# Birth and death evolution of polyphenol oxidase (PPO) gene family in Oryza species

## TL;DR

This study explores the evolution of the PPO gene family in rice species, revealing how gene duplication and mutations have shaped their diversity and function.

## Contribution

The first comprehensive analysis of PPO gene family evolution in the Oryza genus, identifying three PPO types and their evolutionary patterns.

## Key findings

- PPO genes in Oryza are classified into three types, with PPO3 reported for the first time.
- Tandem duplications and truncations drive PPO gene family expansion and diversity.
- Domestication and natural selection have shaped PPO mutations across Oryza species.

## Abstract

Polyphenol oxidases (PPOs) are copper-containing enzymes that catalyze the oxidation of phenolic substrates to quinones. In cereal crops, PPOs contribute to both grain browning and defense responses. During domestication, multiple independent PPO mutations have been selected, creating a trade-off between grain quality and plant fitness. In rice, most PPO-related studies have focused on the reference genome of Oryza sativa ssp. japonica cv. Nipponbare, yet a comprehensive understanding of PPO gene diversity, copy number variation, and evolutionary history across the Oryza genus remains lacking.

We systematically identified PPO genes in 21 fully sequenced wild and cultivated Oryza species, along with three close relatives. PPOs were classified into three types (PPO1–3), with PPO1 further divided into two subtypes (PPO1-1 and PPO1-2) and PPO3 is reported here for the first time. Both PPO1 and PPO3 possess thylakoid transfer domains and Tat-specific motifs, whereas PPO2 lacks these features. PPO1 and PPO2 expanded through tandem duplications, forming two major clusters: the PPO1 cluster and the PPO2/PPO3 cluster. Truncated PPO variants were found to be widespread across Oryza, present in roughly half of the surveyed species and often outnumbering intact PPO counterparts. Most truncated PPOs contain multiple indels: those in PPO1-1 and PPO3 arose independently, whereas the truncations in PPO1-2 and PPO2 are conserved. Furthermore, PPO mutations in Nipponbare (PPO1 and PPO3) and O. glaberrima (PPO1-1) are associated with domestication, with PPO1-2.1 in Nipponbare disrupted by transposable-element insertions and O. glaberrima harboring a novel truncated PPO1-1 allele.

This study provides the first comprehensive analysis of the PPO gene family across Oryza, revealing three major PPO types. The expansion of PPOs through tandem duplications, coupled with frequent loss-of-function mutations due to frameshift-indel truncations, is consistent with a birth-and-death model of gene family evolution. Our findings highlight the combined contributions of domestication and natural selection in shaping PPO diversity in Oryza.

The online version contains supplementary material available at 10.1186/s40529-026-00491-5.