# Identification of PP2C gene family and its role in stress and adversity based on T2T flax (Linum usitatissimum L.) genome

## TL;DR

This study identifies and characterizes the PP2C gene family in flax, revealing their roles in stress responses and adaptation.

## Contribution

The first comprehensive analysis of the PP2C gene family in flax using the T2T genome assembly.

## Key findings

- 117 LuPP2C genes were identified and classified into 11 subclades through phylogenetic analysis.
- LuPP2C26 and LuPP2C99 enhance salt tolerance when overexpressed in yeast.
- Stress-responsive cis-regulatory elements and miRNA targets were identified in LuPP2C promoters.

## Abstract

The PP2C gene family plays crucial roles in plant growth, development, and responses to biotic/abiotic stresses. Flax (Linum usitatissimum L.), as an important oilseed and fiber crop, lacks comprehensive characterization of its PP2C genes. In this study, we conducted a genome-wide bioinformatics analysis of the PP2C gene family in flax using the Telomere to Telomere (T2T) genome assembly, identifying 117 LuPP2C genes. Phylogenetic analysis classified these LuPP2C proteins into 11 distinct subclades. Gene structure and motif analyses revealed conserved exon-intron architectures and motif compositions among members within the same phylogenetic branches. Cis-regulatory element analysis of LuPP2C promoters identified abundant stress-responsive elements, including those associated with plant hormones (MeJA and ABA) and abiotic stresses (anaerobic induction, drought responsiveness, and low-temperature adaptation). Genomic duplication events revealed 104 segmental duplication pairs, suggesting expansion through large-scale duplication. miRNA target prediction identified lus-miR395 as the predominant miRNA targeting LuPP2C family members. Expression profiling demonstrated preferential expression of most LuPP2C members in leaf tissues. Quantitative real-time PCR (qRT-PCR) analysis further revealed that subfamily A genes, particularly LuPP2C26 and LuPP2C99, were significantly upregulated under cold, drought, and salt stress conditions. Functional validation through heterologous expression confirmed that overexpression of LuPP2C26 and LuPP2C99 enhances salt tolerance in yeast transformants. These findings systematically characterize the flax PP2C family and provide insights into its potential roles in stress adaptation mechanisms.

The online version contains supplementary material available at 10.1186/s12870-025-07284-1.