Phytophthora receives a new review after 180 years of research

USDA researchers have compiled 180 years of advances in taxonomy and identification of Phytophthora, a genus with 261 valid species and a direct impact on crops, forests, nurseries, urban landscapes, and natural ecosystems. Its scientific review connects potato blight and the Irish famine to the birth of modern plant pathology. It also updates databases for Sanger sequencing, high-throughput technologies, and complete genomes.

The genus includes some of the most important plant pathogens. The best-known case involves Phytophthora infestans, the causal agent of potato blight. The disease struck Ireland between 1845 and 1852. Approximately 1,5 million people died and up to 1,5 million emigrated due to the famine associated with the disease, which was not yet formally described at that time.

The review shows the progress from the first hypotheses about the cause of the disease to the use of genomics. In the 1840s, late blight appeared in North America and Europe. Records indicate an almost simultaneous occurrence in 1841 and 1842 in Philadelphia, in the United States, and in Liège, Belgium. The disease spread to other European regions and culminated in the Irish famine. (Click here and read: Study confirms the origin of Phytophthora infestans)

Miles Joseph Berkeley defended the fungal theory after observing mold-covered potato leaves under a microscope. Heinrich Anton de Bary described Phytophthora infestans in 1876 and coined the name Phytophthora, derived from the Greek words for "plant" and "destruction." This milestone helped solidify phytopathology as a scientific field.

Two phrases

The work divides taxonomic history into two phases. The morphological era spans from 1876 to 1999. It utilized characteristics such as size and shape of sporangia, oogonia, antheridia, chlamydospores, growth in culture media, temperature, and pathogenicity. Despite the large number of species published during this period, only 48 remain valid.

The molecular era began in 2000. Since then, 214 species have been described with integration between morphological and molecular characters. Sanger sequencing has gained a leading role in molecular characterization. The ITS region of ribosomal DNA has historically been used as a marker for species description and identification. Nuclear and mitochondrial genes have also begun to support identification and phylogeny studies.

The study updates the information from "Revision of Phytophthora," published in 2023. The previous survey listed 211 valid species and a representative lineage of Phytophthora palmivora. The new database lists 261 valid species, with 50 additional species published in recent years.

Scientists highlight the importance of ex-types, cultures derived from the reference specimens used in species definition. Their work presents updated databases for identification by Sanger and by second- and third-generation HTS technologies. These databases cover the 261 valid species and a representative lineage of Phytophthora palmivora.

The work also brings together 257 complete genomes available at NCBI, associated with 76 species. Of this total, 46 correspond to ex-types, including 35 reference genomes at NCBI. The genomic assemblies utilize platforms such as Illumina, PacBio, and MinION ONT.

High-performance technologies

High-throughput technologies have expanded diagnostic capabilities. Metabarcoding allows for the identification of organisms from environmental DNA. However, this work points to limitations in short reads, especially in studies with ITS1 of approximately 250 base pairs. Third-generation sequencing, with longer reads, could improve species-level resolution.

Scientists also note challenges. HTS technologies require instruments, reagents, and knowledge in bioinformatics. Identification can face problems with hybrid species, DNA from non-viable organisms, and species with similar sequence profiles. The text also points to the need for standardization of bioinformatics protocols and workflows, especially in areas of quarantine, regulation, and biosafety.

Further information can be found at doi.org/10.1094/PDIS-07-25-1349-FE