Unravelling the ancient stories hidden in DNA

Date:
February 3, 2022
Source:
Okinawa Institute of Science and Technology (OIST) Graduate
University
Summary:
Scientists have compared the chromosomes of three major animal
groups to reveal surprising stability across a time span of more
than 550 million years.



FULL STORY ========================================================================== Scientists have discovered that the genomes of marine invertebrates
have been surprisingly stable across deep time. Published in Science
Advances, this new study provides an overarching analysis of distantly
related animal groups, including sponges, jellyfish, scallops, and
the invertebrates most closely related to humans, and found that their chromosomes are remarkably similar.


========================================================================== Think of a genome as the instruction manual located in each cell and
written in DNA code. It contains all the inherited information for the operation of an organism. This instruction manual is divided into chapters
-- the chromosomes - - and those are, in turn, further subdivided into
pages -- the genes.

"Over deep time -- and by that, I mean at least 550 million years
-- due to random mutations, the order of genes within chromosomes
become scrambled, kind of like mixing up pages within a chapter of a
book. And more dramatically, sometimes we find that two chromosomes
have come together and become mixed, as if the chapters were merged
and shuffled." explained Prof. Daniel Rokhsar, last author of the
paper and principal investigator of the Molecular Genetics Unit at the
Okinawa Institute of Science and Technology Graduate University (OIST)
in Japan. "But overall, we found a remarkable amount of stability. Even
though the last common ancestor of these three groups lived over half a
billion years ago, many of their chromosomes are recognizably similar in
the sense that they contain the same groups of genes." The study compared
the genomes of species from the three vast groups -- sponges (very simple animals with no muscles or nerves), cnidarians (specifically jellyfish
and hydra), and bilaterians (scallops and amphioxus). These genomes had
either been previously sequenced or were first reported in this study.

Although many of these organisms had had "draft" versions of their genomes sequenced before, this early research fell short of being able to study
overall chromosomal organization. Now, with advancements in genetic
technology, researchers are able to put the puzzles together and compare
the way genes are organized into the long threads. In this study, the chromosomes of the hydra were, for the first time, reconstructed, those
of the amphioxus were vastly improved, and a wide-ranging comparative
analysis was completed.

The international group of researchers, which included scientists from
OIST, University of Vienna, the University of California campuses at
Berkeley, Irvine, and Santa Cruz, Ludwig Maximilian University of Munich,
and University College, London, found striking similarities between
the chromosomes of the five different animals, and confirmed that these similarities were also present in other animal genomes. In some cases,
they identified patterns of chromosomal fusion that were specific to
certain sub-groups of animals. For example, the researchers found four
ancient fusions shared by scallops and several other mollusks, which
also resembled a fusion in the draft genome of a marine worm.

"We see that genes can be on the same chromosome in different species but
often in a different order," explained Prof. Rokhsar. "In rare cases where
two chromosomes fuse together and then get mixed up by scrambling across
the newly fused chromosome, this fusion can't be undone, and serves as
a permanent marker of the evolutionary history of the chromosome. It's
like shuffling two packs of cards together. We can keep shuffling them,
but they will never divide into the two exact packs again." When living animals share the same fusions, the researchers infer that the fusions
must have occurred in an ancient common ancestor of these species. They
have now made several testable predictions about yet-to-be-sequenced
genomes.

For example, the team predicts that the genomes of all mollusks and
related "spiralian" animals must show the specific set of fusions seen
in scallops.

These results showcase an interesting paradox. "Mammals have only been
around for about 100 million years," Prof. Rokhsar explained. "But
when we compare the genome of two mammals, say, a human and a mouse,
the chromosomes look like they have been broken up into a few hundred
pieces and then mixed together. The chromosome-scale conservation characteristic that we found in invertebrates is simply not seen in
mammals." He speculated that mammalian chromosomes could have evolved differently because, historically, mammals have lived in smaller groups
than most marine invertebrates. Small groups facilitate the survival of
these random mutations, which could be why chromosomal rearrangements
spread more easily in mammals.

In total, the researchers identified 29 ancestral segments of chromosomes.

Furthermore, the group found that some of these segments were present some
800- 900 million years, before the existence of animals, when all the
organisms were in unicellular or very simple multicellular forms. Thus,
some genes have been travelling together for almost a billion years,
yet the consequence of these ancient gene linkages remains a mystery.

========================================================================== Story Source: Materials provided by Okinawa_Institute_of_Science_and_Technology_(OIST)
Graduate_University. Original written by Lucy Dickie. Note: Content may
be edited for style and length.


========================================================================== Journal Reference:
1. Oleg Simakov, Jessen Bredeson, Kodiak Berkoff, Ferdinand Marletaz,
Therese Mitros, Darrin T. Schultz, Brendan L. O'Connell, Paul
Dear, Daniel E. Martinez, Robert E. Steele, Richard E. Green,
Charles N. David, Daniel S. Rokhsar. Deeply conserved synteny and
the evolution of metazoan chromosomes. Science Advances, 2022; 8
(5) DOI: 10.1126/sciadv.abi5884 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2022/02/220203103038.htm

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