Sequencing the Genome of Mya arenaria, the Soft Shell Clam
This project supports research efforts to finish sequencing the genome of Mya arenaria, the soft shell clam. Specifically, we will collect additional paired end and mate pair data on the Illumina platform. The aims of this proposed project are wholly synergistic with the current Sea Grant research project directed by Drs. Chuck Walker and Michael Lesser. Indeed, this project will enhance my general research efforts aimed at the development of computational methods for eukaryotic genome assembly while supporting the Walker/Lesser project aimed at understanding gene expression in Mya.
With funds from other sources ($7000 College of Life Sciences and Agriculture (COLSA) Dean’s office), Chuck Walker has already sequenced the Mya arenaria genome (estimated size 1.2 Gb) to a coverage of approximately 20X. In brief, modern genome assemblers implementing a de Bruijn graph approach require at least 50-100X coverage, more than double what we currently have. As such, after substantial efforts at assembling the genome with the current data, it remains very fragmented and unusable for the desired purposes (e.g., a maximally powered RNAseq study). To this end, Chuck Walker and Michael Lesser are currently funded by Sea Grant to investigate gene expression following induction of clam leukemia in M. arenaria after experimental exposure to increasing pH and temperatures consistent with predicted climate change scenarios. This project is in its first year and therefore work aimed at generating a high-quality genome assembly is timely. Indeed, having a reference genome would greatly enhance their ability to detect patterns of differential gene expression, and will open up entirely new research directions (e.g., studies of DNA methylation).
Participants in the genome project include Chuck Walker, Michael Lesser and Michael Chambers (outreach) as well as Lindsay Havens, Lauren Kordonowy and Amanda St. Martin, an undergraduate researcher, and potentially other undergraduate and graduate students in the course listed below.
Advantages of expending funds on the project for Sea Grant are:
1. To the current Sea Grant project of Walker and Lesser: A complete and annotated genome will provide them with the ability to perform much more sensitive analyses of gene expression as compared to the current scenario which utilizes a de novo transcriptome assembly.
2. Involving myself, a newly hired UNH professor with expertise in genomics and bioinformatics, in marine research in the Gulf of Maine.
3. This genome will be used for teaching a course entitled, “Eukaryotic Genome Assembly” to interested undergraduate and graduate students via the MCBS 796/896 mechanism. These students will learn how to design a sequencing experiment, assemble and annotate a large genome. Accompanying training in bioinformatics will be significant training in marine sciences and invertebrate biology.
4. Publication of the only in-faunal bivalve genome that is of critical ecological and economic importance in the Gulf of Maine and recognition of N.H. Sea Grant and COLSA as the “home” of this significant genome that is also important as a non-model organism in biomedical research.
N.H. Sea Grant researchers sequence softshell clam genome to understand differences in cancerous vs. non-cancerous clams
In 2015, N.H. Sea Grant-funded researchers sequenced and assembled the genome for the softshell clam Mya arenaria, which will help scientists improve their understanding of gene expression differences in cancerous versus non-cancerous clams.
Relevance: Softshell clam populations in New England experience annual population declines, in part due to clam leukemia. Very little is known about the etiology or origin of clam leukemia, and detailed clam genetics data are needed to understand more about the disease and its impacts on clam populations.
Response: In 2015, N.H. Sea Grant-funded researchers worked to sequence the genome for the softshell clam Mya arenaria. They generated an additional lane of Illumina sequencing to add to previous efforts.
Results: These new sequence data were instrumental in assembling a contiguous M. arenaria genome, which in turn will be used for a functional genomics project aimed at understanding gene expression differences in cancerous versus non-cancerous clams.