Aquaculturomics: bringing the genome revolution to aquaculture. Helen Poynton School for the Environment University of Massachusetts Boston

Transcription

1 Aquaculturomics: bringing the genome revolution to aquaculture Helen Poynton School for the Environment University of Massachusetts Boston

2 Aquaculturomics use of genomic technologies and their scientific products to enhance the health of fish and shellfish and the sustainability of aquaculture. Image: Massachusetts Oyster Project

3 Genes and genomics Our Genome, made up of a 3 billion sequence code, contains the blueprint for every cell in our body. Our genome is made up of 21,000 genes that determine everything from our hair color to whether we are at risk for disease. The genome also contains switches that determine when genes are turned on or off. In some cases, these switches are more important than the genes themselves.

4 Genes to proteins transcription translation OFF ON Gene blueprint for making proteins Messenger RNA - delivers the instructions for ONE gene to protein factory Protein- final product that does a job in the cell (e.g. channels, bridges, enzymes) Protein image credit: Thomas Shafee, CC

5 Genomics to proteomics transcription translation Genome All the genes, blueprints, and switches Transcriptome- all the messages in transit at one time Proteomics all the proteins working away in the cell at a time.

6 Genomics revolution In 2001, the complete human genome sequence was published, launching a genomics revolution. Unbelievable new insights including only 21,000 genes (only 1000 more than a worm and less than many bugs). It made it possible to see find our human roots, the paths we have been on, and our relationships with other peoples in high resolution.

7 Genomics revolution: Health and medicine Advances in understanding disease Genome wide association studies have be able to link specific mutations in DNA to genetic disorders. Infants can now be screened for over 6000 different rare diseases caused by mutations in their DNA sequence. Huge progress has been made with more complex disorders where increased susceptibility for a disease has been linked to specific DNA sequences. Nature Reviews Genetics 6, (May 2005)

8 Genomics revolution: Health and medicine Breakthroughs in cancer treatment Each cancer is different and understanding these differences is essential to treating them. DNA sequencing of cancer cells have identified specific mutations that caused the cancer and have produced potential targets for therapies. Some cancer cells have a mutation that makes too much of a protein called HER2. This causes the cancer cells to divide rapidly. After this mechanism was discovered, drugs were developed that blocked HER2, killing the cancer cells. Image credit: Anne Weston, Cancer Research UK; HER2 diagram,

9 Genomics revolution: Health and medicine New diagnostic tests for infectious disease DNA sequencing methods have now been developed to test for infectious diseases, matching DNA or RNA found in the blood or spit of a sick patient and screening through millions of potential agents. It also has the potential to identify unknown, emerging infectious agents. Bacteria Fungus Parasite Unknown Virus Naccache et al. (2014) Genome Research

10 Genomics revolution: Personalized medicine

11 Aquaculturomics GOAL: Bring the technologies and advances seen in human genomics to the shellfish industry to make healthier, stress- and disease- resistant crops. Image: Massachusetts Oyster Project

12 Genomic resources for shellfish Pacific oyster was the first shellfish genome sequenced (2012) revealing new information about shell formation and intertidal adaptation. A few additional genomes in draft form or still in the pipeline, especially for oysters and mussels. Crassostrea gigas Much more data available for transcriptomes (messenger RNAs) across several commercially important species.

13 Genomic resources for shellfish Common and species name Total number of DNA sequences Bay Scallop (Argopectin irradians) 90,778,257 Razor clam (Ensis directus) 57,966,839 Quahog (Mercenaria mercenaria) 72,946,477 Soft-shell clam (Mya arenaria) 82,920,582 Blue mussel (Mytilus edulis) 440,000,000 Razor clam image credit: Hans Hillewaert; soft-shell clam image credit: Kirsten Poulsen

14 Current applications of genomics in shellfish: disease Marker Assisted Selection Many aquaculture species are selectively bred for disease resistance and other characteristics. Selection based on these characteristics is a long process. However, selective breeding and be sped up if you know the genetic basis of trait.

15 Current applications of genomics in shellfish: disease Marker Assisted Selection Using genomic resources three teams of investigators from Louisiana, Rhode Island, and New Jersey uncovered the gene responsible for resistance to Dermo disease in oysters. Serine Proteinase Inhibitor -1 (CvSI-1): immune protein turned on very high in resistant oysters. This up-regulation is caused by a mutation in the gene s switch. Dermo spores, image credit: Roger Williams University Peyre et al. Developmental and Comparative Immunology 34 (2010) 84 92

16 Current applications of genomics in shellfish: disease Diagnostic tools for disease Genomic based tools available for the detection of major bacterial and parasite pathogens including Vibrios, Roseovarius oyster disease (ROD), and Perkinsus marinus (Dermo disease). Current work is focused on creating screening panels for multiple diseases using DNA sequencing technologies. First DNA based diagnostic test for Roseovarius oyster disease (ROD), Malroy et al., 2005 Dis Aquat Org. 67:

17 Current applications of genomics in shellfish: algal toxins Diagnostic tools for disease Toxic algal blooms pose a significant threat to human health and many of these toxins are concentrated in shellfish. New tests based on the shellfish response to algal toxins are being developed by looking for genes that are turned on specifically by the toxin. Detree et al PLoS ONE 11(10): e Saxitoxin (paralytic shellfish poisoning) monitoring. Blue mussels were exposed to the pure toxin as well as two species of Alexandrium. A number of genes were turned on specifically by the toxin and could form the basis of a monitoring tool.

18 Current applications of genomics in shellfish: environmental stress Detection tools for stress and contamination Pollution is an environmental stressor that can hurt the growth of shellfish. Through metal exposures and transcriptomic analysis we have identified genes that are turned on and indicate the presence of contamination and animal stress. Unfolded protein stress response No metals Metal contamination

19 Current applications of genomics in shellfish: environmental stress Detection tools for stress and contamination Pollution is an environmental stressor that can hurt the growth of shellfish. Particular compounds called endocrine disrupting compounds (EDCs) interfere with the mussels ability to grow and reproduce and may be responsible for gender reversal. Two genes play an important role in reproduction, a female gene VERL and a male gene VCL. When exposed to the estrogen EE2, mussels turn on the VERL gene and switch off the VCL gene. Therefore, these important genes are excellent indicators of EDCs and are suggestive of reproductive impacts. decrease

20 Current applications of genomics in shellfish: environmental stress Detection tools for stress and contamination Pollution is an environmental stressor that can hurt the growth of shellfish. Particular compounds called endocrine disrupting compounds interfere with the mussels ability to grow and reproduce and may be responsible for gender reversal. When exposed to the estrogen EE2, more mussels turn on the female only gene, suggesting that they are becoming more female.

21 Where can we go? Potential applications Novel markers for selection and indicators of health Identification of markers for fast growth and increased fitness. Resistance to environmental stress including thermal and acidification stress. Screening tools that can predict larvae survival and settlement success.

22 Where can we go? Resources for the diversity of shellfish Expanding resources Selection markers stress markers genomes transcriptomes Disease markers oysters mussels soft-shell clam quahog scallop s Resources available

23 Making the tools assessable: following the human example Genetic testing for disease or cancer are currently done in labs where samples are taken in a hospital or doctor s office and sent to a molecular diagnostic lab for testing. Image credit: IBM In Aquaculture, genetic testing and disease detection could be conducted in a similar manner where samples of tissue or blood are sent to a lab for analysis. Image credit: Alan Mearns/NOAA

24 Making the tools assessable: following the human example There are also a number of diagnostic tests that have moved out of the doctor s office and lab. These are anti-body based tests and have been developed for everything from home drug testing to tests for strep throat. These simple, inexpensive, and on the farm type of tests are our goal, but they will require more research for development.

25 Working together Aquaculturomics is still in its veliger stage and there are many steps involved until we can harvest its benefits. Working together to set the seeds of this field is critical. We want to work with you and on the major concerns you are facing. Image credit: Chesapeake Bay Program Through collaboration, we can make and provide tools to enhance the health of shellfish and the sustainability of aquaculture.

26 Acknowledgements Collaborators at the MWRA Bonnie Blalock William Robinson Robyn Hannigan Brian Duphily Keegan Krick... and the many shellfish biologists of aquaculturomics whose work I cited here. FUNDING Ruth D. Turner Foundation Healey Grants Program Image credit: pinay06 (CC-BY)