Sabine Telle

Towards a universal barcode of oomycetes - a comparison of the cox1 and cox2 loci

Oomycetes are a diverse group of eukaryotes in terrestrial, limnic and marine habitats worldwide and include several devastating plant pathogens, for example Phytophthora infestans (potato late blight). The cytochrome c oxidase subunit 2 gene (cox2) has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. The cox1 locus has been used in some studies of Pythium and Phytophthora, but has rarely been used for other oomycetes, as amplification success of cox1 varies with different lineages and sample ages. To determine which out of cox1 or cox2 is best suited as a universal oomycete barcode, we compared these two genes in terms of (i) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (ii) sequence polymorphism, intra‐ and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding‐type material. Sequence data for several historic type specimens exist for cox2, but there are none for cox1. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. The cox2‐1 spacer could be a useful marker below species level. Improved protocols and universal primers are presented for all genes to facilitate future barcoding efforts.

Phylogenetic relationships of graminicolous downy mildews based on cox2 sequence data

Graminicolous downy mildews (GDM) are an understudied, yet economically important, group of plant pathogens, which are one of the major constraints to poaceous crops in the tropics and subtropics. Here we present a first molecular phylogeny based on cox2 sequences comprising all genera of the GDM currently accepted, with both lasting (Graminivora, Poakatesthia, and Viennotia) and evanescent (Peronosclerospora, Sclerophthora, and Sclerospora) sporangiophores. In addition, all other downy mildew genera currently accepted, as well as a representative sample of other oomycete taxa, have been included. It was shown that all genera of the GDM have had a long, independent evolutionary history, and that the delineation between Peronosclerospora and Sclerospora is correct. Sclerophthora was found to be a particularly divergent taxon nested within a paraphyletic Phytophthora, but without support. The results confirm that the placement of Peronosclerospora and Sclerospora in the Saprolegniomycetidae is incorrect. Sclerophthora is not closely related to Pachymetra of the family Verrucalvaceae, and also does not belong to the Saprolegniomycetidae, but shows close affinities to the Peronosporaceae. In addition, all GDM are interspersed throughout the Peronosporaceae s lat., suggesting that a separate family for the Sclerosporaceae might not be justified.

The inclusion of downy mildews in a multi-locus-dataset and its reanalysis reveals a high degree of paraphyly in Phytophthora.

Pathogens belonging to the Oomycota, a group of heterokont, fungal-like organisms, are amongst the most notorious pathogens in agriculture. In particular, the obligate biotrophic downy mildews and the hemibiotrophic members of the genus Phytophthora are responsible for a huge variety of destructive diseases, including sudden oak death caused by P. ramorum, potato late blight caused by P. infestans, cucurbit downy mildew caused by Pseudoperonospora cubensis, and grape downy mildew caused by Plasmopara viticola. About 800 species of downy mildews and roughly 100 species of Phytophthora are currently accepted, and recent studies have revealed that these groups are closely related. However, the degree to which Phytophthora is paraphyletic and where exactly the downy mildews insert into this genus in relation to other clades could not be inferred with certainty to date. Here we present a molecular phylogeny encompassing all clades of Phytophthora as represented in a multi-locus dataset and two representatives of the monophyletic downy mildews from divergent genera. Our results demonstrate that Phytophthora is at least six times paraphyletic with respect to the downy mildews. The downy mildew representatives are consistently nested within clade 4 (contains Phytophthora palmivora), which is placed sister to clade 1 (contains Phytophthora infestans). This finding would either necessitate placing all downy mildews and Phytopthora species in a single genus, either under the oldest generic name Peronospora or by conservation the later name Phytophthora, or the description of at least six new genera within Phytophthora. The complications of both options are discussed, and it is concluded that the latter is preferable, as it warrants fewer name changes and is more practical.

Phylogenetic investigations in the downy mildew genus Bremia reveal several distinct lineages and a species with a presumably exceptional wide host range

Bremia lactucae is one of the most devastating and widespread pathogens in lettuce production worldwide. Despite its economical importance, uncertainty prevails about the species delimitation in the genus Bremia. Commonly, Bremia is considered to be monotypic, containing only Bremia lactucae, while taxonomists have described additional species, and molecular phylogenetic studies have shown significant sequence divergence between accessions from different hosts. Here, we report that several previously described species are genetically highly distinct from Bremia lactucae parasitic to Lactuca sativa. These include Bremia lapsanae, Bremia sonchicola, and Bremia taraxaci. In addition to these host-specific species, a plurivorous species is revealed, which infects hosts from three different tribes in the Asteraceae subfamilies Asteroideae and Carduoideae. The broad host range of clade 1 is exceptional for downy mildews and only paralleled by Pseudoperonospora cubensis, which infects a broad range of Cucurbitaceae. The taxonomic status of Bremia cirsii and of Bremia centaureae remains unresolved, as the accessions from Cirsium and Centaurea, respectively, did not form a monophylum but were partly contained in the plurivorous clade 1. Bremia lactucae was found to be restricted to Lactuca sativa and Lactuca serriola. Thus, it can be assumed that Bremia infections on weeds apart from Lactuca species do not pose a significant risk for lettuce production. However, it is unlikely that breeding resistance genes from Lactuca serriola into Lactuca sativa will result in durable resistance of lettuce to downy mildew disease, because the current study provides additional evidence that Bremia accessions from both hosts form a population continuum.

Molecular phylogenetic analysis of Peronosclerospora (Oomycetes) reveals cryptic species and genetically distinct species parasitic to maize

Downy mildews are amongst the most widespread and economically important pathogens of cultivated grasses in the tropics and subtropics. Despite their importance, molecular methods, particularly DNA sequence analysis, have rarely been applied to either species identification or to the determination of phylogenetic relationships between species. Here we report the presence of several cryptic species in the genus Peronosclerospora. Further we confirm that maize can be parasitised by several species of Peronosclerospora, including P. eriochloae, which has not been reported previously as a pathogen of maize. The presence of 14 distinct phylogenetic lineages, including three that are parasitic to maize, highlights the current fragmentary knowledge on the diversity and classification of species within Peronosclerospora. Species identification in Peronosclerospora has been traditionally based on the host genus and a set of variable morphological characteristics, which has meant that the identification of species is often unreliable. This situation is primed for the application of molecular techniques for the identification of species. One of the lineages parasitic to maize in Australia has not yet been formally described and its distribution is not known. Future investigation including a broad sampling of downy mildews from maize and other cultivated and native grasses on a world-wide basis is a prerequisite to a re-evaluation of quarantine regulations aimed at restricting or limiting their spread.

Cryptic diversity of Plasmopara viticola (Oomycota, Peronosporaceae) in North America

Plasmopara viticola is the causal agent of grapevine downy mildew and is among the most important diseases in viticulture. It originates from North America, where it coevolved with wild Vitis species. Beginning in the 1870s it turned into a global epidemic that has been causing severe yield losses. It is generally believed that a single species is causing downy mildew on a large variety of economically important cultivars. Here we report, based on one nuclear and two mitochondrial markers, that isolates from vineyards in the United States fall into three highly distinct phylogenetic lineages. One of these contains European strains and affects Vitis vinifera cultivars, while the other two lineages affect also other species of Vitis. The divergence between these lineages is high, and, judging from the genetic variation in other Plasmopara lineages, might reflect distinct species. Due to the potentially significant implications for quarantine regulations and resistance breeding, detailed studies will be necessary to clarify whether these genetically distinct lineages occur outside of North America or are still confined there.

The molecular phylogeny of the white blister rust genus Pustula reveals a case of underestimated biodiversity with several undescribed species on ornamentals and crop plants

Despite their economic importance, the knowledge of the biodiversity of many plant pathogens is still fragmentary. In this study we show that this is true also for the white blister rust genus Pustula that is parasitic on several genera in the asterids, including sunflower and the gentian, Eustoma. It is revealed that several distinct species exist in Pustula, suggesting that species are mostly host genus specific. No geographic patterns were observed in the occurrence of Pustula, the host range of which includes the Araliaceae, Asteraceae, Gentianaceae, and Goodeniaceae. Evidence points to these becoming hosts as a result of jumps from the Asteraceae, with subsequent host-specific adaptation and speciation. Among the undescribed species are pathogens of economic importance, e.g. the white blister rusts of sunflower, or with still restricted geographical ranges, e.g. Pustula centaurii, which could potentially spread with international seed trade, if no quarantine restrictions are implemented.

Reclassification of an enigmatic downy mildew species on lovegrass (Eragrostis) to the new genus Eraphthora, with a key to the genera of the Peronosporaceae

Graminicolous downy mildews affect economical important crops like sorghum, maize and pearl millet, and also a variety of wild grasses, which pathogens have hitherto been much less studied. This also applies to an enigmatic downy mildew from Eragrostis cilianensis, which exhibits a chimeric appearance, with similarities to Basidiophora, Sclerophthora, and Sclerospora. In this study, the phylogenetic relationship of lovegrass downy mildew with respect to other genera of the Peronosporaceae was investigated and the characteristics of genera potentially associated with lovegrass downy mildew summarised from historic studies. A key based on the morphology of asexual stages is presented for all genera of downy mildews hitherto described. Based on morphological characteristics and sequence divergence, Sclerospora butleri is transferred to a new genus, Eraphthora. Lovegrass downy mildew seems to be widely distributed, as in addition to previous records from Malawi, India and Australia, we could now sample one specimen from Europe (Spilimbergo, Italy). Currently, it is unclear if Eraphthora butleri is able to infect the crop species Eragrostis tef, which might be a potential host of economic importance.

A new presumably widespread species of Albugo parasitic to Strigosella spp. (Brassicaceae)

White blister rust is one of the most common diseases in Brassicaceae. Recently, molecular approaches revealed that apart from Albugo candida, several other more specialized species of the genus are causing this disease on Brassicaceae and the diversity of this group still remains largely unexplored. All newly described species have so far been sampled only from a limited geographic range, except for Albugo species which followed their invasive host from Europe to other continents. In this study we show that a previously unknown species of Albugo is causing white blister rust disease on two species of Strigosella. This species can be distinguished from other species of the genus Albugo both by its phylogenetic position and its unique oospore ornamentation that might be an adaptation to the harsh environment of the host plants. As a consequence, Albugo arenosa is described and illustrated as a new species, so far known from Strigosella africana in Iran and Spain, and Strigosella brevipes in Iran. Apart from Albugo candida and Albugo lepidii, this is the third hitherto known species of Albugo s. str. with a confirmed native distribution range of several thousand kilometres.

Ten polymorphic microsatellite loci identified from a small insert genomic library for Peronospora tabacina

Ten polymorphic microsatellite loci for the obligate biotrophic, oomycete pathogen of tobacco, Peronospora tabacina, were identified from a small insert genomic library enriched for GT motifs. Eighty-five percent of the 162 loci identified were composed of dinucleotide repeats, whereas only 4% and 11% were tri-and tetra-nucleotide repeats respectively. About 82% of all the microsatellites were perfect and within the library; only about 7% of the loci were duplicated. Primers were designed for 63 loci; 10 loci were polymorphic, 19 were monomorphic and 34 either failed to amplify or produced ambiguous/inconsistent results. The 10 polymorphic loci were characterized with 44 isolates of P. tabacina collected from tobacco plants growing in Europe, the Near East and North and South America. The number of alleles per locus was either three or four with a mean of 3.2, and the mean number of genotypes per locus was 3.6. Observed heterozygosity was 0.32–0.95, whereas expected heterozygosity was 0.44–0.69 for these loci. All loci except PT054 did not conform to the Hardy-Weinberg distribution. Polymorphic information content (PIC) for the loci was 0.35–0.69 with a mean of 0.50. These microsatellite loci provide a set of markers sufficient to perform genetic diversity and population studies of P. tabacina, and possibly other species of Peronospora.