Marine Genomics

CAS BI 550

Contact the Instructor
Professor John R. Finnerty

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    Computational work

    Students in BI550, including Lukas DeFilippo and Jessie Mathews (foreground) perform bioinformatic analyses on protein sequences. Photo by John Finnerty.

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    Sequencing a coral transcriptome

    With assistance from teaching fellow Liz Burmester, Arianna Medina constructs a "library" for RNA sequencing. Photo by John Finnerty.

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    Field collections

    The students of Marine Genomics accompany Professor Finnerty to Belle Isle Marsh in Boston to collect the sea anemone Nematostella. Photo by Liz Burmester.

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    The view from the observation tower

    Students in Marine Genomics on a visit to Belle Isle Marsh in Boston take in the view from the observation tower. Photo by John Finnerty.

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    Extracting anemones from the sediment

    BI550 students Venus Fung, Caitlin Russell, and Zachary Lepore collect anemones from the soft sediment of a salt marsh pool. Photo by Kimberly Wong.

Course Description

Marine Genomics is a young scientific discipline that involves the application of genomic techniques to investigate the phenotype of marine organisms and the function of marine ecosystems. For example, (1) “metagenomic” approaches are now deemed essential for reconstructing the microbial communities that drive nutrient cycling in marine ecosystems, (2) “transcriptomic” approaches are increasingly being utilized to understand how marine organisms respond to environmental stress at the molecular level, and (3) “population genomic” approaches are being used to investigate the microevolution of animal populations. The theoretical portion of this course will cover the evolution of genomes, the architecture of gene networks, the connection between genotype and phenotype, and the basics of population genetics.

In the practical portion of the course, students use “next-generation” DNA sequencing techniques to characterize the transcriptomes or metagenomes of marine organisms. The focus is on cnidarian model systems (mainly corals and sea anemones) and the responses of their transcriptomes and metagenomes to environmental stress. Students have chosen to work with material they collected in Belize during Tropical Marine Invertebrates (BI 569).

Recent Syllabus: BI550_2014_Syllabus_1119

Example of a student research project in BI 550:

Defilippo & Lorenc (2012) “Variations in the Structure of NF-kappaB —A Key Stress Response Protein — in the Cnidaria” (BI550_2012_Presentation_DeFilippo&Lorenc)

Example of a published paper deriving in part from BI 550:

Stefanik DJ, Lubinski TJ, Granger BR, Byrd AL, Reitzel AM, DeFilippo L, Lorenc A, Finnerty JR (2014) Production of a reference transcriptome and transcriptomic database (EdwardsiellaBase) for the lined sea anemone, Edwardsiella lineata, a parasitic cnidarian. BMC Genomics. 15:71