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UM Researchers Join Alliance to Sequence the Genomes of Invertebrates


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    combjellyfish

    UM biologist William Browne, who studies the comb jelly Mnemiopsis leidyi, has high hopes for the GIGA consortium.

    By Marie Guma-Diaz
    and Annette Gallagher
    UM News

    CORAL GABLES, Fla. (January 6, 2014) – Of the 1.9 million species of creatures that have been described on Earth, more than 1.3 million are invertebrates. They have served as model organisms in many areas of biology.

    There are many examples of the important role of invertebrates in science, including sea urchins for developmental/cancer cell biology, the mollusks Aplysia and Loligo for neurobiology research, the fruit fly Drosophila for genetics, and the nematode worm C. elegans for cell line maturation, development, and genetics. Studies using all of these have received Nobel Prizes.

    Now, to learn more about these remarkable organisms, a cooperative consortium called the Global Invertebrate Genomics Alliance (GIGA) has been formed. The group will provide a network of diverse scientists to promote comparative genomics and bioinformatics research on non-insect/non-nematode invertebrates.

    William Browne, a biologist in the College of Arts and Sciences at the University of Miami, who works on the comb jelly Mnemiopsis leidyi, hopes his participation in GIGA will offer opportunities for interactions with a broader community of researchers delving into invertebrate genomics.

    “The GIGA consortium lays the groundwork, for example, to take work on the genome of Mnemiopsis in our lab and facilitate comparison of the results to work from other labs that are pursuing these same kinds of questions in different organisms,” Browne said. “The hope is that syntheses of large-scale genomic studies across many groups will improve not only our understanding of the metazoan tree of life, but also illuminate repertoires of genetic diversity responsible for the present-day diversity of animals.”

    Earlier this year, Jose Lopez, a professor of biology at Nova Southeastern University’s (NSU) Oceanographic Center, organized the inaugural workshop of expert invertebrate scientists to discuss the plausibility of, and long-term strategies for, sequencing the whole genomes of multiple, targeted invertebrate organisms.

    “There’s so much more we can learn from these animals if we come together to focus and coordinate our research efforts,” Lopez said. “GIGA allows us to work collaboratively as we discover new and exciting details of invertebrate genomics.

    Invertebrates display many unique and outlandish traits among animals. For example:

    ·     Some invertebrates are the longest-living animals on the planet, including Lamellibrachia tube worms (~250 years), Quahog clams Arctica islandica (maximum reported age 507 years), black corals (estimated 2,000 years), and the immortal Hydra.

    ·     Tardigrades (“water bears”) can survive extreme temperatures (-150 ºC to 150 ºC), ionizing solar and galactic radiation, and even interplanetary vacuum.

    ·     Octopi not only have eight arms but three hearts, as well as highly developed brains and visual systems.

    ·     Sponges represent one of the most ancient lineages of animals and, together with corals, produce the largest number of chemical “lead” molecular structures for discovery of novel pharmaceuticals.

    ·     Ctenophores, another ancient lineage of animals, possess a range of unique cell types and are the largest animals that use only cilia for locomotion.

    GIGA was partially inspired by the Genome 10K project, initiated by NSU’s affiliate professor Stephen J. O’Brien and colleagues to sequence genomes from 10,000 vertebrate animals. The organization held its inaugural workshop at NSU’s Oceanographic Center in March 2013.

    Workshop participants came from the U.S., China, and Europe and included more than 40 experts in invertebrate biology, genomics, and systematics from several universities and institutions, including the Smithsonian Institution, Scripps Oceanographic Institute, Harvard and Brown universities, as well as the biotech industries, including Life Technologies, PacBio, and BioNanoGenomics.

    Participants developed the consortium’s framework during in-depth, breakout discussions, such as which specific genomes to prioritize for sequencing, which DNA or RNA sequencing platforms are optimal, standards for collections and sample preparations, and where to specify a particular invertebrate taxon’s place on the evolutionary tree of life. Also discussed were nascent policies on data submittal, and access and sharing within the GIGA consortium.

    Primary funding for the workshop to kick-start GIGA was generously awarded by the American Genetic Association, publisher of the Journal of Heredity. The momentum of the workshop carried forward, leading to the creation of an NSU-hosted website (Giga‐cos.org), more international collaborations (i.e., the GIGA symposium at next summer’s Society for Molecular Biology and Evolution—SMBE  in Puerto Rico), and the white paper published in the current issue of the Journal of Heredity. This article further showcases GIGA’s main goals, ongoing projects, and recommended experimental standards and policies.

     Annette Gallagher can be reached at 304-284-1121.

     

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