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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #428861
Research Project: Championing Improvement of Sorghum and Other Agriculturally Important Species through Data Stewardship and Functional Dissection of Complex Traits

Location: Plant, Soil and Nutrition Research

Title: Visualizing Functional Divergence and Conservation in Gene Families with TBrowse

Author
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item VAN BUREN, PETER - Cold Spring Harbor Laboratory
item WEI, SHARON - Cold Spring Harbor Laboratory
item Gladman, Nicholas
item Ware, Doreen

Submitted to: Conference on Genome Informatics
Publication Type: Abstract Only
Publication Acceptance Date: 11/5/2025
Publication Date: 11/5/2025
Citation: Olson, A., Chougule, K., Kumari, S., Lu, Z., Van Buren, P., Wei, S., Gladman, N.P., Ware, D. 2025. Visualizing Functional Divergence and Conservation in Gene Families with TBrowse. Conference on Genome Informatics . Conference on Genome Informatics.

Interpretive Summary:

Technical Abstract: Gene trees model the evolutionary history of gene families based on sequence homology and a phylogenetic species tree, revealing speciation and duplication events. Integrating functional annotations and other gene attributes in this evolutionary context would allow scientists to explore functional conservation, divergence and dosage effects. TBrowse is a modular, extensible tool for visualizing phylogenetic trees. It is implemented to support rendering trees and augmenting tree nodes with multiple sequence alignments, domain architectures, and synteny data from genetrees.org, as well as arbitrary gene attributes served from external APIs. Designed with pan-genome analysis in mind, TBrowse enables species-level visualization of gene presence, duplication, and diversification. The web service at genetrees.org, powered by Apache Solr, hosts protein coding gene trees built with the Ensembl Compara pipeline across a broad range of taxa, including vertebrates, plants, fungi, protists, metazoa, bacteria, and pan-genomic sets for select crops. Each tree node is stored as a Solr document with fixed fields for structure and dynamic fields for rich annotations, such as InterPro domains. The API provides endpoints for searching gene families and retrieving trees. Subtrees and tree pruning based on arbitrary filters are supported via Solr’s GraphQueryParser. Together, the TBrowse interface, plugin architecture, and genetrees.org backend form a unified platform, adaptable to both broad phylogenomic studies and detailed species-level pan-genome investigations.