Diversity and Pathogenicity of Phytophthora Species Associated with Declining Alder Trees in Italy and Description of Phytophthora alpina sp. nov

Extensive decline and mortality events of alder trees have recently been observed in several riparian ecosystems in Italy. Since there is little information about the aetiology of this disease and given the high ecological relevance of riparian ecosystems, an in-depth study was conducted in three sites spanning from the Mediterranean to Alpine regions. From spring 2019 to spring 2020, 261 samples of bleeding cankers, rhizosphere soil and leaves used as baits along waterways were collected and used for Phytophthora isolation. Based on morphology, colony appearance and DNA sequence data, 10 species belonging to 6 clades were identified. These included P. plurivora (84 isolates), P. pseudocryptogea (50), P. hydropathica (18), P. gonapodyides (14), P. bilorbang (13), P. pseudosyringae (12), P. lacustris (11), P. acerina (7), P. cactorum (1) and one isolate of the hybrid Phytophthora ×serendipita. In addition, two new Phytophthora species, one of which is described here as Phytophthora alpina sp. nov., were isolated. The pathogenicity of P. alpina and other species obtained from samples collected in the green alder stand was assessed on 3-year-old seedlings. All species proved to be pathogenic on green alder causing symptoms congruent with field observations. Results obtained have allowed us to expand knowledge about alder decline aetiology. The diversity of pathogenicity of Phytophthora species associated with symptomatic alder trees suggested that no single agent is responsible for the disease, but that it is the result of multiple infections of different Phytophthora species, variable in assemblages among sites.

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Diversity and Distribution of Phytophthora Species in Protected Natural Areas in Sicily

Forests ◽

10.3390/f10030259 ◽

2019 ◽

Vol 10 (3) ◽

pp. 259 ◽

Cited By ~ 9

Author(s):

Thomas Jung ◽

Federico La Spada ◽

Antonella Pane ◽

Francesco Aloi ◽

Maria Evoli ◽

...

Keyword(s):

Host Plants ◽

Rhizosphere Soil ◽

Stream Water ◽

Its Region ◽

Morphological Characters ◽

Phytophthora Species ◽

Riparian Ecosystems ◽

Forest Stands ◽

Natural Areas ◽

Protected Natural Areas

: The aim of this study was to investigate the occurrence, diversity, and distribution of Phytophthora species in Protected Natural Areas (PNAs), including forest stands, rivers, and riparian ecosystems, in Sicily (Italy), and assessing correlations with natural vegetation and host plants. Fifteen forest stands and 14 rivers in 10 Sicilian PNAs were studied. Phytophthora isolations from soil and stream water were performed using leaf baitings. Isolates were identified using both morphological characters and sequence analysis of the internal transcribed spacer (ITS) region. A rich community of 20 Phytophthora species from eight phylogenetic clades, including three new Phytophthora taxa, was recovered (17 species in rhizosphere soil from forest stands and 12 species in rivers). New knowledge about the distribution, host associations, and ecology of several Phytophthora species was provided.

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Using DNA sequence data to investigate the invasive spotted lanternfly's origin, parasitoids, and microbial associates

10.1603/ice.2016.109017 ◽

2016 ◽

Author(s):

Julie M. Urban

Keyword(s):

Dna Sequence ◽

Sequence Data ◽

Dna Sequence Data

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Taxonomic Re-Examination of Nine Rosellinia Types (Ascomycota, Xylariales) Stored in the Saccardo Mycological Collection

Microorganisms ◽

10.3390/microorganisms9030666 ◽

2021 ◽

Vol 9 (3) ◽

pp. 666

Author(s):

Niccolò Forin ◽

Alfredo Vizzini ◽

Federico Fainelli ◽

Enrico Ercole ◽

Barbara Baldan

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Illumina Miseq ◽

Botanical Garden ◽

Molecular Study ◽

Its2 Sequence ◽

Type Specimens ◽

Its1 Sequence ◽

Dna Sequence Data ◽

Nomen Novum

In a recent monograph on the genus Rosellinia, type specimens worldwide were revised and re-classified using a morphological approach. Among them, some came from Pier Andrea Saccardo’s fungarium stored in the Herbarium of the Padova Botanical Garden. In this work, we taxonomically re-examine via a morphological and molecular approach nine different Roselliniasensu Saccardo types. ITS1 and/or ITS2 sequences were successfully obtained applying Illumina MiSeq technology and phylogenetic analyses were carried out in order to elucidate their current taxonomic position. Only the ITS1 sequence was recovered for Rosellinia areolata, while for R. geophila, only the ITS2 sequence was recovered. We proposed here new combinations for Rosellinia chordicola, R. geophila and R. horridula, while for R. ambigua, R. areolata, R. australis, R. romana and R. somala, we did not suggest taxonomic changes compared to the current ones. The name Rosellinia subsimilis Sacc. is invalid, as it is a later homonym of R. subsimilis P. Karst. & Starbäck. Therefore, we introduced Coniochaeta dakotensis as a nomen novum for R. subsimilis Sacc. This is the first time that these types have been subjected to a molecular study. Our results demonstrate that old types are an important source of DNA sequence data for taxonomic re-examinations.

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Sequence data from isolated lichen-associated melanized fungi enhance delimitation of two new lineages within Chaetothyriomycetidae

Mycological Progress ◽

10.1007/s11557-021-01706-8 ◽

2021 ◽

Vol 20 (7) ◽

pp. 911-927

Author(s):

Lucia Muggia ◽

Yu Quan ◽

Cécile Gueidan ◽

Abdullah M. S. Al-Hatmi ◽

Martin Grube ◽

...

Keyword(s):

Sequence Data ◽

Single Species ◽

Sister Group ◽

Asexual Propagation ◽

Dna Sequence Data ◽

Wide Range ◽

The Family ◽

Rock Inhabiting Fungi ◽

Stable Habitat

AbstractLichen thalli provide a long-lived and stable habitat for colonization by a wide range of microorganisms. Increased interest in these lichen-associated microbial communities has revealed an impressive diversity of fungi, including several novel lineages which still await formal taxonomic recognition. Among these, members of the Eurotiomycetes and Dothideomycetes usually occur asymptomatically in the lichen thalli, even if they share ancestry with fungi that may be parasitic on their host. Mycelia of the isolates are characterized by melanized cell walls and the fungi display exclusively asexual propagation. Their taxonomic placement requires, therefore, the use of DNA sequence data. Here, we consider recently published sequence data from lichen-associated fungi and characterize and formally describe two new, individually monophyletic lineages at family, genus, and species levels. The Pleostigmataceae fam. nov. and Melanina gen. nov. both comprise rock-inhabiting fungi that associate with epilithic, crust-forming lichens in subalpine habitats. The phylogenetic placement and the monophyly of Pleostigmataceae lack statistical support, but the family was resolved as sister to the order Verrucariales. This family comprises the species Pleostigma alpinum sp. nov., P. frigidum sp. nov., P. jungermannicola, and P. lichenophilum sp. nov. The placement of the genus Melanina is supported as a lineage within the Chaetothyriales. To date, this genus comprises the single species M. gunde-cimermaniae sp. nov. and forms a sister group to a large lineage including Herpotrichiellaceae, Chaetothyriaceae, Cyphellophoraceae, and Trichomeriaceae. The new phylogenetic analysis of the subclass Chaetothyiomycetidae provides new insight into genus and family level delimitation and classification of this ecologically diverse group of fungi.

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DNA sonification for public engagement in bioinformatics

BMC Research Notes ◽

10.1186/s13104-021-05685-7 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Heleen Plaisier ◽

Thomas R. Meagher ◽

Daniel Barker

Keyword(s):

Dna Sequence ◽

Public Engagement ◽

Sequence Data ◽

Sensory Perception ◽

Data Representation ◽

Sequence Information ◽

Dna Sequence Data ◽

Public Events ◽

Dna Base ◽

Alternative Means

Abstract Objective Visualisation methods, primarily color-coded representation of sequence data, have been a predominant means of representation of DNA data. Algorithmic conversion of DNA sequence data to sound—sonification—represents an alternative means of representation that uses a different range of human sensory perception. We propose that sonification has value for public engagement with DNA sequence information because it has potential to be entertaining as well as informative. We conduct preliminary work to explore the potential of DNA sequence sonification in public engagement with bioinformatics. We apply a simple sonification technique for DNA, in which each DNA base is represented by a specific note. Additionally, a beat may be added to indicate codon boundaries or for musical effect. We report a brief analysis from public engagement events we conducted that featured this method of sonification. Results We report on use of DNA sequence sonification at two public events. Sonification has potential in public engagement with bioinformatics, both as a means of data representation and as a means to attract audience to a drop-in stand. We also discuss further directions for research on integration of sonification into bioinformatics public engagement and education.

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When DNA sequence data and morphological results fit together: Phylogenetic position of Crenubiotus within Macrobiotoidea (Eutardigrada) with description of Crenubiotus ruhesteini sp. nov

Journal of Zoological Systematics & Evolutionary Research ◽

10.1111/jzs.12449 ◽

2021 ◽

Author(s):

Roberto Guidetti ◽

Ralph O. Schill ◽

Ilaria Giovannini ◽

Edoardo Massa ◽

Sara Elena Goldoni ◽

...

Keyword(s):

Dna Sequence ◽

Sequence Data ◽

Phylogenetic Position ◽

Dna Sequence Data

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A new Liopeltis Fitzinger, 1843 (Squamata: Colubridae) from Pulau Tioman, Peninsular Malaysia

Zootaxa ◽

10.11646/zootaxa.4766.3.6 ◽

2020 ◽

Vol 4766 (3) ◽

pp. 472-484

Author(s):

HANNAH E. SOM ◽

L. LEE GRISMER ◽

PERRY L. JR. WOOD ◽

EVAN S. H. QUAH ◽

RAFE M. BROWN ◽

...

Keyword(s):

Mitochondrial Dna ◽

New Species ◽

Dna Sequence ◽

Rare Species ◽

Sequence Data ◽

Peninsular Malaysia ◽

Tropical Asia ◽

Dna Sequence Data ◽

A New Species ◽

Lines Of Evidence

Liopeltis is a genus of poorly known, infrequently sampled species of colubrid snakes in tropical Asia. We collected a specimen of Liopeltis from Pulau Tioman, Peninsular Malaysia, that superficially resembled L. philippina, a rare species that is endemic to the Palawan Pleistocene Aggregate Island Complex, western Philippines. We analyzed morphological and mitochondrial DNA sequence data from the Pulau Tioman specimen and found distinct differences to L. philippina and all other congeners. On the basis of these corroborated lines of evidence, the Pulau Tioman specimen is described as a new species, L. tiomanica sp. nov. The new species occurs in sympatry with L. tricolor on Pulau Tioman, and our description of L. tiomanica sp. nov. brings the number of endemic amphibians and reptiles on Pulau Tioman to 12.

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