rapid life cycle and small genome make it well suited for genetic research and mapping of key genes that underlie the traits of interest. It led to a multitude of discoveries and in 2000 it became the first plant to have its genome sequenced. This initial genome release was at an excellent level in the chromosomal arms, where most genes are located, but was unable to assemble the highly repetitive and complex regions known as centromeres, telomeres, and ribosomal DNA. Today, thanks to advances in sequencing technologies, these difficult regions have been assembled for the first time.

The study is the first to successfully perform long-term sequencing and assembly of Arabidopsis thaliana centromeres. Since the genome was first sequenced in 2000, long-read sequencing technologies have advanced, allowing researchers to see the genome in more than 100,000 pieces of nucleotides, instead of 100 to 200 pieces of nucleotides. These data, combined with the algorithmic advances that put the readings together, mean that the “genomic puzzle” is suddenly achievable.

“Centromeres are among the most interesting regions of the genome, but also the most difficult to analyze. . “Fortunately, advances in sequencing coupled with advances in computational methods for genome assembly now allow even the most difficult sequences to be assembled with precision,” such as the genetic makeup of the centromere.

For decades, researchers have attempted to understand the paradox of how and why centromeric DNA evolves with extraordinary speed, while remaining stable enough to fulfill its role in cell division. In contrast, other old parts of the cell that have conserved roles, such as ribosomes, which make proteins from mRNA, tend to evolve very slowly. Yet the centromere, despite its retained role in cell division, is the fastest growing part of the genome. This study, by revealing the genetic and epigenetic topography of Arabidopsis centromeres, marks a radical change in our understanding of this paradox.

As part of the study, the centromere maps compiled provide new information about the “repeat ecosystem” found in the centromere. The maps reveal the architecture of repeat networks, which has implications for their evolution, as well as for the chromatin and epigenetic states of centromeres. In the future, scientists want to use these maps as a basis for understanding how and why centromeres evolve so rapidly.

“It’s fantastic to be able to see in centromeres for the first time and use it to understand their unusual evolutionary patterns,” says Professor Ian Henderson, co-corresponding author, Department of Plant Sciences at the University. from Cambridge.

Next, scientists will seek to use this approach to map the centromeres of various Arabidopsis species, and finally more widely through plants.

Other authors include Bradley W. Abramson, Nolan Hartwick, and Kelly Colt of Salk; Matthew Naish, Piotr Wlodzimierz, Andrew J. Tock, Christophe Lambing, Pallas Kuo and Natasha Yelina of the University of Cambridge; Michael Alonge of Johns Hopkins University; Anna Schmücker, Bhagyshree Jamge and Frédéric Berger of the Austrian Academy of Sciences; Terezie Mandáková and Martin A. Lysak from Masaryk University in the Czech Republic; Lisa Smith and Jurriaan Ton of the University of Sheffield; Tetsuji Kakutani of the University of Tokyo; Robert A. Martienssen of the Howard Hughes Medical Institute; Korbinian Schneeberger from LMU Munich; and Alexandros Bousios from the University of Sussex.

Funding has been provided by grants and awards from the British Biotechnology and Biological Sciences Research Council, European Research Council, Marie Curie International Training Network, Human Frontier Science Program, National Institutes of Health, the National Science Foundation, the Royal Society, the Czech Science Foundation, the Gregor Mendel Institute, the Fonds zur Förderung der wissenschaftlichen Forschung (FWF), the Leverhulme Trust and the Howard Hughes Medical Institute.

Published courtesy of the Department of Plant Sciences, University of Cambridge.

About the Salk Institute for Biological Studies:

Each cure has a starting point. The Salk Institute embodies Jonas Salk’s mission to dare to make dreams come true. Its internationally renowned and award-winning scientists explore the very foundations of life, seeking new understandings in neuroscience, genetics, immunology, plant biology and more. The Institute is an independent, non-profit organization and an architectural landmark: small by choice, intimate by nature, and fearless in the face of any challenge. Whether it’s cancer or Alzheimer’s disease, aging or diabetes, Salk is where the cures begin. Find out more at: salk.edu.


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