PlantTribes2: Tools for comparative gene family analysis in plant genomics

Abstract

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

A Haplotype-resolved, Chromosome-scale Genome for Malus domestica 'WA 38'

“…Gene family analysis is performed using PlantTribes2 and the pre-constructed 26Gv2-scaffold orthogroup database (Wafula et al 2022). Out of the 18,110 pre-constructed orthogroups, proteins from all apple annotations [5 published genomes (‘Honeycrisp’ (Khan et al 2022), ‘Gala’ (Sun et al 2020), ‘Hanfu’ (L. Zhang et al 2019), ‘Antonovka’ (Švara et al 2023), and the GDDH13 ‘Golden Delicious’ (Daccord et al 2017) genomes) and the ‘WA 38’ genome from this work] are found in 11,671 orthogroups.…”

“…A full list of genomes analyzed can be found in Supplemental Table S7) following the method described by (Khan et al 2022). Briefly, predicted protein sequences from the selected pome fruit genomes were classified into a pre-computed orthogroup database (26Gv2.0) using the both HMMscan and BLASTp option implemented in the GeneFamilyClassifier tool from PlantTribes2 (Wafula et al 2022). Overlapping orthogroups among M. domestica genomes were calculated and visualized with the UpSet plot function implemented in TBtools v2.030 (Chen C., 2023).…”

“…A Core OrthoGroup (CROG) – Rosaceae gene count analysis was carried out following the method described by Wafula et al 2022. First, a CROG gene count matrix was created by counting genes classified into CORGs from each pome fruit genome.…”

Phylotranscriptomic Analyses of Mycoheterotrophic Monocots Show a Continuum of Convergent Evolutionary Changes in Expressed Nuclear Genes From Three Independent Nonphotosynthetic Lineages

“…Cleaned reads were de novo assembled using Trinity ( Grabherr et al 2011 ; Haas et al 2013 ) with the default parameters. The resulting transcriptome assemblies were post-processed with the PlantTribes tool ( Wafula et al 2022 ) AssemblyPostProcessor ( https://github.com/dePamphilis/PlantTribes ) using Oryza sativa ESTScan score matrices ( Iseli et al 1999 ) to produce non-redundant sets of predicted coding sequences and their corresponding translations ( supplementary table S2, Supplementary Material online). Additional filtering was performed on post-processed assemblies to remove non-plant contaminant sequences by screening transcripts against NCBI non-redundant protein database using BLASTp ( Altschul et al 1990 ) (E-value = 1e−5) as shown in supplementary tables S13 a and S13 b , Supplementary Material online.…”

“…The Arabidopsis thaliana proteome was obtained from Phytozyme 12, and genes were sorted into the 12-genome OrthoMCL gene family circumscriptions using GeneFamilyClassifier in Plant Tribes ( Wafula et al 2022 ). Genes representing the heme and chlorophyll biosynthetic pathway, and light harvesting and photosynthetic pathways were selected following Wickett et al (2011) , and Arabidopsis gene annotations were associated with corresponding orthogroups.…”