NSF Postdoctoral Fellowship in Biology FY 2021: The role of dosage balance in duplicate gene retention

This action funds an NSF Postdoctoral Research Fellowship in Biology for FY 2021, Integrative Research Investigating the Rules of Life Governing Interactions Between Genomes, Environment and Phenotypes. The fellowship supports research and training of the Fellow that will contribute to the area of Rules of Life in innovative ways. Organisms show immense diversity of lifestyles and forms, and this diversity is based on the origins of new genes during evolution.

The main source of new genes is the duplication of older genes. But a central problem is how newly duplicated genes can persist and acquire new functions despite ongoing mutations. Although some duplicate genes are lost quickly, others persist for millions of years.

The central hypothesis to explain gene retention is the need to maintain the proper amount of protein products (dosage balance). This dosage balance hypothesis (DBH) has been found to play a major role in gene retention and loss in plants, yeast, and humans. However, it has not been tested in any insects, which represent the majority of animal diversity.

This project will address why some duplicate genes are retained over time by testing the DBH in aphids. This project will also shed light on the role of gene duplication, and improve understanding of how genomes evolve. Outreach in bioinformatics and genomics will be conducted in undergraduate biology courses, in addition to the mentoring and training of undergraduate researchers from diverse backgrounds.

This project aims to integrate genomics, proteomics, and phenotypic information in aphids to test the DBH as a potential Rule of Life that governs the fate of genes. Aphids are a unique system to test the DBH because they have high fractions of duplicate genes and have not experienced a whole genome duplication. This research will use a comparative genomics approach on chromosome level genome assemblies to reveal the tempo and mode of gene duplications in aphids.

This study will also build a protein interaction network using co-fractionation mass spectrometry to determine the interactions of thousands of proteins in aphids, using supervised machine learning. Predictions from the DBH will be tested under a statistical framework by integrating results from gene duplication history and protein interaction networks.

This project will also test to determine if DBH can affect ecologically important phenotypes by integrating gene duplication history, with protein interactions, and phenotypic information for gene families with ecological roles involving symbiosis, oxidative stress, and coloration. The Fellow will receive technical training in genomics and proteomics at the University of Texas at Austin.

All data and computational resources generated during this project will be freely available to the broader research community through public repositories.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.