PlantTribes2: Tools for comparative gene family analysis in plant genomics

• DOI: 10.3389/fpls.2022.1011199
• Publication Date: 2023-01-31T15:00:26Z
• Authors: Eric K. Wafula; Huiting Zhang; Gregory Von Kuster; James H. Leebens-...; Loren A. Honaas; Claude W. dePamph...
• Keywords: Gene prediction; Comparative Genomics; Gene Annotation

Plant genome-scale resources are being generated at an increasing rate as sequencing technologies continue to improve and raw data costs fall; however, the cost of downstream analyses remains large. This has resulted in a considerable range genome assembly annotation qualities across plant genomes due their varying sizes, complexity, technology used for annotation. To effectively work genomes, researchers increasingly rely on comparative genomic approaches that integrate community types. Such efforts have aided process yielded novel insights into evolutionary history gene families, including complex non-model organisms. The essential tools achieve these family analysis genome-scale, but they not well integrated rapid new data, learning curve can be steep. Here we present PlantTribes2, scalable, easily accessible, highly customizable, broadly applicable framework with multiple entry points user provided data. It uses objective classifications annotated protein sequences from existing, high-quality studies. PlantTribes2 transcript models then sort them, either annotations or individual coding sequences, pre-computed orthologous clusters rich functional information. Then, families interest, performs customizable visualizations including, (1) sequence alignment, (2) phylogeny, (3) estimation synonymous non-synonymous substitution rates among homologous (4) inference large-scale duplication events. We give examples applications studies economically important namely transcriptomics weedy Orobanchaceae core orthogroup (CROG) Rosaceae. is freely available use within main public Galaxy instance downloaded GitHub Bioconda. Importantly, readily adapted transcriptomic any kind organism.