• Squid and octopus genome studies reveal

    From ScienceDaily@1:317/3 to All on Wed May 4 22:30:48 2022
    Squid and octopus genome studies reveal how cephalopods' unique traits
    evolved

    Date:
    May 4, 2022
    Source:
    Marine Biological Laboratory
    Summary:
    Squid, octopus, and cuttlefish -- even to scientists who study them
    - - are wonderfully weird creatures. Known as the soft-bodied or
    coleoid cephalopods, they have the largest nervous system of any
    invertebrate, complex behaviors such as instantaneous camouflage,
    arms studded with dexterous suckers, and other evolutionarily
    unique traits. Now, scientists have dug into the cephalopod genome
    to understand how these unusual animals came to be. Along the way,
    they discovered cephalopod genomes are as weird as the animals
    are. Scientists from the Marine Biological Laboratory (MBL) in
    Woods Hole, the University of Vienna, the University of Chicago,
    the Okinawa Institute of Science and Technology and the University
    of California, Berkeley, reported their findings in two new studies
    in Nature Communications.



    FULL STORY ========================================================================== Squid, octopus, and cuttlefish -- even to scientists who study them --
    are wonderfully weird creatures. Known as the soft-bodied or coleoid cephalopods, they have the largest nervous system of any invertebrate,
    complex behaviors such as instantaneous camouflage, arms studded with
    dexterous suckers, and other evolutionarily unique traits.


    ==========================================================================
    Now, scientists have dug into the cephalopod genome to understand
    how these unusual animals came to be. Along the way, they discovered
    cephalopod genomes are as weird as the animals are. Scientists from
    the Marine Biological Laboratory (MBL) in Woods Hole, the University of
    Vienna, the University of Chicago, the Okinawa Institute of Science and Technology and the University of California, Berkeley, reported their
    findings in two new studies in Nature Communications.

    "Large and elaborate brains have evolved a couple of times," said co-lead author Caroline Albertin, Hibbitt Fellow at the MBL. "One famous example
    is the vertebrates. Another is the soft-bodied cephalopods, which serve as
    a separate example for how a large and complicated nervous system can be
    put together. By understanding the cephalopod genome, we can gain insight
    into the genes that are important in setting up the nervous system, as
    well as into neuronal function." In Albertin et al., published this week,
    the team analyzed and compared the genomes of three cephalopod species --
    two squids (Doryteuthis pealeii and Euprymna scolopes) and an octopus
    (Octopus bimaculoides).

    Sequencing these three cephalopod genomes, never mind comparing them,
    was a tour de force effort funded by the Grass Foundation that took
    place over several years in labs around the world.

    "Probably the greatest advance in this new work is providing
    chromosomal-level assemblies of no less than three cephalopod genomes,
    all of which are available for study at the MBL," said co-author Clifton Ragsdale, professor of Neurobiology and of Biology and Anatomy at the University of Chicago.



    ========================================================================== "Chromosomal-level assemblies allowed us to better refine what genes are
    there and what their order is, because the genome is less fragmented,"
    Albertin said.

    "So now we can start to study the regulatory elements that may be driving expression of these genes." In the end, comparing the genomes led the scientists to conclude that evolution of novel traits in soft-bodied cephalopods is mediated, in part, by three factors:
    * massive reorganization of the cephalopod genome early in evolution
    * expansion of particular gene families * large-scale editing of
    messenger RNA molecules, especially in nervous
    system tissues.

    Most strikingly, they found the cephalopod genome "is incredibly churned
    up," Albertin said.

    In a related study (Schmidbaur et al.), published last week, the team
    explored how the highly reorganized genome in Euprymna scolopes affects
    gene expression.

    The team found that the genome rearrangements resulted in new interactions
    that may be involved in making many of the novel cephalopod tissues,
    including their large, elaborate nervous systems.

    "In many animals, gene order within the genome has been preserved over evolutionary time," Albertin said. "But in cephalopods, the genome has
    gone through bursts of restructuring. This presents an interesting
    situation: genes are put into new locations in the genome, with new
    regulatory elements driving the genes' expression. That might create opportunities for novel traits to evolve." What's so Striking about
    Cephalopod Genomes?


    ==========================================================================
    Key insights into cephalopod genomes that the studies provide include:
    They're large.The Doryteuthisgenome is 1.5 times larger than the human
    genome, and the octopus genome is 90% the size of a human's.

    They're scrambled."Key events in vertebrate evolution, leading to humans, include two rounds of whole-genome duplication," Ragsdale said. "With
    this new work, we now know that the evolution of soft-bodied cephalopods involved similarly massive genome changes, but the changes are not
    whole-genome duplications but rather immense genome rearrangements, as if
    the ancestral genomes were put in a blender." "With this new information,
    we can begin to ask how large-scale genome changes might underlie those
    key unique features that cephalopods and vertebrates share, specifically
    their capacity for large bodies with disproportionately large brains,"
    Ragsdale said.

    Surprisingly, they found the three cephalopod genomes are highly
    rearranged relative to each other -- as well as compared to other animals.

    "Octopus and squid diverged from each other around 300 million years ago,
    so it makes sense that they seem they have very separate evolutionary histories," Albertin said. "This exciting result suggests that the
    dramatic rearrangements in cephalopod genomes have produced new gene
    orders that were important in squid and octopus evolution." They contain
    novel gene families.The team identified hundreds of genes in novel
    gene families that are unique to cephalopods. While some ancient gene
    orders common to other animals are preserved in these new cephalopod gene families, the regulation of the genes appears to be very different. Some
    of these cephalopod-specific gene families are highly expressed in unique cephalopod features, including in the squid brain.

    Certain gene families are unusually expanded."An exciting example of that
    is the protocadherin genes," Albertin said. "Cephalopods and vertebrates independently have duplicated their protocadherins, unlike flies and
    nematodes, which lost this gene family over time. This duplication
    has resulted in a rich molecular framework that perhaps is involved
    in the independent evolution of large and complex nervous systems in vertebrates and cephalopods." They also found species-specific gene
    family expansions, such as the genes involved in making the squid's beak
    or suckers. "Neither of these gene families were found in the octopus. So, these separate groups of animals are coming up with novel gene families
    to accomplish their novel biology," Albertin said.

    An octopus emerges video: https://youtu.be/8F020iUEafU RNA Editing:
    Another Arrow in the Quiver to Generate Novelty Prior research at the
    MBL has shown that squid and octopus display an extraordinarily high rate
    of RNA editing, which diversifies the kinds of proteins that the animals
    can produce. To follow up on that finding, Albertin et al.sequenced RNA
    from 26 different tissues in Doryteuthisand looked RNA editing rates
    across the different tissues.

    "We found a very strong signal for RNA editing that changes the sequence
    of a protein to be restricted to the nervous system, particularly in
    the brain and in the giant fiber lobe," Albertin said.

    "This catalog of editing across different tissues provides a resource to
    ask follow-up questions about the effects of the editing. For example, is
    RNA editing occurring to help the animal adapt to changes in temperature
    or other environmental factors? Along with the genome sequences, having
    a catalog of RNA editing sites and rates will greatly facilitate future
    work." Video: https://youtu.be/uuTMCBErVxg Why did These Cephalopods
    Make the Cut? These three cephalopod species were chosen for study given
    their past and future importance to scientific research. "We can learn
    a lot about an animal by sequencing its genome, and the genome provides
    an important toolkit for any sort of investigations going forward,"
    Albertin said.

    They are:
    * The Atlantic longfin inshore squid (Doryteuthis pealeii). Nearly a
    century of research on this squid at the MBL and elsewhere
    has revealed fundamental principles of neurotransmission (some
    discoveries garnering a Nobel Prize). Yet this is the first report
    of the genome sequence of this well-studied squid (in Albertin et
    al.,funded by the Grass Foundation).

    Two years ago, an MBL team achieved the first gene knockout
    in a cephalopod using Doryteuthis pealeii, taking advantage of
    preliminary genomic sequence data and CRISPr-Cas9 genome editing.

    * The Hawaiian bobtail squid (Euprymna scolopes). A glowing bacterium
    lives
    inside a unique "light organ" in the squid, to the mutual benefit of
    both. This species has become a model system for studying animal-
    bacterial symbiosis and other aspects of development. A draft
    E. scolopes genome assembly was published in 2019.

    * The California two-spot octopus (Octopus bimaculoides). A relative
    newcomer on the block of scientific research, this was the first
    octopus genome ever sequenced. Albertin co-led the team that
    published its draft genome in 2015.


    ========================================================================== Story Source: Materials provided by Marine_Biological_Laboratory. Original written by Diana Kenney. Note: Content may be edited for style and length.


    ========================================================================== Related Multimedia:
    * Images_of_octopuses_and_squid ========================================================================== Journal References:
    1. Caroline B. Albertin, Sofia Medina-Ruiz, Therese Mitros, Hannah
    Schmidbaur, Gustavo Sanchez, Z. Yan Wang, Jane Grimwood, Joshua
    J. C.

    Rosenthal, Clifton W. Ragsdale, Oleg Simakov, Daniel
    S. Rokhsar. Genome and transcriptome mechanisms driving
    cephalopod evolution. Nature Communications, 2022; 13 (1) DOI:
    10.1038/s41467-022-29748-w
    2. Hannah Schmidbaur, Akane Kawaguchi, Tereza Clarence, Xiao Fu, Oi Pui
    Hoang, Bob Zimmermann, Elena A. Ritschard, Anton Weissenbacher,
    Jamie S.

    Foster, Spencer V. Nyholm, Paul A. Bates, Caroline B. Albertin, Elly
    Tanaka, Oleg Simakov. Emergence of novel cephalopod gene regulation
    and expression through large-scale genome reorganization. Nature
    Communications, 2022; 13 (1) DOI: 10.1038/s41467-022-29694-7 ==========================================================================

    Link to news story: https://www.sciencedaily.com/releases/2022/05/220504082333.htm

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