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Mycological herbaria contain important records of plant biodiversity and past outbreaks of plant disease. Mycological herbaria have been used to (1) understand the life history of plant pathogens; (2) identify outbreak strains and track their source; (3) understand the landscape ecology, biodiversity, and distribution of native plants and their dis...
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Context 1
... about the taxonomy and classification of plant pathogens can be resolved with herbarium samples ( Table 1). For example, the taxonomic status of the spinach downy mildew pathogen was resolved using herbarium specimens from four continents ( Choi et al., 2007). ...Context 2
... temporal occurrence of two major wheat pathogens was investigated from specimens collected in the long-term trials on wheat at Rothamsted Research in the United Kingdom over a 160-year period ( Bearchell et al., 2005). The abundance of Phaeosphaeria nodorum and Mycosphaerella graminicola were monitored in wheat from samples from the Broadbalk experiments where systematic sampling from the same sentinel plots at Rothamsted has occurred since 1844 ( Table 1). DNA was extracted from samples and a beta tubulin gene was amplified using real-time PCR to identify each species. ...Citations
... It is very probable that M. ferrinii was accidentally introduced with the host where it is found outside of Asia. Herbarium specimens from plant pathology and mycological herbaria have been widely used to identify fungal plant pathogens and track their distribution and natural host range (Ristaino 2020). The current study shows how herbarium specimens are providing new information on plant pathogens and their host range and distribution. ...
As an agroforestry resource willow species (Salix spp.) becoming increasingly important in the protection of riverbanks, recovery of floodable lands, soil bioremediation, biomass production, and wicker furniture manufacture, Babylon willow (Salix babylonica) is widely planted all over the world and is found throughout Iran as part of the rural landscape and is mostly planted for ornamental or bioremediation purposes. Rust fungi in the genus Melampsora usually cause disease on Salix species. Identification of Melampsora species is often complicated because there are few differences in spore morphology and little publicly available comparative sequence data. Willow trees in Iran have been reported to be infected by 15 Melampsora species; however, most of these records are based on morphological characterization. During surveillance activities carried out in June 2007, a rust species was detected on isolated Babylon willow trees in an area in Northern Iran. Both the rust fungus and the host plant were identified on the basis of morphological features and DNA sequencing. Based on a combination of morphology, large subunit (LSU) rDNA sequencing and phylogenetic analyses, our rust specimen was identified as Melampsora ferrinii, which is newly reported from Iran on Salix babylonica. Melampsora ferrinii was originally described from the Americas and this is the first time this rust has been observed on its telial host, Babylon willow, in Asia. The documentation of the rust fungus was performed using both scanning electron microscopy (SEM) and light microscopy. Additionally, an identification key for Melampsora species reported on Salix spp. in Iran is included.
En tant que ressource agroforestière, les espèces de saules (Salix spp.) deviennent de plus en plus importantes dans la protection des berges, la récupération des terres inondables, la bioremédiation des sols, la production de biomasse et la fabrication de meubles en osier. Le saule de Babylone (Salix babylonica) est largement planté dans le monde entier et se trouve dans tout l’Iran dans le cadre du paysage rural principalement planté à des fins ornementales ou de bioremédiation. Les champignons de la rouille du genre Melampsora provoquent généralement des maladies sur les espèces de Salix. L’identification des espèces de Melampsora est souvent compliquée en raison du peu de différences dans la morphologie des spores et du peu de données de séquence comparative accessibles au public. Des saules en Iran ont été signalés comme étant infectés par 15 espèces de Melampsora, cependant, la plupart de ces signalements sont basés sur la caractérisation morphologique. Au cours des activités de surveillance menées en juin 2007, une espèce de rouille a été détectée sur des arbres isolés de saule de Babylone dans une zone située au nord de l’Iran. Le champignon de la rouille et la plante hôte ont été identifiés sur la base des caractéristiques morphologiques et du séquençage de l’ADN. Sur la base de la combinaison de la morphologie, du séquençage de l’ADNr des grandes sous-unités (LSU) et des analyses phylogénétiques, notre spécimen a été identifié comme Melampsora ferrinii, récemment signalé en Iran sur Salix babylonica. Melampsora ferrinii a été initialement décrite des Amériques et c’est la première fois que cette rouille est observée sur son hôte télien, le saule de Babylone, en Asie. La documentation du champignon de la rouille a été réalisée en utilisant à la fois la microscopie électronique à balayage (MEB) et la microscopie optique. De plus, une clé d’identification des espèces de Melampsora rapportée sur Salix spp. en Iran est inclus.
KEYWORDS: Melampsora ferriniirust fungiSalicaceaetree diseaseUredinalesweeping willow
KEYWORDS: champignons de la rouillemaladie des arbresMelampsora ferriniiSalicaceaesaule pleureurUredinales
... Several sources used by the scientific community define the hierarchy in the following ranks in order of most to the least homogenous: realm, subrealm, kingdom, subkingdom, phylum, subphylum, class, subclass, order, suborder, family, subfamily, genus, and subgenus [26][27][28][29]. However, due to the inconsistencies of the ranking system [25] and other factors [30], discrepancies and disputes in taxonomy also arise [31][32][33][34] such as in the case of Leguminosae [35,36]. ...
The DNA barcoding approach has been used extensively in taxonomy and phylogenetics. The differences in certain DNA sequences are able to differentiate and help classify organisms into taxa. It has been used in cases of taxonomic disputes where morphology by itself is insufficient. This research aimed to utilize hierarchical clustering, an unsupervised machine learning method, to determine and resolve disputes in plant family taxonomy. We take a case study of Leguminosae that historically some classify into three families (Fabaceae, Caesalpiniaceae, and Mimosaceae) but others classify into one family (Leguminosae). This study is divided into several phases, which are: (i) data collection, (ii) data preprocessing, (iii) finding the best distance method, and (iv) determining disputed family. The data used are collected from several sources, including National Center for Biotechnology Information (NCBI), journals, and websites. The data for validation of the methods were collected from NCBI. This was used to determine the best distance method for differentiating families or genera. The data for the case study in the Leguminosae group was collected from journals and a website. From the experiment that we have conducted, we found that the Pearson method is the best distance method to do clustering ITS sequence of plants, both in accuracy and computational cost. We use the Pearson method to determine the disputed family between Leguminosae. We found that the case study of Leguminosae should be grouped into one family based on our research.
... Furthermore, herbarium specimens can be used to find evidence and/or patterns of diseases associated with rare plants. Ristaino (2020) has demonstrated this with both crop and non-crop plants. Two additional examples can be seen on the leaves of bracted twistflower with powdery mildew and harbinger of spring (Erigenia bulbosa) with rust (Puccinia erigeniae; Box 2). ...
Funding for rare plant conservation is limited. In addition, many aspects of the biology and ecology of rare plants are unknown. Therefore, low-cost data generation approaches to fill these gaps should be pursued. Herbarium specimens can be used as a low-cost alternative to learn about the basic biology and ecology of rare plant species. The information provided on herbarium labels has dramatically increased in recent decades to include precise locality (i.e., latitude/longitude), exact dates, habitat, associated species, and substrate. In addition, herbarium specimens are being digitized and the resulting images and data are available via clearinghouses such as GBIF and SEINet. Already, herbarium specimens of rare plants have been used to develop habitat suitability models, predict range shifts, and assess changes in flower phenology due to climate change. Herbarium specimens can also provide a wealth of information about the reproductive biology and biotic interactions of rare plants. In this paper, we will demonstrate how this information can be accessed and present a practical application for using this information to populate an important federal listing document in the USA, Species Status Assessments (SSA). We will provide examples from the literature, as well as case studies from our own research, to demonstrate how this information can be collected from herbarium specimens and how and where to incorporate this information into SSAs. More generally, data gleaned from herbarium specimens can become part of a conservationist’s tool kit to further our knowledge of past, present, and future trends for rare plants. Additional knowledge of a species’ biology and ecology allows land managers and conservationists to make more informed decisions and allows for greater protection of listed species.
... Through the sequencing of 19th-centuryinfected specimens, the strain which caused the great potato famine in 1845-1849 has been identified and its genome characterized. Phylogeny reconstruction showed the historical strain to have originated from a secondary diversification area of the pathogen in North America from where one or a few dispersal events caused P. infestans emergence in Europe [14][15][16][17][18][19] . Similar studies reconstructing the evolutionary history of crop pathogens from full genomes have been successfully realized on viruses as well [20][21][22][23] . ...
Herbarium collections are an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography can shed light on the emergence and evolutionary history of plant pathogens. Here, we reconstruct 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected Citrus herbarium specimens. Following authentication based on ancient DNA damage patterns, we compare them with a large set of modern genomes to estimate their phylogenetic relationships, pathogenicity-associated gene content and several evolutionary parameters. Our results indicate that Xci originated in Southern Asia ~11,500 years ago (perhaps in relation to Neolithic climate change and the development of agriculture) and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world (probably via human-driven expansion of citriculture through early East-West trade and colonization).
... To enhance the timeliness and accuracy of notification of plant pathogens occurrences internationally and strengthen the food and nutrition security among all reporting countries, more data exchange and real-time observation of new plant diseases are needed.6. Monitoring and Understanding Spread of diseases using Geospatial IntelligenceIn order to respond to possible disease risks in landscapes and agricultural systems, geographic information systems (GIS) are a vital tool for mapping and evaluating data regarding normal and infected hosts(Fry et al., 2013;Ristaino, 2020). Numerous disease predictions in agricultural areas are reliant on regular pest and disease surveillance using sentinel plots, as well as meteorological analysis and monitoring(Isard et al., 2007). ...
... For example, real-time monitoring is used to map outbreaks, genotype lineages, and detect fungicide sensitivity of pathogen lineages in the United States (https://usablight.org/) and Europe (https:// agro.au.dk/ forskning/internationale-platforme/euroblight/)(Fry et al., 2013;Ristaino, 2020). When the pathogen is found, USABlight.org ...
... When the pathogen is found, USABlight.org sends text or email alerts to surrounding farms(Fry et al., 2013;Ristaino, 2020). Growers saved $3,706 to $4,201 per hectare using a late blight decision support tool to target fungicide applications, depending on the variety planted(Liu et al., 2018). ...
Throughout many areas of the globe, phyto-pathogens epidemics are on
the rise, posing a major threat to crop production for the impoverished.
A worldwide human epidemic is now endangering the health of millions
of people around the world. To pull people out of poverty and promote
wellness a reliable, nutritious food source will be required. Changing
climate, spreading through worldwide food trade route, pathogen spillover
as well as the creation of novel disease groups are all contributing to the
expansion and exacerbation of phyto-pathogens both endemic and newly
developing. To address the above broad concerns, a novel set of tools
is required encompassing surveillance system and enhanced diagnostic
devices such as pathogen detectors, as well as forecasting and data
analytics. Here in this book chapter, we present comprehensive studies
that can really aid in the prevention of emerging crop diseases outbreaks
... These models and research can benefit from the improved understanding of underlying disease distribution that our web map provides. Parameterization of these models is in turn informed by genomic and bioinformatic disciplines, which could use both archival and present geospatial information on the presence of F. oxysporum to track movement of plant pathogens by elucidating the origins, evolution, and migration routes of past outbreak strains and identifying where the highest and greatest threats to crop populations may exist (Bieker and Martin 2018;Ristaino 2020). Furthermore, the detection of global hot spots of emerging diseases along with genotyping and race information will be useful to guide breeding efforts to deploy resistant varieties and to effectively implement quarantine measures and other eradication methods at landscape level. ...
... Through the sequencing of 19 th century 63 infected specimens, the strain which caused the great potato famine in 1845-1849 has been identified 64 and its genome characterized. Phylogeny reconstruction showed the historical strain to have 65 originated from a secondary diversification area of the pathogen in North America from where one or 66 a few dispersal events caused P. infestans emergence in Europe (Martin et al. 2013, Ristaino 2020 important economic losses, both by decreasing fruit yield and quality, and because of Xci quarantine 76 organism status (Gottwald et al. 2002, Talon et al. 2020. Xci comprises three major pathotypes, 77 discriminated by genetic diversity and host range. ...
Over the past decade, the field of ancient genomics has triggered considerable progress in the study of various pathogens, including those affecting crops. In this context, herbarium collections have been an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography may shed light into the emergence and evolutionary history of plant pathogens. In this study, we reconstructed 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected citrus herbarium specimens using a shotgun-based deep sequencing strategy. Following authentication of the historical genomes based on ancient DNA damage patterns, we compared them to a large set of modern genomes to reconstruct their phylogenetic relationships, pathogeny-associated genes content and estimate several evolutionary parameters, using Bayesian tip-dating calibration and phylogeography inferences. Our results reveal that Xci originated in Southern Asia ~11,500 years ago and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world. This updated scenario links Xci specialization to Neolithic climatic change and the development of agriculture, and its diversification to the human-driven expansion of citriculture through the early East-West trade and later colonization. The analysis of data obtained from such historical specimens is challenging and must undergo adapted treatment before being compared to modern samples. Nevertheless, we confirm here that herbarium collections are a precious tool to improve the knowledge of the evolutionary history of plant pathogens.
... Evaluating herbarium specimens of plant pathogens can provide valuable insights into the history of a plant pathogen system and can be crucial for testing ecological, evolutionary, and plant pathological hypotheses (Martin et al., 2013;Yoshida et al., 2014;Ristaino., 2020;Bradshaw et al., 2021;Labuschagne et al., 2021). Currently, over 4000 herbaria (Index Herbariorum, 2022) are located throughout the world, some of which contain fungal specimens up to 2500 yr old (Harvard University, 2020). ...
... Sequencing old herbarium specimens can be instrumental in answering important ecological, evolutionary, taxonomic, and plant pathological inquiries (Martin et al., 2013;Yoshida et al., 2013;Ristaino., 2020;Bradshaw et al., 2021;Labuschagne et al., 2021). In the current study, we generated primers for sequencing rust specimens up to at least 211 yr old and proceeded to use the primers to evaluate herbarium specimens of a common biological control agent for creeping thistle. ...
Sequencing herbarium specimens can be instrumental in answering ecological, evolutionary, and taxonomic inquiries. We developed a protocol for sequencing herbarium specimens of rust fungi (Pucciniales) and proceeded to sequence specimens ranging from 4 to 211 yr old from five different genera.
We then obtained sequences from an economically important biological control agent, Puccinia suaveolens, to highlight the potential of sequencing herbarium specimens in an ecological sense and to evaluate the following hypotheses: (1) The population structure of a plant pathogen changes over time, and (2) introduced pathogens are more diverse in their native range.
Our efforts resulted in sequences from 87 herbarium specimens that revealed a high level of diversity with a population structure that exhibited spatial–temporal patterns. The specimens sequenced from Europe showed more diversity than the ones from North America, uncovering an invasion pattern likely related to its European native host in North America. Additionally, to the best of our knowledge, the specimen from France collected in c. 1811 is the oldest herbarium specimen sequenced from kingdom Fungi.
In conclusion, sequencing old herbarium specimens is an important tool that can be extrapolated to better understand plant–microbe evolution and to evaluate old type specimens to solidify the taxonomy of plant pathogenic fungi.
... de Bary causes late blight, a devastating disease of potato and tomato worldwide. Phytophthora infestans is a heterothallic oomycete plant pathogen and infects a wide range of Solanum species (Ristaino 2020). Yield losses caused by late blight and the cost of its control measures have been estimated to exceed 6 billion Euros annually (Haverkort et al. 2008). ...
... With the introduction of A2 mating-type strains, sexual reproduction became possible and the concomitant increase in phenotypic and genotypic diversity of populations of P. infestans in Europe. First introductions of P. infestans into Europe were largely confined to a single clonal lineage of the Ia mtDNA haplotype FAM-1 (Martin et al 2013;Ristaino et al. 2001;May and Ristaino 2004;Ristaino 2006Ristaino , 2020Ristaino and Hu 2009;Saville and Ristaino 2021). Over time, other clonal lineages of the A1 mating type migrated to Europe (including US-1, Ib mtDNA haplotype) and then these lineages were gradually replaced by more aggressive populations with both A1 and A2 mating-type strains (Day and Shattock 1997;Cooke et al. 2012;Ristaino 2020). ...
... First introductions of P. infestans into Europe were largely confined to a single clonal lineage of the Ia mtDNA haplotype FAM-1 (Martin et al 2013;Ristaino et al. 2001;May and Ristaino 2004;Ristaino 2006Ristaino , 2020Ristaino and Hu 2009;Saville and Ristaino 2021). Over time, other clonal lineages of the A1 mating type migrated to Europe (including US-1, Ib mtDNA haplotype) and then these lineages were gradually replaced by more aggressive populations with both A1 and A2 mating-type strains (Day and Shattock 1997;Cooke et al. 2012;Ristaino 2020). In some European countries, low genetic diversity has been detected in some populations with both A1 and A2 mating types. ...
Phytophthora infestans causes a devastating disease of potato and tomato. P. infestans can reproduce asexually and sexually; and both mating types have been detected in several European countries since the early 1980s. Previous work in the Netherlands showed that population is highly diverse due to sexual reproduction and that oospores can overwinter in the soil. In Southern Flevoland, the genotypic diversity was analyzed by characterizing isolates from conventional and organic potato fields, potato refuse piles, and allotment gardens for mating type and DNA fingerprints between 1994 and 1996. Refuse piles were identified as the most important infection source for commercial fields in 1994 and 1995 and some organic fields were identified as a source of mid-season infection of conventional fields; however, only RFLP fingerprint patterns were used for the analysis. We sampled DNA from these populations and amplified two regions of a single-copy nuclear ras gene (intron 1 -224 bp and exon 3-6 -542 bp) containing both coding and noncoding regions to elucidate gene flow between organic and conventional fields. Multiple isolates were sampled from 5 organic, 17 conventional and 7 refuse pile sites. There were 5 heterozygous sites in the intron 1 region and 5 heterozygous sites in the exon 3-6 region that were phylogenetically informative. Only two isolates from an organic and conventional field were homozygous. Five haplotypes were found among the fields and three of these were found in our previous world wide study of Andean migration. Further analyses of additional mitochondrial gene regions are underway to investigate the migration of P. infestans between these fields.
... Preservation Methods for Fungal Herbarium Specimens. MH, like the botanical herbarium for plants, serve as a repository of preserved fungi in the form of pressed and dried fungal specimens mounted on a sheet of paper or placed in paper packets or in jars with alcohol or glycerin (Ristaino, 2020). Tadiosa and Soriano (2004) described the procedures from the isolation up to the preservation of fungal specimens as presented in the workbook on Tropical Fungi: Collection, Isolation, and Identification, written by T.H. . ...
Mycology in the Tropics: Updates on Philippine Fungi comprehensively discusses the current state of Philippine mycology, including historical developments in the field, listings of fungi with diverse utilizations or applications, and those that cause economic impact on crop production in the country. Specifically, the chapters in the book introduce tropical mycology, describe different fungal groups, their biodiversity and conservation, and give insights into the applications of mycology in agriculture, health, industry and the environment. The book also includes quarantine regulations on economically important diseases and describes the importance of developing local studies on fungi.
