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

Submission information

Submission Number: 123

Submission ID: 216

Submission UUID: 441ea3e2-ee59-461b-be6c-af1b112aae33

Submission URI: /form/project

Created: Tue, 11/02/2021 - 06:12

Completed: Tue, 11/02/2021 - 06:12

Changed: Mon, 11/21/2022 - 14:26

Remote IP address: 74.103.220.121

Submitted by: Gaurav Khanna

Language: English

Is draft: No

Webform: Project

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

Program CAREERS

Project Image

Tags bioinformatics (277), biology (515), genomics (537)

Status Complete

Project Leader

Project Leader Roxanne Beinart

Email rbeinart@uri.edu

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Project Personnel

Mentor(s) Roxanne Beinart

Student-facilitator(s) Johana Rotterova

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Project Information

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.

Project Information Subsection

Project Deliverables The main deliverable of this CyberTeams project is a working and tested workflow to execute genomic methods on URI and MGHPCC HPC systems for faster throughput.

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Student Facilitator Programming Skill Level Some hands-on experience

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Project Institution University of Rhode Island -- Bay Campus

Project Address Rhode Island. 02881

Anchor Institution CR-University of Rhode Island

Preferred Start Date 01/01/2022

Start as soon as possible. No

Project Urgency Already behind3Start date is flexible

Expected Project Duration (in months) 6 months

Launch Presentation

Copy of Careers.project.launch7.pptx

Launch Presentation Date 02/09/2022

Wrap Presentation

WGACareers.project.wrap11092022_0.pptx

Wrap Presentation Date 11/09/2022

Project Milestones

Milestone Title: Milestone #1
Milestone Description: Assess available HPC resources and get access; get organized using GitHub; prepare project “launch” presentation.
Completion Date Goal: 2022-02-15
Actual Completion Date: 2022-02-15
Milestone Title: Milestone #2
Milestone Description: Get experience and training on selected HPC resource(s); get research workflow set up; run some key tests.
Completion Date Goal: 2022-03-31
Actual Completion Date: 2022-03-31
Milestone Title: Milestone #3
Milestone Description: Utilize the established and tested bioinformatics computational workflow for scientific productivity.
Completion Date Goal: 2022-05-15
Actual Completion Date: 2022-05-15
Milestone Title: Milestone #4
Milestone Description: Assemble and organize results; commit final codes to GitHub repo; deliver “wrap” presentation.
Completion Date Goal: 2022-06-30
Actual Completion Date: 2022-11-09

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Final Report

What is the impact on the development of the principal discipline(s) of the project? Studying symbioses between unicellular eukaryotes (protists) and intracellular methanogenic archaea is critical to our understanding of the evolution of eukaryotic life without oxygen, as well as the impact of these multi-domain holobionts on global methane production. Nearly all anaerobic ciliates, ecologically important protists commonly found in oxygen depleted environments, host methanogenic endosymbionts, but their host-symbiont specificity patterns and intraspecific variability remain largely unknown. We bring the first large-scale genomic analysis of the population structure of both host and symbionts in this partnership, providing key insights into the specificity of these symbioses, and building a foundation for future studies of eukaryotic-prokaryotic liasons in anoxia.

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Lessons Learned I have learned to work at the URI Andromeda research cluster, how to properly schedule and plan large computing jobs using several nodes but also to back up all data on a regular basis.

Overall results I was able to use and adapt computational software pipelines to assemble and analyze new transcriptomic and large-scale metagenomic data that we have sequenced. I have assembled a eukaryotic transcriptome from the target organism (ciliate hosting archaeal endosymbiont) and genomes from 78 single-cell metagenomic samples from various populations of the archaeal endosymbiont (Methanocorpusculum sp.) from the same ciliate host species. I have analyzed the genomic data to assess the symbiont-host co-diversification and genetic variation. In addition, I have reconstructed mitochondrial genomes from the selected ciliate host populations and performed a mitochondrial phylogenomic analysis to confirm the host phylogeny.