Genetic validation of historical plant pathology records – a case study based on the fungal genus Phoma from the ICMP culture collection

Abstract

Fungal taxonomy and classification, and fungal identification tools, are increasingly based on DNA sequencing technologies. In contrast, many historical records of fungi are based on morphologically identified specimens. Scientific collections of specimens or living cultures provide a resource to enable these early records to be genetically validated using modern techniques. This project uses a set of cultures deposited prior to 2008 in the International Collection of Microorganisms from Plants (ICMP) culture collection as Phoma, a genus of high biosecurity importance that is notoriously difficult to identify accurately using morphological characters. Of the 265 cultures sequenced, 23% had been misidentified. These misidentifications mean that six species previously thought to be present in New Zealand probably do not occur there. Fifty specimens had not previously been identified to species level; amongst these were eight species newly reported from New Zealand. Genetic validation projects such as this, using existing scientific collections, are essential for maintaining a robust global biosecurity system. Keywords: barcoding, biosecurity, DNA sequencing, ICMP culture collection, phylogeny, plant pathology IntroductionNew Zealand has strict biosecurity regulations aimed at minimizing risk associated with the importation of unwanted organisms, especially pathogens of plants and animals (Ministry for Primary Industries, 2017). The import of new material of species not known to occur in New Zealand needs a strong case that satisfies the Hazardous Substances and New Organisms Act (Environmental Protection Authority, 2017). Part of the purpose of the Act was to protect the environment, as well as the health and safety of people and communities, by preventing or managing the adverse effects of organisms new to New Zealand.An important tool for the government departments regulating these acts in relation to fungal pathogens is the NZFungi database (http://nzfungi2.landcareresearch.c o.nz/), the most complete catalogue for the fungi of New Zealand. NZFungi attempts to list all of the fungal names that have been used in a New Zealand context, along with the current name for those fungi. It also provides an opinion on whether these fungi actually occur in New Zealand, based on evidence from voucher specimens, cultures, DNA sequences, and literature reports. Most of the 'present in New Zealand' opinions are based on historical identifications made using morphological comparisons. However, for many fungal genera of biosecurity importance, morphologically based identifications are notoriously difficult and unreliable. Current fungal taxa are increasingly distinguished on the basis of DNA sequences, making the genetic validation of records based on morphologically identified specimens desirable.For plant-associated fungi, scientific collections such as the New Zealand Fungarium (PDD, www.landcareresea rch.co.nz/resources/collections/pdd), the International Collection of Microorganisms from Plants (the ICMP culture collection...

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

“…Perceived lack of phenotypical divergence can also stem from failure to properly observe diagnostic characters (Moncada et al 2014;Lücking et al 2017;Merényi et al 2017). This is particularly obvious in microfungi; for instance, Johnston et al (2017) showed that 23% of historical Phoma cultures determined based on phenotype had been misidentified.…”

Isolation and evaluation of culture media for mycelia growth of an emerging faba bean (Vicia faba L.) gall-forming disease causal agent in Ethiopia

“…Besides, the diagnosis of microscopic structures showed that the chlamydospore (Figure 3 C) and conidia (Figure 3 B) of the isolates were similar to Peyronellaea pinodella. Peyronellaea pinodella is associated with a black stem (summer back stem) of clover and peas (Johnston et al, 2017).…”

“…The microscopic examinations were carried with the 40X objective lens of the compound light microscope (MAX BINO BELGIUM). Macroscopic and microscopic morphological characters were used to compare the fungal isolates with the assistance of current mycological literature (Johnston et al, 2017).…”

Detection of the Phoma pathogens Plenodomus biglobosus subclades ‘brassicae’ and ‘canadensis’ on wasabi, and ‘canadensis’ in Europe

“…Moreover, this study also represents, to the best of the authors' knowledge, new discoveries for both Pbb and Pbc as causal agents of Phoma disease on wasabi plants. Prior to this study, based on available sequence data, P. biglobosus subclade 'occiaustralensis' appears to be the predominant subclade on Phoma-symptomatic wasabi, with reports from Canada, New Zealand and Taiwan (de Gruyter et al, 2013;Johnston et al, 2017;Punja et al, 2017). Thus, it is evident that multiple genetic subclades of P. biglobosus are pathogenic to wasabi.…”