BIVALVE GENOMICS

PI: Fabrizio Ghiselli [e-mail]

Mollusca is the largest marine Phylum for number of species, the second among Metazoa after Arthropoda. The Class Bivalvia is a highly successful and ancient taxon—the second largest inside Mollusca—including ~25,000 living species. Bivalves are an extremely interesting group for numerous branches of biology: evolution, biodiversity and conservation, ecology, ecotoxicology, physiology, cell biology, reproduction, and genetics. During their long evolutionary history—their first appearance in the fossil record dates back to Middle Cambrian, 500+ Mya—bivalves adapted to a wide range of physical-chemical conditions (e.g.: salinity, temperature, pH, oxygen concentration, pressure), substrates (e.g.: buried into sediments, attached to hard surfaces), habitats (e.g.: rivers, lakes, estuaries, intertidal zones, coral reefs, ocean banks, continental shelves, deep waters), biological interactions (e.g.: free-living, in symbiosis with dinoflagellates or seagrasses, parasites of fish), and feeding habits (e.g.: filtering, scraping, predation). Bivalves can have strikingly different dimensions (from less than 1 millimeter to 1+ meter), and despite their apparently simple body plan, they evolved very different shell shapes, and complex anatomic structures, such as eyes and mantle modifications for host-attraction. One of the most striking feature of this class of animals is their peculiar mitochondrial biology: bivalves have facultatively anaerobic mitochondria that allow them to survive prolonged periods of anoxia/hypoxia; moreover they show the only known evolutionarily stable exception to the strictly maternal inheritance of mitochondria. Such phenomenon is called doubly uniparental inheritance, and has been reported, so far, in ~100 species (for further details see: Breton et al. 2007, Passamonti & Ghiselli 2009, Milani et al. 2011, Breton et al. 2014, Milani et al. 2016). Another field of biological research that involves bivalves is the study of ageing: the ocean quahog (Arctica islandica) is the longest living non-colonial metazoan, with an authenticated lifespan up to 507 years. Bivalves are also good bioindicators and can be used as sentinel species for monitoring the concentration of pollutants, heavy metals, and environmental contamination by microorganisms. Furthermore, the remarkable ability of some species to adapt to a wide range of environmental conditions make them excellent models for studying adaptation to environmental changes (see for example: Matozzo et al 2013, Milan et al 2013, Milan et al 2015, Milan et al 2016). From an applied point of view, bivalves make up an important source of food all over the world: more than 14 million metric tons of bivalves are produced annually through aquaculture, corresponding to ~20% of the global aquaculture yield; clams are first in production, followed by oysters, mussels, and scallops (FAO Aquaculture and Fishery Yearbook 2015). The demand for bivalve meat is increasing worldwide, and aquaculture—one of the fastest growing food production industries in the world—needs to collaborate with scientific research in order to develop in a sustainable and environment-friendly way, and face the threats of global warming, ocean acidification, water pollution, and diseases. Some biological features of bivalves are interesting also for the fields of materials science and engineering, specifically, the biomineralization process (e.g.: for the development of high-performance inorganic-organic composites), and the formation of the byssus/cement (e.g.: production of water- resistant adhesives, or bio-adhesives for medical and technical applications). Lastly, pearl farming is another economically important industry based on bivalves, and today more than 99% of all pearls sold worldwide are cultured pearls. (For more information about Bivalves see Gosling 2007). All such interesting biological features and economic value are in sharp contrast with the lack of genomics resources about bivalve molluscs.

The main focus of this research line is to produce genomics and transcriptomics data to be analyzed in a comparative framework for studying bivalve genomes under both evolutionary and applied perspectives.

 

ONGOING PROJECTS

 

Development of a transcriptome annotation pipeline for non-model organisms

 

 

 

 

 

 

Sequencing, Analysis, and Characterization of Ruditapes philippinarum Genome

 

 

 

 

Reproductive Biology of Bivalves

 

 

 

 

 

 

 

Effects of Water Chemical Contamination and Adaptation to Environmental Changes in R. philippinarum

 

 

 

 

 

 

 

Biomineralization

 

 

 

 

 

SELECTED PUBLICATIONS

 

  • Renaut S, Guerra D, Hoeh WR, Stewart DT, Bogan AE, GHISELLI F, Milani L, Passamonti M, Breton S. Genome survey of the freshwater mussel Venustaconcha ellipsiformis (Bivalvia: Unionida) using a hybrid de novo assembly approach. Genome biology and evolutionhttps://doi.org/10.1093/gbe/evy117
  • GHISELLI F.*, Iannello M.*, Puccio G., Chang P.L., Plazzi F., Nuzhdin S.V.*, Passamonti M*. (2018). Comparative transcriptomics in two bivalve species offers different perspectives on the evolution of sex-biased genes. Genome Biology and Evolution, 10: 1389–1402. (* equally contributing authors) LINK
  • Capt C., Renaut S., GHISELLI F., Milani L., Johnson N.A., Sietman B., Stewart D.T., Breton S. Deciphering the link between doubly uniparental inheritance of mtDNA and sex determination in bivalves: clues from comparative transcriptomics. Genome Biology and Evolution, 10:577–590. LINK
  • Punzi E., Milani L., GHISELLI F.*, Passamonti M*. Lose it or keep it: (how bivalves can provide) insights into mitochondrial inheritance mechanisms. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 330:41–51. (* equally contributing authors) LINK
  • GHISELLI F., Milani L., Iannello M., Procopio E., Chang P.L., Nuzhdin S.V., Passamonti M. (2017). The complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus (Bivalvia, Veneridae). PeerJ5 e3692. LINK
  • Voolstra, C., Worheide, G., Lopez, J.V., GHISELLI F., et al. (2017). Advancing genomics through the Global Invertebrate Genomics Alliance (GIGA). Invertebrate Systematics, 31(1):1–7. LINK
  • Milani L., GHISELLI F. (2015). Mitochondrial activity in gametes and transmission of viable mtDNA. Biology Direct, 10:22. LINK
  • GHISELLI F., Milani L., Guerra D., Chang P.L., Breton S., Nuzhdin S.V., Passamonti M. (2013). Structure, transcription and variability of metazoan mitochondrial genome. Perspectives from an unusual mitochondrial inheritance system. Genome Biology and Evolution, 5(8): 1535-1554. LINK
  • Milani L., GHISELLI F., Nuzhdin S., Passamonti M. (2013). Nuclear genes with sex bias in Ruditapes philippinarum (Bivalvia Veneridae): mitochondrial inheritance and sex determination in DUI species. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 320B: 442-454. LINK
  • GHISELLI F., Milani L., Chang P.L., Hedgecock D., Davis J.P., Nuzhdin S.V., Passamonti M. (2012). De novo assembly of the Manila clam Ruditapes philippinarum trascriptome provides new insights into expression bias, mitochondrial doubly uniparental inheritance and sex determination. Molecular Biology and Evolution, 29(2): 771-786. LINK

 

 

All the mentioned research activity and other upcoming projects are integrated in the GLOBAL INVERTEBRATE GENOMICS ALLIANCE (GIGA) project. Click on the logo below for more information.