Genomics of Fish and Shellfish
Genomics of Fish and Shellfish
Genomic technologies are enabling new applications in fisheries by providing a detailed understanding of population structure, migration patterns and adaptations to local environments. Genomics also provides insight into the genetic basis of susceptibility or resistance to disease and the capacity to adapt to changing marine environments. Sequencing the genomes of commercially important species will not only enhance our understanding of the biology and ecology of these animals, but will enable the development of high resolution genomic tools to provide the best information on fisheries resources to the community.
American Lobster Genome
GMGI, in collaboration with Dovetail Genomics LLC (Santa Cruz, CA) and David Walt’s laboratory at Tufts University, has embarked on a project to sequence the iconic local lobster (Homarus americanus). Sequencing the lobster genome is a challenge due to its large size (larger than the human genome) and the presence of many repetitive DNA sequences. Thus, obtaining the sequence of the Lobster genome will represent a major accomplishment, and provide an important foundation for all future scientific studies of the lobster and other crustaceans.
In addition to supporting a vitally important fishery, the lobster has been a model animal for scientists studying development and evolution of the nervous system. The American lobster is also reported to be a long-lived animal, estimated to live for up to 100 years. The genome sequence will not only provide an important resource for fisheries, but will help scientists understand the genes associated with nervous system function and longevity.
North Atlantic Cod Genome
For over 400 years, the cod fishery has been an important part of the New England economy, with families in major fishing communities, such as Gloucester recalling as many as seven generations of fishermen. Recently, cod populations have been challenged and there has been a significant reduction in the cod fishery quotas in New England, resulting in serious threats to the socio-economic health of the region.
Genetic analysis of populations can identify distinct sub-populations and map their spatial boundaries providing important information to consider in management strategies. Using traditional approaches, it is known that Atlantic cod (Gadus morhua) vary genetically across the North Atlantic ocean. To build on this knowledge and provide an improved understanding of the local cod population structure, GMGI set out to sequence the whole genome of North Atlantic cod and to identify genetic variations in populations collected from three key commercial fisheries locations off the Massachusetts coast:
1. Gulf of Maine (winter spawning, Dec 2013)
2. Gulf of Maine (spring spawning, May 2014)
3. Georges Bank (winter spawning, Mar 2014)
GMGI’s cod genome sequencing project was funded by the Massachusetts Division of Marine Fisheries and carried out in collaboration with scientists from the Annisquam River Marine Fisheries Station (Gloucester, MA) who provided the cod specimens; SeqWell LLC (Beverly, MA) who conducted the DNA sequencing; and the laboratory of Stephen Palumbi at Hopkins Marine Station (Stanford University) who provided the bioinformatics analysis and significant computing power required for this effort.
Whole genome sequencing was conducted for 31 individual cod from the three locations (estimated genome size 800 megabases). Analysis of the DNA sequences identified over three million Single Nucleotide Polymorphisms (variants) throughout the genome, detected three large clusters of linkage disequilibrium and identified the genes contained within these clusters. Across these genes, significant population differentiation was detected among spawning groups in the Gulf of Maine and between Georges Bank and the Gulf of Maine. This analysis revealed local adaptations of cod populations from different spawning groups, adding to previous evidence of spatial and temporal genetic variation that occurs across the North Atlantic, Greenland and Newfoundland fisheries.
This work resulted in GMGI’s first peer-reviewed scientific publication:
Barney, B.T., Munkholm, C., Walt, D.R. and Palumbi, S.R. (2017) Highly localized divergence within supergenes in Atlantic cod (Gadus morhua) within the Gulf of Maine. BMC Genomics 18:271
Bivalves such as oysters, clams and mussels are important species for environmental and commercial applications. Many bivalves feed by filtering small food particles from the water column and as a result serve as monitors of marine pollution. In areas with poor water quality conditions, scientists have observed declines in bivalve populations. This is not only an economic loss, but also an ecological one, since bivalves provide valuable ecosystem functions including the formation of protective nursery habitat for many fish.
The application of genomics to the study of bivalves can improve our understanding of how these organisms interact with their environment by elucidating the genes underlying biological responses to changing conditions. Genomics also enables the identification of genes and genetic markers associated with favorable traits such as increased growth rate and disease resistance. This information can translate into production practices for enhanced efficiency, sustainability and product quality of farmed species.
GMGI is seeking partners to provide genomics based solutions to monitor health and improve production characteristics of these important species.
Genome Mining for Novel Therapeutics and Commercial Products >>
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