Multilocus DNA Sequence Research Articles

Colletotrichum species causing Glomerella leaf spot and apple bitter rot in the southeastern United States exhibit disparities in relative frequency, morphological phenotype, and QoI sensitivity.

Glomerella leaf spot (GLS), Glomerella fruit rot (GFR) and apple bitter rot (ABR), caused by Colletotrichum spp. are amongst the most devastating apple diseases in the southeastern United States. While several species have been identified as causal pathogens of GLS, GFR, and ABR, their relative frequency and fungicide sensitivity status in the southeastern U.S. is unknown. In total, 381 Colletotrichum isolates were obtained from symptomatic leaves and fruit from 18 conventionally managed apple orchards and two baseline populations in western North Carolina and Georgia in 2016 and 2017. Multilocus DNA sequence analysis revealed that C. chrysophilum was the predominant cause of GLS and GFR, and C. fioriniae was the causal agent of ABR. Baseline and commercial populations of Colletotrichum spp. were evaluated for sensitivity to pyraclostrobin and trifloxystrobin and no statistical differences in sensitivity between the two species were observed for conidial germination. However, EC50 values were significantly lower for C. fioriniae compared to C. chrysophilum for both fungicides regarding mycelial inhibition. Isolates recovered from commercial orchards revealed that 5 populations of C. chrysophilum and 1 population of C. fioriniae had reduced sensitivity to trifloxystrobin, and 1 C. fioriniae population had reduced sensitivity to pyraclostrobin via conidial germination assays. The cytb gene for 27 isolates of C. fioriniae, C. chrysophilum, and C. fructicola with different QoI sensitivities revealed the G143A mutation in a single isolate of C. chrysophilum with insensitivity to both fungicides. Results of these studies suggest that two Colletotrichum spp. predominantly cause GLS and ABR in the southeastern U.S. and that a reduction in sensitivity to some QoI fungicides may be responsible for control failures. This study also provides basis for monitoring shifts in QoI sensitivity in Colletotrichum spp. causing disease on apple in the southeastern U.S.

First report of Morchella galilaea, an autumn species from Pakistan, based on multilocus DNA sequences, light microscopy, and scanning electron microscopy analyses.

Morchella is highly prized for its distinct and delicious taste, making it one of the most sought-after and valuable macrofungi. Despite Pakistan exporting morels to various European countries, Morchella's diversity in this South Asian country has not been cataloged using multilocus DNA sequence data. Realizing the need for their scientific identity, various collections were commissioned, including those from the low and high altitudinal zones of the Charsadda, Swat, and Poonch districts of Pakistan during autumn of 2015 through 2019. Specimens were identified by sequencing the internal transcribed spacer (ITS) region and portions of the RNA polymerase II largest subunit (RPB1), second largest subunit (RPB2), and translation elongation factor 1-α (TEF1) loci. Multigene molecular phylogenetic analysis revealed the autumnal collections were Morchella galilaea Masaphy & Clowez. The species was previously documented in the United States, China, Israel, and Turkey. A detailed taxonomic description, light and scanning electron microscopy, and multigene molecular phylogenetic analyses of the species are reported here for the first time from Pakistan. The study underscores the necessity for further surveys of unexplored areas of Pakistan and systematics of Morchella to augment species diversity and their geographic distribution. RESEARCH HIGHLIGHTS: Specimens of Morchella were collected from low and high altitudinal zones in Pakistan during the autumn. Specimens were assessed using multigene (ITS, RPB1, RPB2, and TEF1) molecular phylogenetic analyses for the first time in Pakistan. The specimens were identified as Morchella galilaea based on multigene molecular phylogenetic analysis. Updated taxonomic descriptions of macro- and microanatomical characters were provided for clarity and precision. Hitherto-unreported shapes of paraphyses and acroparaphyses are observed and thoroughly reported. Scanning electron microscopy (SEM) of an ascospore is provided.

Species diversity in Pseudocercospora.

Species of Pseudocercospora are commonly associated with leaf and fruit spots on diverse plant hosts in sub-tropical and tropical regions. Pseudocercospora spp. have mycosphaerella-like sexual morphs, but represent a distinct genus in Mycosphaerellaceae (Mycosphaerellales, Dothideomycetes). The present study adds a further 29 novel species of Pseudocercospora from 413 host species representing 297 host genera occurring in 60 countries and designates four epitypes and one lectotype for established names. This study recognises 329 species names, with an additional 69 phylogenetic lineages remaining unnamed due to difficulty in being able to unambiguously apply existing names to those lineages. To help elucidate the taxonomy of these species, a phylogenetic tree was generated from multi-locus DNA sequence data of the internal transcribed spacers and intervening 5.8S nuclear nrRNA gene (ITS), partial actin (actA), and partial translation elongation factor 1-alpha (tef1), as well as the partial DNA-directed RNA polymerase II second largest subunit (rpb2) gene sequences. Novel species described in this study include those from various countries as follows: Australia, Ps. acaciicola from leaf spots on Acacia sp., Ps. anopter from leaf spots on Anopterus glandulosus, Ps. asplenii from leaf spots on Asplenium dimorphum, Ps. australiensis from leaf spots on Eucalyptus gunnii, Ps. badjensis from leaf spots on Eucalyptus badjensis, Ps. erythrophloeicola from leaf spots on Erythrophleum chlorostachys, Ps. grevilleae from leaf spots on Grevillea sp., Ps. lophostemonigena from leaf spots on Lophostemon confertus, Ps. lophostemonis from leaf spots on Lophostemon lactifluus, Ps. paramacadamiae from leaf spots on Macadamia integrifolia, Ps. persooniae from leaf spots on Persoonia sp., Ps. pultenaeae from leaf spots on Pultenaea daphnoides, Ps. tristaniopsidis from leaf spots on Tristaniopsis collina, Ps. victoriae from leaf spots on Eucalyptus globoidea. Brazil, Ps. musigena from leaf spots on Musa sp. China, Ps. lonicerae-japonicae from leaf spots on Lonicera japonica, Ps. rubigena leaf spots on Rubus sp. France (Réunion), Ps. wingfieldii from leaf spots on Acacia heterophylla. Malaysia, Ps. musarum from leaf spots on Musa sp. Netherlands, Ps. rhododendri from leaf spots on Rhododendron sp. South Africa, Ps. balanitis from leaf spots on Balanites sp., Ps. dovyalidicola from leaf spots on Dovyalis zeyheri, Ps. encephalarticola from leaf spots on Encephalartos sp. South Korea, Ps. grewiana from leaf spots on Grewia biloba, Ps. parakaki from leaf spots on Diospyros kaki, Ps. pseudocydoniae from leaf spots on Chaenomeles lagenaria, Ps. paracydoniae from leaf spots on Chaenomeles speciosa. Thailand, Ps. acerigena from leaf spots on Acer sp., Ps. tectonigena from leaf spots on Tectona grandis. Epitypes are designated for Cercospora bonjeaneae-rectae, Cercospora halleriae, Ps. eucleae, and an epitype as well as a lectotype for Ps. macadamiae. Results obtained in the present study contribute to a better understanding of the host specificity and distribution in Pseudocercospora spp., many of which represent important pathogens of food or fibre crops, or organisms of quarantine concern. Citation: Groenewald JZ, Chen YY, Zhang Y, Roux J, Shin H-D, Shivas RG, Summerell BA, Braun U, Alfenas AC, Ujat AH, Nakashima C, Crous PW (2024). Species diversity in Pseudocercospora. Fungal Systematics and Evolution 13: 29-89. doi: 10.3114/fuse.2024.13.03.

Taxonomy and phylogeny of the family Suberitidae (Porifera: Demospongiae) in California

This study presents a comprehensive taxonomic revision of the family Suberitidae (Porifera: Demospongiae) for California, USA. We include the three species previously known from the region, document two additional species previously known from other regions, and formally describe four new species as Pseudosuberites latke sp. nov., Suberites californiana sp. nov., Suberites kumeyaay sp. nov., and Suberites agaricus sp. nov. Multi-locus DNA sequence data is presented for seven of the nine species, and was combined with all publicly available data to produce the most comprehensive global phylogeny for the family to date. By integrating morphological and genetic data, we show that morphological characters may be sufficient for regional species identification but are likely inadequate for global classification into genera that reflect the evolutionary history of the family. We therefore propose that DNA sequencing is a critical component to support future taxonomic revisions.

Diversity and biogeography of South American mud turtles elucidated by multilocus DNA sequencing (Testudines: Kinosternidae)

Kinosternon is the most speciose genus of extant turtles, with 22 currently recognized species, distributed across large parts of the Americas. Most species have small distributions, but K. leucostomum and K. scorpioides range from Mexico to South America. Previous studies have found discordance between mitochondrial and nuclear phylogenies in some kinosternid groups, with the current taxonomy following the nuclear-based results. Herein, based on extended molecular, geographic, and taxonomic sampling, we explore the phylogeographic structure and taxonomic limits for K. leucostomum and the K. scorpioides group and present a fossil-calibrated nuclear time tree for Kinosternon. Our results reveal contrasting differentiation patterns for the K. scorpioides group and K. leucostomum, despite overlapping distributions. Kinosternon leucostomum shows only shallow geographic divergence, whereas the K. scorpioides group is polyphyletic with up to 10 distinct taxa, some of them undescribed. We support the elevation of K. s. albogulare and K. s. cruentatum to species level. Given the deep divergence within the genus Kinosternon, we propose the recognition of three subgenera, Kinosternon, Cryptochelys and Thyrosternum, and the abandonment of the group-based classification, at least for the K. leucostomum and K. scorpioides groups. Our results show an initial split in Kinosternon that gave rise to two main radiations, one Nearctic and one mainly Neotropical. Most speciation events in Kinosternon occurred during the Quaternary and we hypothesize that they were mediated by both climatic and geological events. Additionally, our data imply that at least three South American colonizations occurred, two in the K. leucostomum group, and one in the K. scorpioides group. Additionally, we hypothesize that discordance between mitochondrial and nuclear phylogenetic signal is due to mitochondrial capture from an extinct kinosternine lineage.

Molecular delineation and genetic diversity of Fusarium species complex causing tea dieback in India and their sensitivity to fungicides

Fusarium dieback is a prevalent disease of tea (Camellia sinensis (L.) Kuntze) in India and China. The pathogen affects plucking shoots and causes complete crop loss under favourable conditions. Although, other fungal diseases that infect tea were widely explored for pathogen identification and characterization, little is known about Fusarium dieback in major tea growing regions of India. Therefore, in this study 24 isolates of Fusarium species causing dieback on tea in 24 tea gardens of Assam and North Bengal were isolated and characterized through micro-morphological and molecular analysis using multi-locus DNA sequences to determine whether multiple species of Fusarium are responsible for dieback disease. Molecular analysis revealed the association of four species of Fusarium, namely F. concentricum, F. solani, F. fujikuroi, and F. oxysporum. The most dominant species was F. concentricum (62.5%), whereas the occurrence frequencies of F. solani, F. fujikuroi, and F. oxysporum were 20.8%, 12.5%, and 0.04%, respectively. All Fusarium isolates were pathogenic to tea leaves when individually and co-inoculated, with F. concentricum HPE0F10 and NHT0F17 exhibiting 19.3 mm lesion length being the most virulent isolates. The growth rate of the pathogen was positively correlated with lesion lengths (P < 0.001). Co-infection of two or multiple Fusarium species enhanced the disease severity and quicker disease development compared to single inoculation. All the isolates showed diverse genetic backgrounds based on Inter Simple Sequence Repeat (ISSR) primers and principal coordinate analysis. In fungicide screening test, all isolates except HPE0F10, NDS0F18, and SNY0F22 were insensitive to M1 fungicide (copper oxychloride). Isolates GNP0F8 and LKW0F16 were insensitive to MBC + M3 (Carbendazim + Mancozeb), whereas HPE0F10, NLG0F11, IND0F13, and NLW0F19 were insensitive to DMI (respective each two to Hexaconazole and Valextra) fungicides. Notably, all the isolates were susceptible to propiconazole. Further, ISSR segregated isolates insensitive to MBC + M3 and M1 fungicides into two separate clusters, representing their distinctiveness. The fungicide screening results indicate that fungicide resistance can be managed by rotating different modes of action of fungicides against multiple Fusarium species causing tea dieback.

Syncephalastrum massiliense sp. nov. and Syncephalastrum timoneanum sp. nov. Isolated from Clinical Samples.

Mucormycosis is known to be a rare opportunistic infection caused by fungal organisms belonging to the Mucorales order, which includes the Syncephalastrum species. These moulds are rarely involved in clinical diseases and are generally seen as contaminants in clinical laboratories. However, in recent years, case reports of human infections due to Syncephalastrum have increased, especially in immunocompromised hosts. In this study, we described two new Syncephalastrum species, which were isolated from human nails and sputum samples from two different patients. We used several methods for genomic and phenotypic characterisation. The phenotypic analysis relied on the morphological features, analysed both by optical and scanning electron microscopy. We used matrix-assisted laser desorption-ionization time-of-flight mass spectrometry, energy-dispersive X-ray spectroscopy, and BiologTM technology to characterise the proteomic, chemical mapping, and carbon source assimilation profiles, respectively. The genomic analysis relied on a multilocus DNA sequence analysis of the rRNA internal transcribed spacers and D1/D2 large subunit domains, fragments of the translation elongation factor-1 alpha, and the β-tubulin genes. The two novel species in the genus Syncephalastrum, namely S. massiliense PMMF0073 and S. timoneanum PMMF0107, presented a similar morphology: irregular branched and aseptate hyphae with ribbon-like aspects and terminal vesicles at the apices all surrounded by cylindrical merosporangia. However, each species displayed distinct phenotypic and genotypic features. For example, S. timoneanum PMMF0107 was able to assimilate more carbon sources than S. massiliense PMMF0073, such as adonitol, α-methyl-D-glucoside, trehalose, turanose, succinic acid mono-methyl ester, and alaninamide. The polyphasic approach, combining the results of complementary phenotypic and genomic assays, was instrumental for describing and characterising these two new Syncephalastrum species.

Revision of Seriphium plumosum (Gnaphalieae: Asteraceae) in southern Africa with description of new species in Seriphium

Seriphium plumosum L. from southern Africa has been shown to comprise at least seven distinct species based on analysis of morphological, environmental, and multilocus DNA sequence data. On that evidence, Stoebe burchellii Levyns, Stoebe virgata Thunb., and Stoebe vulgaris Levyns are reinstated in Seriphium, and four new species are described, viz., Seriphium alto-argillaceum Z.Shaik, Se. burrowsii Z.Shaik, Se. crypticum Z.Shaik, and Se. dunensis Z.Shaik. Four of these species are endemic to the Cape Floristic Region of South Africa, and one is so far known from a single high-elevation locality. We present a key to species in the Seriphium plumosum complex, and for each species provide a formal description with accompanying images, typification and synonymy, with distribution maps based on verified field-collected and herbarium specimens.

Ganoderma from Cuba: an approach to some species based on morphology and phylogenetic analyses

Abstract Ganoderma is a genus of wood-decaying polypores fungi with several species, in which morphological delimitation has been challenging due to its large plasticity. Knowledge of the taxonomic diversity of Ganoderma in Cuba remains incomplete. Here, we identified some species, mainly laccate, of Ganoderma present in Cuba based on morphological and phylogenetic data and investigated their relationships with other species. Type specimens, recently collected materials, herbarium specimens and in vitro cultures were studied to delimit morphological species. The phylogenetic affinities of ten species were inferred based on multilocus (ITS rDNA, rpb2, tef1-α) DNA sequences to delimit phylogenetic species. In this work, 14 species of Ganoderma were recognized in Cuba, of which G. amazonense, G. curtisii, G. dussii and G. multiplicatum are reported for the first time. Ganoderma rodriguezii sp. nov. is described as a novel species. We confirmed G. amazonense is a non-laccate species although it is phylogenetically affine to laccate species. An identification key for studied species, nomenclatural information, updated descriptions and geographical distributions are presented. The lectotypification in second step of G. perzonatum, G. pulverulentum and G. zonatum was made here. To correctly interpret G. perzonatum, recent collections, including live strains from the type locality, are described. We confirm G. lucidum is not present in Cuba, despite previous records from the country.

Multigene Phylogeny and Pathogenicity Trials Revealed Alternaria alternata as the Causal Agent of Black Spot Disease and Seedling Wilt of Pecan (Carya illinoinensis) in South Africa.

The pecan (Carya illinoinensis) industry in South Africa is growing rapidly, and it is becoming increasingly crucial to understand the risks posed to pecans by fungal pathogens. Black spots on leaves, shoots, and nuts in shucks caused by Alternaria species have been observed since 2014 in the Hartswater region of the Northern Cape Province of South Africa. Species of Alternaria include some of the most ubiquitous plant pathogens on earth. The aim of this study was to use molecular techniques to identify the causative agents of Alternaria black spot and seedling wilt isolated from major South African pecan-production areas. Symptomatic and non-symptomatic pecan plant organs (leaves, shoots, and nuts-in-shucks) were collected from pecan orchards, representing the six major production regions in South Africa. Thirty Alternaria isolates were retrieved from the sampled tissues using Potato Dextrose Agar (PDA) culture media and molecular identification was conducted. The phylogeny of multi-locus DNA sequences of Gapdh, Rpb2, Tef1, and Alt a 1 genes revealed that the isolates were all members of Alternaria alternata sensu stricto, forming part of the Alternaria alternata species complex. The virulence of six A. alternata isolates were tested on detached nuts of Wichita and Ukulinga cultivars, respectively, as well as detached leaves of Wichita. The A. alternata isolates were also evaluated for their ability to cause seedling wilt in Wichita. The results differed significantly between wounded and unwounded nuts of both cultivars, but not between the cultivars. Similarly, the disease lesions on the wounded detached leaves were significantly different in size from the unwounded leaves. The seedling tests confirmed that A. alternata is pathogenic and that A. alternata causes black spot disease and seedling wilt of pecans. This study is one of the first documentations of Alternaria black spot disease of pecan trees and its widespread occurrence in South Africa.

Taxonomy and Phylogeny of Cystolepiota (Agaricaceae, Agaricales): New Species, New Combinations and Notes on the C. seminuda Complex

Species of Cystolepiota are known as diminutive lepiotaceous fungi with a worldwide distribution. Previous studies revealed that Cystolepiota is not monophyletic and preliminary DNA sequence data from recent collections suggested that several new species exist. Based on multi-locus DNA sequence data (the nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2, ITS; the D1-D2 domains of nuc 28S rDNA, LSU; the most variable region of the second-largest subunit of RNA polymerase II, rpb2 and a portion of the translation-elongation factor 1-α. tef1), C. sect. Pulverolepiota forms a distinct clade separating from Cystolepiota. Therefore, the genus Pulverolepiota was resurrected and two combinations, P. oliveirae and P. petasiformis were proposed. With the integration of morphological characteristics, multi-locus phylogeny, and information on geography and habitat, two new species, viz. C. pseudoseminuda and C. pyramidosquamulosa, are described and C. seminuda was revealed to be a species complex containing at least three species, viz. C. seminuda, C. pseudoseminuda, and Melanophyllum eryei. In addition, C. seminuda was re-circumscribed and neo-typified based on recent collections.

Late Cenozoic history and the role of Beringia in assembling a Holarctic cestode species complex

The dynamic climate history that drove sea level fluctuation during past glacial periods mediated the movement of organisms between Asia and North America via the Bering Land Bridge. Investigations of the biogeographic histories of small mammals and their parasites demonstrate facets of a complex history of episodic geographic colonization and refugial isolation that structured diversity across the Holarctic. We use a large multi-locus nuclear DNA sequence dataset to robustly resolve relationships within the cestode genus Arostrilepis (Cyclophyllidea: Hymenolepididae), a widespread parasite of predominantly arvicoline rodents (voles, lemmings). Using this phylogeny, we confirm that several Asian Arostrilepis lineages colonized North America during up to four distinct glacial periods in association with different rodent hosts, consistent with taxon-pulse dynamics. A previously inferred westward dispersal across the land bridge is rejected. We also refine interpretations of past host colonization, providing evidence for several distinct episodes of expanding host range, which probably contributed to diversification by Arostrilepis. Finally, Arostrilepis is shown to be paraphyletic with respect to Hymenandrya thomomyis, a parasite of pocket gophers, confirming that ancient Arostrilepis species colonized new host lineages upon arriving in North America.

Four new species and three taxonomic adjustments in Lachenalia (Asparagaceae: Scilloideae) from southern and western South Africa

A novel phylogenetic hypothesis for Lachenalia (Asparagaceae; Scilloideae; Hyacintheae) based on multilocus DNA sequence data has revealed the existence of four morphologically, ecologically and/or geographically distinct species, and supports the elevation of three existing subspecies to the species level. The new species and combinations are presented here. The new species are Lachenalia komsbergensis from the Komsberg in the southern Great Karoo (Northern Cape), Lachenalia inflata from the Hantam-Roggeveld escarpment in the western Great Karoo (Northern Cape), Lachenalia granitica from the Cape West Coast (Western Cape) and Lachenalia filamentosa from the Cape West Coast, Breede River Valley and Overberg (Western Cape). The taxa elevated from subspecies to species level are Lachenalia rogersii (previously L. mediana subsp. rogersii) from the Breede River Valley (Western Cape), Lachenalia glaucina (previously L. orchioides subsp. glaucina) from the southern Cape Peninsula (Western Cape) and Lachenalia parviflora (previously L. orchioides subsp. parviflora) from the northeastern Cape Peninsula (Western Cape).

Diversity of fungi associated with Monochamusalternatus larval habitats in Bursaphelenchusxylophilus-infected Pinusmassoniana and identification of two new ophiostomatalean species (Ascomycota, Ophiostomatales).

Bursaphelenchusxylophilus, a pathogenic pine wood nematode (PWN), is responsible for pine wilt disease (PWD), which has caused significant economic and ecological damage worldwide, particularly in East Asia. Multiple biological factors, such as the beetle vector Monochamus, symbiotic bacteria and associated fungi, are involved in the disease infection cycle. This study isolated and identified the fungal communities of Monochamusalternatus larval galleries and pupal chambers from different instars through field investigation, morphological observation and multi-locus DNA sequence analyses in Zhejiang Province, China. A total of 255 and 454 fungal strains were isolated from M.alternatus galleries and pupal chambers infected with PWN, from the 2nd-3rd and 4th-5th instar larvae, respectively. A total of 18 species of fungi were identified, 14 species were isolated from the 2nd-3rd instar larval galleries and six species from the galleries and pupal chambers of the 4th-5th instar larvae. Amongst them were six species belonging to four genera of ophiostomatalean fungi, including two novel species, Graphilbumxianjuensis sp. nov. and Ophiostomataizhouense sp. nov. and four known species, Ceratocystiopsisweihaiensis, Ophiostomaips, Sporothrixzhejiangensis and S.macroconidia. The findings revealed that the fungal diversity and abundance of the 2nd-3rd instar larvae differed markedly from those of the 4th-5th instar larvae. This difference could be the result of fungal succession. This study provides a thorough understanding of the fungi associated with PWD and lays the groundwork for future research.

Diversity and Distribution of Calonectria Species from Plantation and Forest Soils in Fujian Province, China.

To meet the growing demand for wood and pulp products, Eucalyptus plantations have expanded rapidly during the past two decades, becoming an integral part of the southern China landscape. Leaf blight caused by various Calonectria spp., is a serious threat to these plantations. In order to explore the diversity and distribution of Calonectria spp. in Fujian Province soils, samples were collected in Eucalyptus plantations and adjacent plantings of Cunninghamia lanceolata, Phyllostachys heterocycle and Pinus massoniana as well as in natural forests. Three hundred and fifty-three Calonectria isolates were recovered from soil samples and they were identified based on a comparison of multilocus DNA sequence data for the act (actin), cmdA (calmodulin), his3 (histone H3), rpb2 (the second largest subunit of RNA polymerase), tef1 (translation elongation factor 1-alpha) and tub2 (β-tubulin) gene regions, as well as morphological characteristics. Six known taxa including Calonectria aconidialis, Ca. hongkongensis, Ca. ilicicola, Ca. kyotensis, Ca. pacifica, Ca. pseudoreteaudii and one novel species described here as Ca. minensis sp. nov. were identified. Of these, Ca. aconidialis and Ca. kyotensis were the most prevalent species, and found in eight and seven sites, and four and five forest types, respectively. Calonectria spp. were most abundant in soils from Eucalyptus stands, followed by P. heterocycle and natural forests. Relatively few species were found in the soils associated with Cunninghamia lanceolata and Pinus massoniana. The abundance of known Calonectria spp. suggests that these fungi have been relatively well sampled in Fujian. The results are also consistent with the fact that most Calonectria diseases are found on Angiosperm as opposed to Gymnosperm plants.

Morphological and Molecular Characterization of Pseudocercospora chionanthi-retusi Causing Leaf Spot on Chionanthus retusus in Korea

Leaves of Chionanthus retusus were found to be damaged by leaf spot disease associated with a fungus in Iksan, Korea. Leaf spots were angular to irregular, vein-limited, scattered, 1–8 mm diameter, brownish-gray to dark brown when dry, with heavy fructification. The pathogen causes premature defoliation of C. retusus plant and was identified as Pseudocercospora chionanthi-retusi based on morphological and molecular-phylogenetic analyses. The phylogenetic tree was constructed using multi-locus DNA sequence data of partial actin (actA), partial translation elongation factor 1-alfa (ef1A), partial DNA-directed RNA polymerase II second largest subunit (rpb2) genes, and internal transcribed spacer regions. Current study provides detail morphological description of P. chionanthi-retusi on C. retusus in Korea, with supports of phylogenetic analysis and pathogenicity test.

A phylogenetic survey of the ascomycete genus Arthrorhaphis (Arthrorhaphidaceae, Lecanoromycetes) including new species in Arthrorhaphis citrinella sensu lato

AbstractThe genus Arthrorhaphis is a group of ascomycetes comprising lichenised and non‐lichenised taxa from temperate to arctic‐alpine regions in both hemispheres. Nine species and two infraspecific taxa are currently recognised. Their delimitation, inter‐relationships, and phylogenetic placement remain poorly understood. We have used an integrative taxonomic approach to assess taxon limits, phylogenetic placement of the family, and to test the hypothesis that transition to lichenisation has happened only once. We present a first molecular phylogenetic hypothesis of all but one known Arthrorhaphis species based on Bayesian inference and maximum likelihood analyses of multilocus DNA sequence data. Our results support monophyly of Arthrorhaphis, phylogenetic placement in the Ostropomycetidae, and lichenisation having evolved from lichenicolous ancestors only once. The lichenicolous Arthrorhaphis species are well‐defined both morphologically and genetically. The lichenised A. alpina s.l. and A. citrinella s.l., however, include multiple genetic clades that are partly supported by phenotypic data. We split A. citrinella s.l. into the following five species: (1) A. bullata sp. nov., (2) A. catolechioides comb. &amp; stat. nov., (3) A. citrinella, (4) A. farinosa sp. nov., and (5) A. vulgaris comb. &amp; stat. nov. A sixth phylogenetic clade from the Neotropics remains undescribed herein due to insufficient data. Five circumarctic accessions of A. alpina s.l. form a genetically distinct but morphologically poorly understood clade sister to the alpina‐vacillans clade, which we preliminarily name “A. septentrionalis”. Jointly, our multispecies coalescence analyses, of both single‐locus (bGMYC) and multilocus (bPtP, bP&amp;P) datasets, largely support our proposed species hypotheses in Arthrorhaphis.

Multilocus phylogeny, natural history traits and classification of natricine snakes (Serpentes: Natricinae)

Abstract Natricine snakes are geographically widespread, species rich (with ~250 extant species) and both morphologically and ecologically diverse. We present a multilocus DNA sequence phylogeny for 249 natricine specimens representing 189 named species, including 69 specimens and 21 species not previously sampled. Our inferred Bayesian and maximum likelihood trees form the basis for evaluations of genus-level classification, historical biogeography, lineage diversification, and dietary, habit and reproductive-mode diversity and evolution, although several, mostly deeper, relationships remain poorly resolved. The optimal trees support natricine origins in Asia, with dispersals to Australo-Melanesia, sub-Saharan Africa (including Seychelles Archipelago, excluding Aldabra), Europe and North Africa and into North and Central America. Viviparity appears to have evolved independently three times in Natricinae but was not significantly associated with an aquatic habit. We found limited associations between habit and diet categories. We propose generic reallocations for four natricine species and highlight other points of uncertainty in natricine classification.

Colletotrichum fioriniae and Colletotrichum godetiae Causing Postharvest Bitter Rot of Apple in South Tyrol (Northern Italy).

South Tyrol (northern Italy) harbors one of the largest interconnected apple farming areas in Europe, contributing approximately 10% to the apple production of the European Union. Despite the availability of sophisticated storage facilities, postharvest diseases occur, one of which is bitter rot of apple. In Europe, this postharvest disease is mainly caused by the Colletotrichum acutatum species complex. This study aimed to characterize the Colletotrichum spp. isolated from decayed apple fruit collected in 2018 and 2019 in South Tyrol. The characterization of Colletotrichum spp. was accomplished based on multilocus DNA sequences of four different genomic regions-actin (ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone H3 (HIS3), and the internal transcribed spacer (ITS) region-as well as morphological and pathogenicity assessment. A phylogenetic analysis based on multilocus DNA sequences showed that the isolates obtained from apples with symptoms of bitter rot belonged to the species Colletotrichum godetiae and Colletotrichum fioriniae, which are part of the Colletotrichum acutatum species complex. A third species isolated from apples belonging to the same species complex, Colletotrichum salicis, was described in this area. Moreover, the Colletotrichum isolates found in this study proved to be virulent on Cripps Pink, Golden Delicious, and Roho 3615/Evelina. To the best of our knowledge, C. godetiae and C. fioriniae have so far never been mentioned as postharvest pathogens of apple in Italy, although the reanalysis of samples collected in the past indicates that these pathogens have been occurring in Italy for at least a decade. So far, bitter rot seems to play a minor role as a postharvest disease in South Tyrol, but it was disproportionately represented on a few scab-resistant apple cultivars, which are increasingly planted in organically managed orchards. Considering that the expansion of organic apple production and the conversion to new potentially Colletotrichum-susceptible cultivars will continue, the present study represents an important contribution toward a better understanding of bitter rot in this geographic area.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Phylogeny and biogeography of the pantropical whip spider family Charinidae (Arachnida: Amblypygi)

AbstractThe present contribution addresses the phylogeny and biogeography of the pantropical whip spider family Charinidae Quintero, 1986, the most species-rich in the arachnid order Amblypygi Thorell, 1883, based on morphology and multilocus DNA sequences, analysed simultaneously using parsimony, maximum likelihood and Bayesian inference. The morphological matrix comprises 138 characters, scored for four outgroup taxa and 103 ingroup terminals representing all genera and 64% of the species of Charinidae. The multilocus dataset comprises sequences from two nuclear and three mitochondrial gene loci for four outgroup taxa and 48 ingroup representing 30 (23%) taxa of Charinidae. Charinidae are monophyletic, with Weygoldtia Miranda et al., 2018 sister to a monophyletic group comprising Charinus Simon, 1892 and Sarax Simon, 1892, neither of which are reciprocally monophyletic. Charinidae diverged from other amblypygid families in the Late Carboniferous, c. 318 Mya, on the supercontinent Pangaea. Weygoldtia diverged from the common ancestor of Charinus and Sarax during the Late Permian, c. 257 Mya, when changes in climate reduced tropical forests. The divergence of Charinus and Sarax coincides with the fragmentation of Pangaea, c. 216 Mya. Sarax colonized South-East Asia via Australia. The charinid fauna of New Caledonia originated before the Oligocene, when the island separated from Australia, c. 80 Mya.