MSGID: 1:317/3 6273532a   
   PID: hpt/lnx 1.9.0-cur 2019-01-08   
   TID: hpt/lnx 1.9.0-cur 2019-01-08   
    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   
      
   --- up 9 weeks, 2 days, 10 hours, 51 minutes   
    * Origin: -=> Castle Rock BBS <=- Now Husky HPT Powered! (1:317/3)   
   SEEN-BY: 15/0 106/201 114/705 123/120 129/330 331 153/7715 218/700   
   SEEN-BY: 229/110 111 317 400 426 428 470 664 700 292/854 298/25 305/3   
   SEEN-BY: 317/3 320/219 396/45   
   PATH: 317/3 229/426