Two domesticated species of rice shaped the population structure of Xanthomonas oryzae pv. oryzae in Africa
11 affiliations
- 1Plant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
- 2Laboratoire de Biologie Moléculaire Appliquée, Faculté des Sciences et Techniques, Université des Sciences et Techniques et des technologies de Bamako, Bamako, Mali
- 3Institut Supérieur Agronomique et Vétérinaire « Valéry Giscard d’Estaing » de Faranah (ISAV « VGE »/F), Faranah, République de Guinée
- 4Pathogens Genomic Diversity Network Africa, Bamako, Mali
- 5Université de Tilaberi, Tillabéri, Niger
- 6Laboratoire de Biologie Moléculaire Appliquée, Faculté de Médecine et d'Odontostomatologie, Université des Sciences et Techniques et des Technologies de Bamako, Bamako, Mali
- 7Institut Sénégalais de Recherches Agricoles, Tambacounda, Senegal
- 8Centre National de Recherche Scientifique et Technologique (CNRST)/ Institut de l’Environnement et de Recherches Agricoles (INERA), Bobo Dioulasso, Burkina Faso
- 9Laboratoire de Biologie Moléculaire Appliquée et Centre de Recherche en Santé Globale, Bamako, Mali
- 10Laboratoire de Physiologie Végétale, Université Félix Houphouët-Boigny, Abidjan, Côte d'Ivoire
- 11Centre Régional de Recherche Agricole de Niono, Institut d'Economie Rurale, Bamako, Mali
Abstract
African rice (Oryza glaberrima) was independently domesticated in West Africa around 3000 years ago, and has long been intertwined in the history of the region. Asian rice (Oryza sativa), which was introduced in Africa when European settlers arrived, gradually replaced African rice and has since dominated rice cultivation in the continent. Domesticated rice species are affected by bacterial leaf blight (BLB), which is caused by the pathogen Xanthomonas oryzae pv. oryzae (Xoo). Here we show that the bacterial leaf blight pathogen in Africa (AfXoo) belongs to a distinct phylogroup from the one circulating in Asia (AsXoo), and has a different evolutionary history. Analysis of 87 AfXoo genomes identified five main populations, including highly clonal ones, and a more diverse and recombinant population. Tip-dating analysis revealed that the AfXoo population went through a period of expansion, then decline and more recent recovery. We hypothesize this followed the rise and fall of African rice, and that the introduction of O. sativa served as a bottleneck leading to the emergence of current AfXoo populations. We show that AfXoo has a highly conserved repertoire of type III effectors (T3E), but that nonetheless there is variation especially between populations. In the case of transcription activator-like effectors (TALEs), variation can arise quickly through rearrangements, and we hypothesize that the TALE repertoire of AfXoo has been selected to allow the bacteria to colonize both species of cultivated rice found in the continent. Our research provides an attempt to decipher the genetic history of bacterial blight in West Africa, and its past and present impact on rice cultivation in the region. Author summary: For thousands of years, rice cultivation has been an integral part of African agriculture. However, the cultivation of the locally domesticated African rice cultivar (Oryza glaberrima) has gradually shifted towards Asian rice varieties (Oryza sativa), likely altering associated microbe populations. One of these microbes is the causal agent of bacterial leaf blight, Xanthomonas oryzae pv. oryzae (Xoo). We performed a population genomics analysis to understand the evolutionary history of African strains of Xoo (AfXoo). We show that current populations of AfXoo have relatively low genetic diversity, have distinct virulence genes, and have historically gone through expansion and decline. We propose AfXoo was first adapted to African rice at least a thousand years ago. The introduction of O. sativa then shaped the recent population dynamics of AfXoo. Our results highlight the interplay between crop domestication and cultivation and pathogen evolution.
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BibTeX
@article{quibod2026domesticated,
title = {{Two domesticated species of rice shaped the population structure of Xanthomonas oryzae pv. oryzae in Africa}},
author = {Ian Lorenzo Quibod and Coline Sciallano and Florence Auguy and Laurent Brottier and Alexis Dereeper and Diariatou Diagne and Amadou Diallo and Hinda Doucouré and Solely Issaka Mayaki and Ibrahim Keita and Lazeni Konate and Hamidou Tall and Cheick Tékété and Sylvain Zougrana and Mathilde Hutin and Ousmane Koita and Daoudou Kone and Soungalo Sarra and Valérie Verdier and Issa Wonni and Boris Szurek and Sébastien Cunnac and Alvaro L. Pérez-Quintero},
journal = {PLOS Pathogens},
year = {2026},
month = sep,
doi = {10.1371/journal.ppat.1014015},
url = {https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014015},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Two domesticated species of rice shaped the population structure of Xanthomonas oryzae pv. oryzae in Africa
AU - Ian Lorenzo Quibod
AU - Coline Sciallano
AU - Florence Auguy
AU - Laurent Brottier
AU - Alexis Dereeper
AU - Diariatou Diagne
AU - Amadou Diallo
AU - Hinda Doucouré
AU - Solely Issaka Mayaki
AU - Ibrahim Keita
AU - Lazeni Konate
AU - Hamidou Tall
AU - Cheick Tékété
AU - Sylvain Zougrana
AU - Mathilde Hutin
AU - Ousmane Koita
AU - Daoudou Kone
AU - Soungalo Sarra
AU - Valérie Verdier
AU - Issa Wonni
AU - Boris Szurek
AU - Sébastien Cunnac
AU - Alvaro L. Pérez-Quintero
PY - 2026
DA - 2026/09/17
JO - PLOS Pathogens
DO - 10.1371/journal.ppat.1014015
UR - https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014015
AB - African rice (Oryza glaberrima) was independently domesticated in West Africa around 3000 years ago, and has long been intertwined in the history of the region. Asian rice (Oryza sativa), which was introduced in Africa when European settlers arrived, gradually replaced African rice and has since dominated rice cultivation in the continent. Domesticated rice species are affected by bacterial leaf blight (BLB), which is caused by the pathogen Xanthomonas oryzae pv. oryzae (Xoo). Here we show that the bacterial leaf blight pathogen in Africa (AfXoo) belongs to a distinct phylogroup from the one circulating in Asia (AsXoo), and has a different evolutionary history. Analysis of 87 AfXoo genomes identified five main populations, including highly clonal ones, and a more diverse and recombinant population. Tip-dating analysis revealed that the AfXoo population went through a period of expansion, then decline and more recent recovery. We hypothesize this followed the rise and fall of African rice, and that the introduction of O. sativa served as a bottleneck leading to the emergence of current AfXoo populations. We show that AfXoo has a highly conserved repertoire of type III effectors (T3E), but that nonetheless there is variation especially between populations. In the case of transcription activator-like effectors (TALEs), variation can arise quickly through rearrangements, and we hypothesize that the TALE repertoire of AfXoo has been selected to allow the bacteria to colonize both species of cultivated rice found in the continent. Our research provides an attempt to decipher the genetic history of bacterial blight in West Africa, and its past and present impact on rice cultivation in the region. Author summary: For thousands of years, rice cultivation has been an integral part of African agriculture. However, the cultivation of the locally domesticated African rice cultivar (Oryza glaberrima) has gradually shifted towards Asian rice varieties (Oryza sativa), likely altering associated microbe populations. One of these microbes is the causal agent of bacterial leaf blight, Xanthomonas oryzae pv. oryzae (Xoo). We performed a population genomics analysis to understand the evolutionary history of African strains of Xoo (AfXoo). We show that current populations of AfXoo have relatively low genetic diversity, have distinct virulence genes, and have historically gone through expansion and decline. We propose AfXoo was first adapted to African rice at least a thousand years ago. The introduction of O. sativa then shaped the recent population dynamics of AfXoo. Our results highlight the interplay between crop domestication and cultivation and pathogen evolution.
SN - 1553-7374
ER -