Pan-genome analysis of the glutathione S-transferase gene family reveals the core and dispensable components of GST evolution in Arachis
- 1Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences
- 2Yunnan Key Laboratory of Genetic Improvement of Herbal Oil Crops, Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences
- 3College of Agriculture, Yunnan University
Abstract
Introduction: Gene-family identification and comparative analyses have largely relied on a single reference genome and therefore cannot capture presence/absence variation among genomes.
Methods: The glutathione S-transferase (GST) family was analysed computationally across 20 Arachis genomes, 16 allotetraploid and four from the diploid progenitor lineages, using orthologous gene groups (OGGs) as the unit of analysis. Gene structure, phylogeny, duplication, collinearity, Ka/Ks and expression in tissue and stress transcriptomes were compared among OGG categories.
Results: The 1,436 GSTs carrying both canonical domains were assigned to 57 OGGs, comprising 18 core OGGs present in all 20 genomes and 39 dispensable OGGs (softcore, shell and line-specific). The family was structurally uniform, and its uniformity declined from the core to the shell OGGs. The OGGs fell into the Tau, Phi, Theta and Lambda subfamilies, 53 of the 57 belonging to Tau. WGD/segmental duplicates predominated in core and softcore OGGs, making up 65.2% of core genes, whereas tandem duplicates predominated among shell genes at 42.0%, and WGD/segmental duplicates made up a far larger share of the GSTs in the tetraploids than in the diploids. Core and softcore OGGs occupied syntenic positions shared with the progenitor diploids, about half of the cross-genome syntenic links connecting the A and B subgenomes. Among 23,399 within-OGG gene pairs, mean Ka/Ks was below 1 in 43 of the 46 OGGs for which it could be estimated, consistent with predominantly purifying selection; no pair with Ka/Ks above 1 departed significantly from neutrality, and neither Ka, Ks nor Ka/Ks differed between core and dispensable OGGs. Across 22 tissues of the cultivar NDH108, all 35 core genes were expressed, the nine silent genes belonged to softcore or shell OGGs, and the calyx was the most frequent tissue of peak expression. Under drought, cold or salt, 74 of the 84 NDH108 GSTs responded, at similar rates in core and dispensable OGGs.
Discussion: All results are computational and were not validated experimentally. The OGG-based analysis resolves variation in GST content and genomic organisation across the Arachis panel that a single reference genome does not capture, and the genes it highlights are candidates for experimental study.
Related
- Glutathione S transferase assembled gold silver nanoclusters activate cGAS STING immunity in breast cancer
- Drosophila glutathione S-transferase S1 exacerbates phenotypes of the gain-of-function voltage-gated sodium channel mutant paraShu through a hemocyte-mediated mechanism
- Proteolytic dissection of eIF4G reveals that closed-loop mRNP formation is dispensable for bulk translation in mammalian cells
- Gene functional-state covariance reveals modular structure in the Arabidopsis thaliana dispensable genome
- A systematic investigation reveals dissociable effects of ageing on implicit and explicit components of sensorimotor learning
BibTeX
@article{huang2026pangenome,
title = {{Pan-genome analysis of the glutathione S-transferase gene family reveals the core and dispensable components of GST evolution in Arachis}},
author = {Congbo Huang and Yusong Zhang and Yuan Jiang and Yanqing Luo and Kaiqin Zhao and Genze Li and Xiaoyan Yuan and Minglian Fu},
journal = {Frontiers in Plant Science},
year = {2026},
month = oct,
doi = {10.3389/fpls.2026.1986683},
url = {https://www.frontiersin.org/articles/10.3389/fpls.2026.1986683/full},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Pan-genome analysis of the glutathione S-transferase gene family reveals the core and dispensable components of GST evolution in Arachis
AU - Congbo Huang
AU - Yusong Zhang
AU - Yuan Jiang
AU - Yanqing Luo
AU - Kaiqin Zhao
AU - Genze Li
AU - Xiaoyan Yuan
AU - Minglian Fu
PY - 2026
DA - 2026/10/26
JO - Frontiers in Plant Science
DO - 10.3389/fpls.2026.1986683
UR - https://www.frontiersin.org/articles/10.3389/fpls.2026.1986683/full
AB - Introduction: Gene-family identification and comparative analyses have largely relied on a single reference genome and therefore cannot capture presence/absence variation among genomes. Methods: The glutathione S-transferase (GST) family was analysed computationally across 20 Arachis genomes, 16 allotetraploid and four from the diploid progenitor lineages, using orthologous gene groups (OGGs) as the unit of analysis. Gene structure, phylogeny, duplication, collinearity, Ka/Ks and expression in tissue and stress transcriptomes were compared among OGG categories. Results: The 1,436 GSTs carrying both canonical domains were assigned to 57 OGGs, comprising 18 core OGGs present in all 20 genomes and 39 dispensable OGGs (softcore, shell and line-specific). The family was structurally uniform, and its uniformity declined from the core to the shell OGGs. The OGGs fell into the Tau, Phi, Theta and Lambda subfamilies, 53 of the 57 belonging to Tau. WGD/segmental duplicates predominated in core and softcore OGGs, making up 65.2% of core genes, whereas tandem duplicates predominated among shell genes at 42.0%, and WGD/segmental duplicates made up a far larger share of the GSTs in the tetraploids than in the diploids. Core and softcore OGGs occupied syntenic positions shared with the progenitor diploids, about half of the cross-genome syntenic links connecting the A and B subgenomes. Among 23,399 within-OGG gene pairs, mean Ka/Ks was below 1 in 43 of the 46 OGGs for which it could be estimated, consistent with predominantly purifying selection; no pair with Ka/Ks above 1 departed significantly from neutrality, and neither Ka, Ks nor Ka/Ks differed between core and dispensable OGGs. Across 22 tissues of the cultivar NDH108, all 35 core genes were expressed, the nine silent genes belonged to softcore or shell OGGs, and the calyx was the most frequent tissue of peak expression. Under drought, cold or salt, 74 of the 84 NDH108 GSTs responded, at similar rates in core and dispensable OGGs. Discussion: All results are computational and were not validated experimentally. The OGG-based analysis resolves variation in GST content and genomic organisation across the Arachis panel that a single reference genome does not capture, and the genes it highlights are candidates for experimental study.
SN - 1664-462X
ER -