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.

Towards identification of postharvest fruit quality transcriptomic markers in Malus domestica

“…2.9.1 Criteria for gene selection. The top 45 genes identified as being predictive of texture loss from the RF regression model were selected and classified into orthogroups pre-computed with the 26Gv2.0 scaffold using PlantTribes2 [51]. Orthogroup multiple sequence alignment, phylogenetic tree estimation, homology inference, and gene model evaluation were performed using genes from 16 Rosaceae genomes (the same 15 from [52] plus Malus baccata [53]) plus the scaffolding species following methods from [52].…”

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

“…The adoption of standardized nomenclature for plant genomes represents a significant advancement in the field of plant genomics as it helps reduce confusion and potential errors, thereby enhancing the reliability and reproducibility of genomic research. In addition, we followed a previouslyestablished gene family classification protocol (Wafula et al 2022;Khan et al 2022) that circumscribed genes into pre-computed orthogroups. Such a practice not only reduces computational resource requirements, but also allows researchers to more easily compare findings across studies.…”

“…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 CROGs from each pome fruit genome.…”

“…large inversions on chromosomes 1, 11, 13 (Supplemental Figure S5 and S7), they have minor effects on gene order (Figure 4), likely due to the small number of genes annotated from those inverted regions. Gene family analysis is performed using PlantTribes2 and the pre-constructed 26Gv2.0 scaffold orthogroup database (Wafula et al 2022). Out of the 18,110 pre-constructed orthogroups, proteins from all apple annotations (including 6 published scion cultivar genomes, 2 rootstock genomes, and the 'WA 38' genome from this work) are found in 11,698 orthogroups.…”

“…The 'WA 38' + 'Honeycrisp' group is clustered with 'GDDH13', as expected based on pedigree (Howard et al 2017). Interestingly, a strong 'publication bias', first mentioned by Wafula et al, 2022, is observed: genomes released in the same publication or annotated by the same researcher clustered together. Such groups are: 'Gala', Malus sieversii, and M. sylvestris (Sun et al, 2021); 'Fuji', 'M9', and 'MM106' (Li et al, 2024); M. fusca (Mansfeld et al 2023) and…”