Location: Physiology and Pathology of Tree Fruits ResearchTitle: PlantTribes: Galaxy tools for comparative gene family analysis in plant genomics [abstract]
|WAFULA, ERIC - Pennsylvania State University|
|VON KUSTER, GREG - Pennsylvania State University|
|DER, JOSHUA - California State University|
|AYYAMPALAYAM, SARAVANARAJ - University Of Georgia|
|WICKETT, NORMAN - Chicago Botanical Garden|
|LEEBENS-MACK, JIM - University Of Georgia|
|DEPAMPHILLIS, CLAUDE - Pennsylvania State University|
Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 5/20/2019
Publication Date: 5/31/2019
Citation: Wafula, E., Von Kuster, G., Der, J.P., Honaas, L.A., Ayyampalayam, S., Wickett, N., Leebens-Mack, J., dePamphillis, C. 2019. PlantTribes: Galaxy tools for comparative gene family analysis in plant genomics [abstract]. Plant and Animal Genome Conference. p. 12.
Technical Abstract: Galaxy PlantTribes is a collection of automated modular analysis pipelines that utilize objective classifications of complete protein sequences from sequenced genomes for comparative and evolutionary analyses of genome-scale gene families and transcriptomes. It post-processes de novo assembly transcripts into putative coding sequences and their corresponding amino acid translations, estimates paralogous/orthologous pairwise synonymous/nonsynonymous substitution rates for a set of gene sequences, classifies gene sequences into pre-computed orthologous plant gene family clusters, and builds gene family multiple sequence alignments and their corresponding phylogenies. A user provides de novo assembly transcripts and Galaxy PlantTribes produces: (1) predicted coding sequences and their corresponding translations, (2) a table of pairwise synonymous/nonsynonymous substitution rates for either orthologous or paralogous transcript pairs, (3) results of significant duplication components in the distribution of Ks (synonymous substitutions) values, (4) a summary table for transcripts classified into orthologous plant gene family clusters with their corresponding functional annotations, (4) gene family amino acid and nucleotide fasta sequences, (6) multiple sequence alignments, and (5) inferred maximum likelihood phylogenies. Optionally, a user can provide an external gene family scaffold and/or externally predicted coding sequences derived from a transcriptorne assembly or gene predictions from a sequenced genome. Galaxy PlantTribes is freely available on the Galaxy main portal (https://usegalaxy.org). In addition, the standalone version of the pipeline is available for download on GitHub (https://github.corn/dePamphilis/PlantTribes) as a command-line interface for batch processing of many datasets.