Host-symbiont population genomics - analyzing the intraspecific variability of methanogenic archaeal endosymbionts of genus Methanocorpusculum hosted by a marine anaerobic ciliate Metopus sp. (Metopida)

Project Information

bioinformatics, biology, genomics
Project Status: Complete
Project Region: CAREERS
Submitted By: Gaurav Khanna
Project Email: rbeinart@uri.edu
Project Institution: University of Rhode Island -- Bay Campus
Anchor Institution: CR-University of Rhode Island
Project Address: Rhode Island. 02881

Mentors: Roxanne Beinart
Students: Johana Rotterova

Project Description

This project aims to deepen our knowledge of the diversity of archaea-ciliate symbioses that are ubiquitous in anoxic coastal sediments. Using bioinformatic approaches, we plan to assess the intraspecific diversity and population structure of methanogenic archaeal endosymbionts hosted by a marine anaerobic ciliate Metopus sp. (Metopida). We have prepared a nested experimental design for sequencing of 96 single-cell metagenomes of 15 cultivated and uncultivated strains of this ciliate species, isolated from various locations across coastal New England, as well as one from a geographically remote location on the other side of the Atlantic Ocean. Using comparative and population genomics methods, we will uncover host-symbiont specificity patterns, which will provide insight into the evolution of this unique symbiotic relationship. The main goal of this CyberTeams project is to get assistance in setting up these genomic methods on URI and MGHPCC HPC systems for faster throughput.

Additional Resources

Launch Presentation:
Wrap Presentation: 6 months

Project Information

bioinformatics, biology, genomics
Project Status: Complete
Project Region: CAREERS
Submitted By: Gaurav Khanna
Project Email: rbeinart@uri.edu
Project Institution: University of Rhode Island -- Bay Campus
Anchor Institution: CR-University of Rhode Island
Project Address: Rhode Island. 02881

Mentors: Roxanne Beinart
Students: Johana Rotterova

Project Description

This project aims to deepen our knowledge of the diversity of archaea-ciliate symbioses that are ubiquitous in anoxic coastal sediments. Using bioinformatic approaches, we plan to assess the intraspecific diversity and population structure of methanogenic archaeal endosymbionts hosted by a marine anaerobic ciliate Metopus sp. (Metopida). We have prepared a nested experimental design for sequencing of 96 single-cell metagenomes of 15 cultivated and uncultivated strains of this ciliate species, isolated from various locations across coastal New England, as well as one from a geographically remote location on the other side of the Atlantic Ocean. Using comparative and population genomics methods, we will uncover host-symbiont specificity patterns, which will provide insight into the evolution of this unique symbiotic relationship. The main goal of this CyberTeams project is to get assistance in setting up these genomic methods on URI and MGHPCC HPC systems for faster throughput.

Additional Resources

Launch Presentation:
Wrap Presentation: 6 months