Shining a light into 'black holes' in the Arabidopsis genome

Date:
November 11, 2021
Source:
Salk Institute
Summary:
Scientists have sequenced the genome of the world's most widely
used model plant species, Arabidopsis thaliana, at a level of
detail never previously achieved. The study reveals the secrets
of Arabidopsis chromosome regions called centromeres. The findings
shed light on centromere evolution and provides insights into the
genomic equivalent of black holes.



FULL STORY ==========================================================================
Salk scientists, collaborating with researchers from the University of Cambridge 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 previously achieved. The study, published in Science
on November 12, 2021, reveals the secrets of Arabidopsischromosome regions called centromeres. The findings shed light on centromere evolution and provides insights into the genomic equivalent of black holes.


========================================================================== "Just over 20 years ago the Arabidopsis genome was published, and it has
been the gold standard plant genome since giving rise to amazing advances
from models to crops," says Todd Michael, a research professor in the
Plant Molecular and Cellular Biology Laboratory. "Our new assembly
resolves the final missing pieces of the genome, paving the way for
exciting research on chromosome architecture and evolution, which will
be critical for our efforts to engineer plants to address climate change
in the future." Arabidopsis thaliana was adopted as a model plant due
to its short generation time, small size, ease of growth and prolific
seed production through self- pollination. Its fast life cycle and small
genome make it well suited for genetics research and to map key genes
that underpin traits of interest. It has led to a multitude of discoveries
and in 2000 it became the first plant to have its genome sequenced. This initial genome release was of an excellent standard in the chromosome
arms, where most of the genes are located, but was unable to assemble the highly repetitive and complex regions known as centromeres, telomeres
and ribosomal DNA. Now, due to advances in sequencing technologies,
these challenging regions have been assembled for the first time.

The study is the first to successfully perform long-read sequencing and assembly of the Arabidopsis thaliana centromeres. Since the genome was
first sequenced in 2000, long-read sequencing technologies have advanced, allowing researchers to see the genome in greater than 100,000 nucleotide pieces, instead of 100-200 nucleotide pieces. These data, combined with algorithmic advances that assemble the reads, means that the "genomic
jigsaw puzzle" is suddenly now completable.

"The centromeres are some of the most interesting, but also the most
difficult, regions of the genome to analyse -- they are like endless
'blue sky' within a jigsaw puzzle," says co-corresponding author Professor
Mike Schatz, from Johns Hopkins University. "Fortunately, advances in sequencing paired with advances in the computational methods for genome assembly now make it possible to accurately assemble even the most
challenging of sequences," such as the genetic makeup of the centromere.

For decades, researchers have been trying to understand the paradox of
how and why centromeric DNA evolves with extraordinary rapidity, whilst remaining stable enough to perform its job during cell division. In
contrast, other ancient parts of the cell that have conserved roles,
such as ribosomes, which make proteins from mRNA, tend to be very slow evolving. Yet the centromere, despite its conserved role in cell division,
is the fastest evolving part of the genome. This study, by revealing
the genetic and epigenetic topography of Arabidopsis centromeres, marks
a step change in our understanding of this paradox.

As part of the study, the compiled centromere maps provide new insights
into the "repeat ecosystem" found in the centromere. The maps reveal
the architecture of the repeat arrays, which has implications for
how they evolve, and for the chromatin and epigenetic states of the centromeres. Moving forward the scientists want to use these maps as a foundation to understand how and why centromeres are evolving so rapidly.

"It's fantastic to be able to see into the centromeres for the first
time and use this to understand their unusual modes of evolution," says co-corresponding author Professor Ian Henderson, from the University of Cambridge's Department of Plant Sciences.

Next, the scientists will be looking at using this approach to map
centromeres from diverse Arabidopsis species, and ultimately more widely throughout plants.

========================================================================== Story Source: Materials provided by Salk_Institute. Note: Content may
be edited for style and length.


========================================================================== Journal Reference:
1. Matthew Naish, Michael Alonge, Piotr Wlodzimierz, Andrew J. Tock,
Bradley
W. Abramson, Anna Schmu"cker, Terezie Manda'kova', Bhagyshree Jamge,
Christophe Lambing, Pallas Kuo, Natasha Yelina, Nolan Hartwick,
Kelly Colt, Lisa M. Smith, Jurriaan Ton, Tetsuji Kakutani, Robert A.

Martienssen, Korbinian Schneeberger, Martin A. Lysak, Fre'de'ric
Berger, Alexandros Bousios, Todd P. Michael, Michael C. Schatz,
Ian R. Henderson.

The genetic and epigenetic landscape of the Arabidopsis centromeres.

Science, 2021; 374 (6569) DOI: 10.1126/science.abi7489 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2021/11/211111154226.htm

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