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101. The diversity of Banana streak virus isolates in Uganda

Author

Harper, G., Hart, D., Moult, S., Hull, R., Geering, Andrew D. W., Thomas, John E., Harper, G., Hart, D., Moult, S., Hull, R., Geering, Andrew D. W., and Thomas, John E.

Abstract

In a study of the variation among isolates of Banana streak virus (BSV) in Uganda, 140 sequences were obtained from 49 samples by PCR across the conserved reverse transcriptase/RNaseH region of the genome. Pairwise comparison of these sequences suggested that they represented 15 different species and phylogenetic analyses showed that all species fell into three major clades based on 28% sequence difference. In addition to the Ugandan sequences, clade I also contained BSV species that are known as both integrated sequences and episomal viruses; clade II also contained integrated BSV sequences but which have not previously been identified as episomal viruses. Clade III comprised of Sugarcane bacilliform virus isolates and Ugandan BSV sequences and for which there is no evidence of integration. The possible reasons for the extraordinary levels of virus sequence variation and the potential origins and epidemiology of these viruses causing banana streak disease are discussed.

Published
2005

105. Banana and plantain

Author

Loebenstein, Gad, Thottappilly, George, Thomas, John E., Geering, Andrew D. W., Dahal, G., Lockhart, B.E.L., Loebenstein, Gad, Thottappilly, George, Thomas, John E., Geering, Andrew D. W., Dahal, G., and Lockhart, B.E.L.

Abstract

Banana and plantain (Musa spp.) are grown in more than 125 countries (Anon., 2001) and are a major source of carbohydrate for more than 400 million people (Swennen et al, 1995). The progenitors of almost all domesticated Musa are two wild species, Musa acuminata and M. balbisiana, whose genomes are represented using the letter codes A and B, respectively. The most commonly cultivated cultivars have the triploid genotypes AAA, AAB or ABB.

Published
2003

107. Identification of Rubus yellow net virus as a distinct badnavirus and its detection by PCR in Rubus species and in aphids

Author

Jones, A.Teifion, McGavin, Wendy J., Geering, Andrew D. W., Lockhart, B.E.L., Jones, A.Teifion, McGavin, Wendy J., Geering, Andrew D. W., and Lockhart, B.E.L.

Abstract

Rubus yellow net virus (RYNV) infects Rubus species and cultivars worldwide and is an essential component of raspberry veinbanding mosaic (RVBMD), a virus disease complex that causes serious decline in plant vigour and productivity. The virus is transmitted, probably in a semi-persistent manner, by the large raspberry aphid, Amphorophora idaei in Europe, and A. agathonica in North America. The particles of RYNV are bacilliform in shape and measure 80–150 × 25–30 nm, similar to those of badnaviruses. A1.7 kb fragment of the viral DNA was amplified by PCR and then directly sequenced. Analysis of this sequence suggests that RYNV is possibly a distinct species in the genus Badnavirus and is most closely related to Gooseberry vein banding associated virus (GVBAV) and Spiraea yellow leaf spot virus, two other badnaviruses described recently. Using the sequence derived from the PCR-amplified viral DNA fragment, RYNV-specific primers were designed and used in PCR to assay for RYNV in a range of Rubus germplasm infected with RYNV, with other unrelated viruses and virus-like diseases found in Rubus, and in healthy plants. RYNV was detected in all glasshouse cultures of RYNV-infected plants, whether alone or in complex infections with other viruses, but not from healthy Rubus plants, nor from plants infected with other viruses. It was also detected in field-grown raspberry plants with and without symptoms of RVBMD and in raspberry plants infected with RYNV by viruliferous A. idaei. RYNV was also detected by PCR in A. idaei following access feeds on RYNV-infected plants of 1 h or more. PCR failed to amplify DNA from gooseberry infected with GVBAV confirming the specificity of the RYNV analysis. PCR detection of RYNV in dormant raspberry buds allows assays to be made outside the natural growing season, providing a useful application for plant introduction and quarantine programmes.

Published
2002

108. Partial characterization of two aphid-transmitted viruses associated with yellow leafspot of Spiraea

Author

Lockhart, B.E.L., Geering, Andrew D. W., Lockhart, B.E.L., and Geering, Andrew D. W.

Abstract

Two previously undescribed viruses were associated with a yellow leafspot disease of spiraea (Spiraea spp.) in the midwestern USA. The first virus, named spiraea leafspot virus (SLSV), is a badnavirus which has a 7.4 kb dsDNA genome and resembles other badnaviruses in particle and genome properties, but is unusual in being transmitted by an aphid (Aphis spiraecola) rather than by mealybugs. The second virus, which is also transmitted by A. spiraecola, has spherical 30-35 nm particles containing a 7.2 kb ds RNA genome. This virus was named spiraea leafspot spherical virus (SLSSV). In particle morphology and genome type SLSSV resembles some members of the family Totiviridae, none of which have been reported to infect plants or higher organisms. In the majority of cases SLSV and SLSSV occurred in mixed infections. Early-season symptoms were associated with the presence of SLSSV and absence of SLSV, whereas late-season symptoms were associated with the presence of SLSV and absence or greatly reduced levels of SLSSV.

Published
2002

110. The effect of Banana streak virus on the growth and yield of dessert bananas in tropical Australia

Author

Daniells, J. W., Geering, Andrew D. W., Bryde, N. J., Thomas, J. E., Daniells, J. W., Geering, Andrew D. W., Bryde, N. J., and Thomas, J. E.

Abstract

We have examined the effect of a strain of Banana streak virus (BSV-Cav) on the growth and yield of dessert bananas (Musa AAA group, Cavendish subgroup cv. Williams) in north Queensland, Australia. Healthy and infected plants were compared in a replicated field experiment over plant and first ratoon crops. In both crops, symptom expression followed a similar pattern, increasing to a maximum near the estimated time of bunch initiation, then decreasing in the period prior to bunch emergence. There was no evidence of plant-to-plant spread of virus, but the rate of transmission through suckers was 100%. In the plant crop, the mean bunch weights of healthy and infected plants were not significantly different. However, BSV-Cav infection resulted in an 18 day delay in harvest, causing a 6% reduction in yield per annum. In the ratoon crop, the mean bunch weight of infected plants was 7% less than that of healthy plants, and the interval between the harvest of plant and ratoon crops was delayed by 9 days, resulting in a 11% reduction in yield per annum. Also, the mean length of fruit from infected plants was 5% less than that of healthy plants, resulting in a smaller percentage of fruit in the extra large size category. We conclude that in horticulturally favourable conditions typical of the tropical Australian banana industry, the effects of BSV-Cav infection on the growth and yield of Cavendish bananas are small. [References: 21]

Published
2001

111. A new badnavirus in Ribes species, its detection by PCR, and its close association with gooseberry vein banding disease

Author

Teifion Jones, A., McGavin, W.J., Geering, Andrew D. W., Lockhart, B.E.L., Teifion Jones, A., McGavin, W.J., Geering, Andrew D. W., and Lockhart, B.E.L.

Abstract

Gooseberry vein banding disease (GVBD) affects Ribes species and cultivars worldwide. It is the second most important virus-like disease in these crops after black currant reversion disease. In this paper, we describe a bacilliform virus, Gooseberry vein banding associated virus (GVBAV), which is associated closely with GVBD, and provide evidence that GVBAV is a distinct species within the genus Badnavirus. Purified GVBAV particles were ca. 120 × 30 nm in size and contained dsDNA. The sequence of a 1.5-kb DNA fragment amplified from viral genomic DNA was similar to those of a wide range of badnaviruses and contained motifs characteristic of the RNase H domain of the badnavirus open reading frame (ORF) III polyprotein. Phylogenetic analyses suggest that GVBAV is most closely related to Spiraea yellow leaf spot virus. Using sequence derived from the polymerase chain reaction (PCR)-amplified DNA fragment, virus-specific primers were designed. These primers were used in PCR to assay for GVBAV in a range of Ribes germplasm affected with GVBD, with other unrelated virus-like diseases and viruses found in Ribes, and in healthy plants. GVBAV was detected in all of 58 GVBD-affected plants from diverse sources, but not from healthy Ribes plants nor from plants infected with other viruses.

Published
2001

112. Genetic Diversity Among Banana streak virus Isolates from Australia

Author

Geering, A. D. W., McMichael, L. A., Dietzgen, R. G., Thomas, J. E., Geering, A. D. W., McMichael, L. A., Dietzgen, R. G., and Thomas, J. E.

Abstract

Banana streak virus (BSV) is an important pathogen of bananas and plantains (Musa spp.) throughout the world. We have cloned and sequenced part of the genomes of four isolates of BSV from Australia, designated BSV-RD, BSV-Cav, BSV-Mys, and BSV-GF. These isolates originated from banana cvs. Red Dacca, Williams, Mysore, and Goldfinger, respectively. All clones contained a sequence covering part of open reading frame III and the intergenic region of the badnavirus genome. The sequences were compared with those of other badnaviruses, including BSV-Onne, a previously characterized isolate from Nigeria. The BSV-RD sequence was virtually identical to that of BSV-Onne, differing by only two nucleotides over 1,292 bp. However, BSV-Cav, -Mys, and -GF were divergent in nucleotide sequence. Phylogenetic analyses using conserved sequences in the ribonuclease H domain revealed that all BSV isolates were more closely related to each other than to any other badnavirus. BSV-Cav was most closely related to BSV-Onne, and there was 95.1% identity between the two amino acid sequences. Other relationships between the BSV isolates were less similar, with sequence identities ranging from 66.4 to 78.2%, which is a magnitude comparable to the distance between some of the recognized badnavirus species. Immunocapture-polymerase chain reaction assays have been developed, allowing specific detection and differentiation of the four isolates of BSV.

Published
2000

114. First records of Banana streak virus on the island of New Guinea

Author

Davis, R.I., Geering, Andrew D. W., Thomas, J. E., Gunua, T.G., Rahamma, S., Davis, R.I., Geering, Andrew D. W., Thomas, J. E., Gunua, T.G., and Rahamma, S.

Abstract

Banana streak virus is identified for the first time in Papua New Guinea and Irian Jaya, Indonesia.

Published
2000

116. Banana streak virus: a unique virus-Musa interaction?

Author

Frison, E.A., Sharrock, S.L., Thomas, J. E., Geering, Andrew D. W., Daniells, J. W., McMichael, L. A., Frison, E.A., Sharrock, S.L., Thomas, J. E., Geering, Andrew D. W., Daniells, J. W., and McMichael, L. A.

Published
1998

118. Search for alternative hosts of banana bunchy top virus in Australia

Author

Geering, Andrew D. W., Thomas, John E., Geering, Andrew D. W., and Thomas, John E.

Abstract

A range of plant species that are either cultivated, naturalised or indigenous to sub-tropical eastern Australia and are also able to sustain feeding by Pentalonia nigronervosa, the vector of banana bunchy top virus (BBTV), were investigated as possible hosts of the virus. Alocasia brisbanensis, Alpinia arundelliana. Alpinia caerulea, Alpinia zerumbet, Canna indica, Colocasia esculenta, Hedychiumcoronarium and Heliconia psittacorum cv. Red Parakeet were aphidinoculated with BBTV and none became systemically infected. Furthermore, no BBTV was detected in surveys of field plants of Alocasia brisbanensis, Alpinia caerulea, Cannaindica, Canna × generalis, Canna × orchiodes,Colocasia esculenta and Strelitzia reginae found growing in or near banana plantations affected by BBTV. It is therefore concluded that hosts other than Musa spp. probably do not play a role as reservoirs of BBTV in Australia.

Published
1997

119. Purification, properties, and diagnosis of banana bract mosaic potyvirus and its distinction from abaca mosaic potyvirus

Author

Thomas, John E., Geering, Andrew D. W., Gambley, C>F., Kessling, A.F., White, M., Thomas, John E., Geering, Andrew D. W., Gambley, C>F., Kessling, A.F., and White, M.

Abstract

Using biochemical, serological, and cytopathological evidence, we have confirmed that banana bract mosaic virus (BBrMV) is a distinct member of the family Potyviridae. Virions of a Philippine isolate of BBrMV were purified from field-infected banana cv. Cardaba. Particles were approximately 725-nm long, banded at a density equivalent to 1.29 to 1.31 g/ml in cesium chloride equilibrium gradients, and had an A260/280 of 1.17. Yields of about 4 mg/kg were obtained from fresh or frozen leaf midrib or lamina tissue. Three major protein species with sizes of 31, 37, and 39 kDa were resolved from dissociated virions, and all reacted specifically with polyclonal antibodies to BBrMV. Infected leaf cells contained typical pinwheel inclusions. Virus-specific cDNA was amplified from field samples by reverse transcription-polymerase chain reaction (RT-PCR) assay using potyvirus degenerate primers. In plate-trapped antigen-enzyme-linked immunosorbent assay (ELISA), weak serological relationships were demonstrated between BBrMV and other members of the family Potyviridae, including abaca mosaic (AbaMV), dasheen mosaic, maize dwarf mosaic, sorghum mosaic, sugarcane mosaic, and wheat streak mosaic viruses. Despite similarities in the symptoms caused by the two viruses, AbaMV was serologically distinct from BBrMV and reacted only weakly, or not at all, with BBrMV antibodies in double-antibody sandwich (DAS)-ELISA. No cross reactions were observed when RT-PCR products from the two viruses were examined by Southern blot hybridization using BBrMV- and AbaMV-specific digoxigenin-labeled DNA probes. BBrMV was consistently associated with banana bract mosaic disease, as assessed by DAS-ELISA and Southern blot hybridization using DNA probes. The known geographical distribution of BBrMV was extended to include India (Kokkan disease) and Sri Lanka.

Published
1997

125. Development of a Multiplexed Bead-Based Suspension Array for the Detection and Discrimination of Pospiviroid Plant Pathogens.

Author

van Brunschot, Sharon L., Bergervoet, Jan H. W., Pagendam, Daniel E., de Weerdt, Marjanne, Geering, Andrew D. W., Drenth, André, and van der Vlugt, René A. A.

Subjects
POSPIVIROIDAE, PHYTOPATHOGENIC microorganisms, PLANT diseases, PLANT biotechnology, GENOMICS, BOTANY
Abstract

Efficient and reliable diagnostic tools for the routine indexing and certification of clean propagating material are essential for the management of pospiviroid diseases in horticultural crops. This study describes the development of a true multiplexed diagnostic method for the detection and identification of all nine currently recognized pospiviroid species in one assay using Luminex bead-based suspension array technology. In addition, a new data-driven, statistical method is presented for establishing thresholds for positivity for individual assays within multiplexed arrays. When applied to the multiplexed array data generated in this study, the new method was shown to have better control of false positives and false negative results than two other commonly used approaches for setting thresholds. The 11-plex Luminex MagPlex-TAG pospiviroid array described here has a unique hierarchical assay design, incorporating a near-universal assay in addition to nine species-specific assays, and a co-amplified plant internal control assay for quality assurance purposes. All assays of the multiplexed array were shown to be 100% specific, sensitive and reproducible. The multiplexed array described herein is robust, easy to use, displays unambiguous results and has strong potential for use in routine pospiviroid indexing to improve disease management strategies. [ABSTRACT FROM AUTHOR]

Published
2014
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128. Panel of real-time PCRs for the multiplexed detection of two tomato-infecting begomoviruses and their cognate whitefly vector species.

Author

Brunschot, S. L., Gambley, C. F., Barro, P. J., Grams, R., Thomas, J. E., Henderson, J., Drenth, A., and Geering, A. D. W.

Subjects
TOMATO yellow leaf curl virus, PLANT disease research, SWEETPOTATO whitefly, BEGOMOVIRUSES, BIOSECURITY, AGRICULTURAL research
Abstract

A new approach for the simultaneous identification of the viruses and vectors responsible for tomato yellow leaf curl disease ( TYLCD) epidemics is presented. A panel of quantitative multiplexed real-time PCR assays was developed for the sensitive and reliable detection of Tomato yellow leaf curl virus-Israel ( TYLCV- IL), Tomato leaf curl virus (To LCV), Bemisia tabaci Middle East Asia Minor 1 species ( MEAM1, B biotype) and B. tabaci Mediterranean species ( MED, Q biotype) from either plant or whitefly samples. For quality-assurance purposes, two internal control assays were included in the assay panel for the co-amplification of solanaceous plant DNA or B. tabaci DNA. All assays were shown to be specific and reproducible. The multiplexed assays were able to reliably detect as few as 10 plasmid copies of TYLCV- IL, 100 plasmid copies of To LCV, 500 fg B. tabaci MEAM1 and 300 fg B. tabaci MED DNA. Evaluated methods for routine testing of field-collected whiteflies are presented, including protocols for processing B. tabaci captured on yellow sticky traps and for bulking of multiple B. tabaci individuals prior to DNA extraction. This work assembles all of the essential features of a validated and quality-assured diagnostic method for the identification and discrimination of tomato-infecting begomovirus and B. tabaci vector species in Australia. This flexible panel of assays will facilitate improved quarantine, biosecurity and disease-management programmes both in Australia and worldwide. [ABSTRACT FROM AUTHOR]

Published
2013
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129. The classification and nomenclature of endogenous viruses of the family Caulimoviridae.

Author

Geering, Andrew D. W., Scharaschkin, Tanya, and Teycheney, Pierre-Yves

Subjects
*GENOMICS, *CAULIMOVIRIDAE, *DNA viruses, *BIOLOGICAL evolution, *ANIMAL classification
Abstract

Endogenous members of the family Caulimoviridae have now been found in the genomes of many plant species. Although these sequences are usually fragmented and rearranged and show varying degrees of decay, the genomes of the ancestral viruses can often be reassembled in silico, allowing classification within the existing viral taxonomic framework. In this paper, we describe analyses of endogenous members of the family Caulimoviridae in the genomes of Oryza sativa, Nicotiana tabacum and Solanum spp. and on the basis of phylogeny, genome organization and genetic distance within the pol gene, propose two new virus genera called Orendovirus and Solendovirus. A system of nomenclature for endogenous virus sequences in plants is also proposed. [ABSTRACT FROM AUTHOR]

Published
2010
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131. Identification of Rubus yellow net virus as a distinct badnavirus and its detection by PCR in Rubusspecies and in aphids

Author

JONES, A TEIFION, McGAVIN, WENDY J, GEERING, A D W, and LOCKHART, B E L

Abstract

Rubus yellow net virus (RYNV) infects Rubusspecies and cultivars worldwide and is an essential component of raspberry veinbanding mosaic (RVBMD), a virus disease complex that causes serious decline in plant vigour and productivity. The virus is transmitted, probably in a semi-persistent manner, by the large raspberry aphid, Amphorophora idaeiin Europe, and A. agathonicain North America. The particles of RYNV are bacilliform in shape and measure 80-150 × 25-30 nm, similar to those of badnaviruses. A1.7 kb fragment of the viral DNA was amplified by PCR and then directly sequenced. Analysis of this sequence suggests that RYNV is possibly a distinct species in the genus Badnavirusand is most closely related to Gooseberry vein banding associated virus (GVBAV) and Spiraea yellow leaf spot virus, two other badnaviruses described recently. Using the sequence derived from the PCR-amplified viral DNA fragment, RYNV-specific primers were designed and used in PCR to assay for RYNV in a range of Rubusgermplasm infected with RYNV, with other unrelated viruses and virus-like diseases found in Rubus, and in healthy plants. RYNV was detected in all glasshouse cultures of RYNV-infected plants, whether alone or in complex infections with other viruses, but not from healthy Rubus plants, nor from plants infected with other viruses. It was also detected in field-grown raspberry plants with and without symptoms of RVBMD and in raspberry plants infected with RYNV by viruliferous A. idaei. RYNV was also detected by PCR in A. idaeifollowing access feeds on RYNV-infected plants of 1 h or more. PCR failed to amplify DNA from gooseberry infected with GVBAV confirming the specificity of the RYNV analysis. PCR detection of RYNV in dormant raspberry buds allows assays to be made outside the natural growing season, providing a useful application for plant introduction and quarantine programmes.

Published
2002
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133. Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution

Author

Rod A. Wing, Simone Scalabrin, Matthias Zytnicki, Nathalie Choisne, Pierre-Yves Teycheney, Hadi Quesneville, Silvia Vezzulli, Derrick J. Zwickl, Andrew D. W. Geering, Dario Copetti, Florian Maumus, Alistair R. McTaggart, Geering, Andrew D W, Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland [Brisbane], Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), University of Arizona, International Rice Research Institute [Philippines] (IRRI), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Department of Ecology and Evolutionary Biology, Istituto di Genomica Applicata, Research and Innovation Centre, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), European Regional Development Fund, and OEDC

Subjects
0106 biological sciences, Phylogénie, plant genome, Introgression, Populus trichocarpa, Virologie, Gene Dosage, endogenous florendoviruses, General Physics and Astronomy, Caulimoviridae, Évolution, Virus Replication, 01 natural sciences, Genome, F30 - Génétique et amélioration des plantes, Jatropha curcas, Phylogeny, Genomic organization, Genetics, 0303 health sciences, Multidisciplinary, Vegetal Biology, biology, virus evolution, horizontal gene-transfer, double-stranded-RNA, transposable elements, maximum-likelihood, divergence times, mixed models, sequence, DNA, rice, expression, food and beverages, Settore AGR/07 - GENETICA AGRARIA, Viral evolution, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Horizontal gene transfer, Espèce nouvelle, Plante, Genome, Plant, Transposable element, Séquence nucléotidique, Genomics, Article, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, 03 medical and health sciences, Phylogenetics, Virology, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Transfert de gène, H20 - Maladies des plantes, 030304 developmental biology, Génome, Oryza, Virus des végétaux, General Chemistry, biology.organism_classification, Introns, Retroviridae, Genetic Loci, Vitis vinifera, Biologie végétale, Microsatellite Repeats, Ricinus communis, 010606 plant biology & botany
Abstract

The extent and importance of endogenous viral elements have been extensively described in animals but are much less well understood in plants. Here we describe a new genus of Caulimoviridae called ‘Florendovirus’, members of which have colonized the genomes of a large diversity of flowering plants, sometimes at very high copy numbers (>0.5% total genome content). The genome invasion of Oryza is dated to over 1.8 million years ago (MYA) but phylogeographic evidence points to an even older age of 20–34 MYA for this virus group. Some appear to have had a bipartite genome organization, a unique characteristic among viral retroelements. In Vitis vinifera, 9% of the endogenous florendovirus loci are located within introns and therefore may influence host gene expression. The frequent colocation of endogenous florendovirus loci with TA simple sequence repeats, which are associated with chromosome fragility, suggests sequence capture during repair of double-stranded DNA breaks., Endogenous viral elements have been extensively described in animals but their significance in plants is less well understood. Here, Geering et al. describe a new group of endogenous pararetroviruses, called florendoviruses, which have colonized the genomes of many important crop species.

Published
2014

134. Fungal Planet description sheets: 1284-1382.

Author

Crous PW, Osieck ER, Jurjević Ž, Boers J, van Iperen AL, Starink-Willemse M, Dima B, Balashov S, Bulgakov TS, Johnston PR, Morozova OV, Pinruan U, Sommai S, Alvarado P, Decock CA, Lebel T, McMullan-Fisher S, Moreno G, Shivas RG, Zhao L, Abdollahzadeh J, Abrinbana M, Ageev DV, Akhmetova G, Alexandrova AV, Altés A, Amaral AGG, Angelini C, Antonín V, Arenas F, Asselman P, Badali F, Baghela A, Bañares A, Barreto RW, Baseia IG, Bellanger JM, Berraf-Tebbal A, Biketova AY, Bukharova NV, Burgess TI, Cabero J, Câmara MPS, Cano-Lira JF, Ceryngier P, Chávez R, Cowan DA, de Lima AF, Oliveira RL, Denman S, Dang QN, Dovana F, Duarte IG, Eichmeier A, Erhard A, Esteve-Raventós F, Fellin A, Ferisin G, Ferreira RJ, Ferrer A, Finy P, Gaya E, Geering ADW, Gil-Durán C, Glässnerová K, Glushakova AM, Gramaje D, Guard FE, Guarnizo AL, Haelewaters D, Halling RE, Hill R, Hirooka Y, Hubka V, Iliushin VA, Ivanova DD, Ivanushkina NE, Jangsantear P, Justo A, Kachalkin AV, Kato S, Khamsuntorn P, Kirtsideli IY, Knapp DG, Kochkina GA, Koukol O, Kovács GM, Kruse J, Kumar TKA, Kušan I, Læssøe T, Larsson E, Lebeuf R, Levicán G, Loizides M, Marinho P, Luangsa-Ard JJ, Lukina EG, Magaña-Dueñas V, Maggs-Kölling G, Malysheva EF, Malysheva VF, Martín B, Martín MP, Matočec N, McTaggart AR, Mehrabi-Koushki M, Mešić A, Miller AN, Mironova P, Moreau PA, Morte A, Müller K, Nagy LG, Nanu S, Navarro-Ródenas A, Nel WJ, Nguyen TH, Nóbrega TF, Noordeloos ME, Olariaga I, Overton BE, Ozerskaya SM, Palani P, Pancorbo F, Papp V, Pawłowska J, Pham TQ, Phosri C, Popov ES, Portugal A, Pošta A, Reschke K, Reul M, Ricci GM, Rodríguez A, Romanowski J, Ruchikachorn N, Saar I, Safi A, Sakolrak B, Salzmann F, Sandoval-Denis M, Sangwichein E, Sanhueza L, Sato T, Sastoque A, Senn-Irlet B, Shibata A, Siepe K, Somrithipol S, Spetik M, Sridhar P, Stchigel AM, Stuskova K, Suwannasai N, Tan YP, Thangavel R, Tiago I, Tiwari S, Tkalčec Z, Tomashevskaya MA, Tonegawa C, Tran HX, Tran NT, Trovão J, Trubitsyn VE, Van Wyk J, Vieira WAS, Vila J, Visagie CM, Vizzini A, Volobuev SV, Vu DT, Wangsawat N, Yaguchi T, Ercole E, Ferreira BW, de Souza AP, Vieira BS, and Groenewald JZ

Abstract

Novel species of fungi described in this study include those from various countries as follows: Antartica , Cladosporium austrolitorale from coastal sea sand. Australia , Austroboletus yourkae on soil, Crepidotus innuopurpureus on dead wood, Curvularia stenotaphri from roots and leaves of Stenotaphrum secundatum and Thecaphora stajsicii from capsules of Oxalis radicosa. Belgium , Paraxerochrysium coryli (incl. Paraxerochrysium gen. nov.) from Corylus avellana. Brazil , Calvatia nordestina on soil, Didymella tabebuiicola from leaf spots on Tabebuia aurea, Fusarium subflagellisporum from hypertrophied floral and vegetative branches of Mangifera indica from a grassland. Microdochium maculosum from living leaves of Digitaria insularis. from a rotten Canada , Cuphophyllus bondii from a grassland. Croatia , Mollisia inferiseptata from a rotten Laurus nobilis trunk. Cyprus , Amanita exilis on calcareous soil. Czech Republic , Cytospora hippophaicola among grass on a lawn. Vaccinium corymbosum. Denmark , Lasiosphaeria deviata on pieces of wood and herbaceous debris. Dominican Republic , Calocybella goethei among grass on a lawn. France (Corsica) , Inocybe corsica on wet ground. France (French Guiana) , Trechispora patawaensis on decayed branch of unknown angiosperm tree and Trechispora subregularis from the gut of a Germany , Paramicrothecium sambuci (incl. Paramicrothecium gen. nov.) on dead stems of Sambucus nigra. India , Aureobasidium microtermitis from the gut of a Microtermes sp. termite, Laccaria diospyricola on soil and Phylloporia tamilnadensis on branches of Catunaregam spinosa . Iran , Pythium serotinoosporum from soil under Prunus dulcis. Italy , Pluteus brunneovenosus on twigs of broadleaved trees on the ground. Japan , Heterophoma rehmanniae on leaves of Rehmannia glutinosa f. hueichingensis. Kazakhstan , Murispora kazachstanica from healthy roots of Triticum aestivum. Namibia , Caespitomonium euphorbiae (incl. Caespitomonium gen. nov.) from stems of an Euphorbia sp. Netherlands , Alfaria junci, Myrmecridium junci, Myrmecridium juncicola, Myrmecridium juncigenum, Ophioceras junci, Paradinemasporium junci (incl. Paradinemasporium gen. nov.), Phialoseptomonium junci, Sporidesmiella juncicola, Xenopyricularia junci and Zaanenomyces quadripartis (incl. Zaanenomyces gen. nov.), from dead culms of Juncus effusus, Cylindromonium everniae and Rhodoveronaea everniae from Evernia prunastri, Cyphellophora sambuci and Myrmecridium sambuci from Sambucus nigra, Kiflimonium junci, Sarocladium junci, Zaanenomyces moderatricis-academiae and Zaanenomyces versatilis from dead culms of Juncus inflexus, Microcera physciae from Physcia tenella, Myrmecridium dactylidis from dead culms of Dactylis glomerata, Neochalara spiraeae and Sporidesmium spiraeae from leaves of Spiraea japonica, Neofabraea salicina from Salix sp., Paradissoconium narthecii (incl. Paradissoconium gen. nov.) from dead leaves of Narthecium ossifragum, Polyscytalum vaccinii from Vaccinium myrtillus, Pseudosoloacrosporiella cryptomeriae (incl. Pseudosoloacrosporiella gen. nov.) from leaves of Cryptomeria japonica, Ramularia pararhabdospora from Plantago lanceolata, Sporidesmiella pini from needles of Pinus sylvestris and Xenoacrodontium juglandis (incl. Xenoacrodontium gen. nov. and Xenoacrodontiaceae from a biofilm covering a deteriorated limestone wall. Juglans regia . New Zealand , Cryptometrion metrosideri from twigs of Metrosideros sp., Coccomyces pycnophyllocladi on a dry dead branch of Phyllocladus alpinus, Hypoderma aliforme from fallen leaves Fuscopora solandri on litter in a mixed forest, Hypoderma subiculatum from dead leaves Phormium tenax. Norway , Neodevriesia kalakoutskii from permafrost and Variabilispora viridis from driftwood of Picea abies. Portugal , Entomortierella hereditatis from a biofilm covering a deteriorated limestone wall. Russia , Colpoma junipericola from needles of Juniperus sabina, Entoloma cinnamomeum on soil in grasslands, Entoloma verae on soil in grasslands, Hyphodermella pallidostraminea on a dry dead branch of Actinidia sp., Lepiota sayanensis on litter in a mixed forest, Papiliotrema horticola from Malus communis , Paramacroventuria ribis (incl. Paramacroventuria gen. nov.) from leaves of Ribes aureum and Paramyrothecium lathyri from a blackened metal railing of an industrial warehouse and Lathyrus tuberosus. South Africa , Harzia combreti from leaf litter of Combretum collinum ssp. sulvense, Penicillium xyleborini from Xyleborinus saxesenii , Phaeoisaria dalbergiae from bark of Dalbergia armata, Protocreopsis euphorbiae from indoor air in a hospital, Euphorbia ingens and Roigiella syzygii from twigs of Syzygium chordatum . Spain gen. nov.) from a tombstone, Genea zamorana from air in a store, Gymnopus nigrescens on Scleropodium touretii, Hesperomyces parexochomi from air in a brick room, Parexochomus quadriplagiatus, Paraphoma variabilis from air in a classroom, Phaeococcomyces kinklidomatophilus from a blackened metal railing of an industrial warehouse and Tuber suaveolens from sludge in a water reservoir. Quercus faginea. Svalbard and Jan Mayen , Inocybe nivea associated with Salix polaris. Thailand , Biscogniauxia whalleyi on corticated wood. UK , Parasitella quercicola from Quercus robur. USA , Aspergillus arizonicus from indoor air in a hospital, Caeliomyces tampanus (incl. Caeliomyces gen. nov.) from office dust, Cippumomyces mortalis (incl. Cippumomyces gen. nov.) from a tombstone, Cylindrium desperesense from air in a store, Tetracoccosporium pseudoaerium from air sample in house, Toxicocladosporium glendoranum from air in a brick room, Toxicocladosporium losalamitosense from air in a classroom, Valsonectria portsmouthensis from air in men's locker room and Varicosporellopsis americana from sludge in a water reservoir. Vietnam , Entoloma kovalenkoi on rotten wood, Fusarium chuoi inside seed of Musa itinerans , Micropsalliota albofelina on soil in tropical evergreen mixed forests and Phytophthora docyniae from soil and roots of Docynia indica. Morphological and culture characteristics are supported by DNA barcodes. Citation : Crous PW, Osieck ER, Jurjević Ž, et al. 2021. Fungal Planet description sheets: 1284-1382. Persoonia 47: 178-374. https://doi.org/10.3767/persoonia.2021.47.06., (© 2021 Naturalis Biodiversity Center & Westerdijk Fungal Biodiversity Institute.)

Published
2021
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135. Fungal Planet description sheets: 371-399.

Author

Crous PW, Wingfield MJ, Le Roux JJ, Richardson DM, Strasberg D, Shivas RG, Alvarado P, Edwards J, Moreno G, Sharma R, Sonawane MS, Tan YP, Altés A, Barasubiye T, Barnes CW, Blanchette RA, Boertmann D, Bogo A, Carlavilla JR, Cheewangkoon R, Daniel R, de Beer ZW, de Jesús Yáñez-Morales M, Duong TA, Fernández-Vicente J, Geering AD, Guest DI, Held BW, Heykoop M, Hubka V, Ismail AM, Kajale SC, Khemmuk W, Kolařík M, Kurli R, Lebeuf R, Lévesque CA, Lombard L, Magista D, Manjón JL, Marincowitz S, Mohedano JM, Nováková A, Oberlies NH, Otto EC, Paguigan ND, Pascoe IG, Pérez-Butrón JL, Perrone G, Rahi P, Raja HA, Rintoul T, Sanhueza RM, Scarlett K, Shouche YS, Shuttleworth LA, Taylor PW, Thorn RG, Vawdrey LL, Solano-Vidal R, Voitk A, Wong PT, Wood AR, Zamora JC, and Groenewald JZ

Abstract

Novel species of fungi described in the present study include the following from Australia: Neoseptorioides eucalypti gen. & sp. nov. from Eucalyptus radiata leaves, Phytophthora gondwanensis from soil, Diaporthe tulliensis from rotted stem ends of Theobroma cacao fruit, Diaporthe vawdreyi from fruit rot of Psidium guajava, Magnaporthiopsis agrostidis from rotted roots of Agrostis stolonifera and Semifissispora natalis from Eucalyptus leaf litter. Furthermore, Neopestalotiopsis egyptiaca is described from Mangifera indica leaves (Egypt), Roussoella mexicana from Coffea arabica leaves (Mexico), Calonectria monticola from soil (Thailand), Hygrocybe jackmanii from littoral sand dunes (Canada), Lindgomyces madisonensis from submerged decorticated wood (USA), Neofabraea brasiliensis from Malus domestica (Brazil), Geastrum diosiae from litter (Argentina), Ganoderma wiiroense on angiosperms (Ghana), Arthrinium gutiae from the gut of a grasshopper (India), Pyrenochaeta telephoni from the screen of a mobile phone (India) and Xenoleptographium phialoconidium gen. & sp. nov. on exposed xylem tissues of Gmelina arborea (Indonesia). Several novelties are introduced from Spain, namely Psathyrella complutensis on loamy soil, Chlorophyllum lusitanicum on nitrified grasslands (incl. Chlorophyllum arizonicum comb. nov.), Aspergillus citocrescens from cave sediment and Lotinia verna gen. & sp. nov. from muddy soil. Novel foliicolous taxa from South Africa include Phyllosticta carissicola from Carissa macrocarpa, Pseudopyricularia hagahagae from Cyperaceae and Zeloasperisporium searsiae from Searsia chirindensis. Furthermore, Neophaeococcomyces is introduced as a novel genus, with two new combinations, N. aloes and N. catenatus. Several foliicolous novelties are recorded from La Réunion, France, namely Ochroconis pandanicola from Pandanus utilis, Neosulcatispora agaves gen. & sp. nov. from Agave vera-cruz, Pilidium eucalyptorum from Eucalyptus robusta, Strelitziana syzygii from Syzygium jambos (incl. Strelitzianaceae fam. nov.) and Pseudobeltrania ocoteae from Ocotea obtusata (Beltraniaceae emend.). Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.

Published
2015
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136. A bead-based suspension array for the multiplexed detection of begomoviruses and their whitefly vectors.

Author

van Brunschot SL, Bergervoet JH, Pagendam DE, de Weerdt M, Geering AD, Drenth A, and van der Vlugt RA

Subjects
Animals, Plant Diseases virology, Begomovirus genetics, Hemiptera genetics, Hemiptera virology, Insect Vectors genetics, Plant Diseases genetics
Abstract

Bead-based suspension array systems enable simultaneous fluorescence-based identification of multiple nucleic acid targets in a single reaction. This study describes the development of a novel approach to plant virus and vector diagnostics, a multiplexed 7-plex array that comprises a hierarchical set of assays for the simultaneous detection of begomoviruses and Bemisia tabaci, from both plant and whitefly samples. The multiplexed array incorporates genus, species and strain-specific assays, offering a unique approach for identifying both known and unknown viruses and B. tabaci species. When tested against a large panel of sequence-characterized begomovirus and whitefly samples, the array was shown to be 100% specific to the homologous target. Additionally, the multiplexed array was highly sensitive, efficiently and concurrently determining both virus and whitefly identity from single viruliferous whitefly samples. The detection limit for one assay within the multiplexed array that specifically detects Tomato yellow leaf curl virus-Israel (TYLCV-IL) was quantified as 200fg of TYLCV-IL DNA, directly equivalent to that of TYLCV-specific qPCR. Highly reproducible results were obtained over multiple tests. The flexible multiplexed array described in this study has great potential for use in plant quarantine, biosecurity and disease management programs worldwide., (Copyright © 2014 Elsevier B.V. All rights reserved.)

Published
2014
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137. A review of the Ustilago-Sporisorium-Macalpinomyces complex.

Author

McTaggart AR, Shivas RG, Geering AD, Vánky K, and Scharaschkin T

Abstract

The fungal genera Ustilago, Sporisorium and Macalpinomyces represent an unresolved complex. Taxa within the complex often possess characters that occur in more than one genus, creating uncertainty for species placement. Previous studies have indicated that the genera cannot be separated based on morphology alone. Here we chronologically review the history of the Ustilago-Sporisorium-Macalpinomyces complex, argue for its resolution and suggest methods to accomplish a stable taxonomy. A combined molecular and morphological approach is required to identify synapomorphic characters that underpin a new classification. Ustilago, Sporisorium and Macalpinomyces require explicit re-description and new genera, based on monophyletic groups, are needed to accommodate taxa that no longer fit the emended descriptions. A resolved classification will end the taxonomic confusion that surrounds generic placement of these smut fungi.

Published
2012
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138. Taxonomic revision of Ustilago, Sporisorium and Macalpinomyces.

Author

McTaggart AR, Shivas RG, Geering AD, Vánky K, and Scharaschkin T

Abstract

Morphological characters within the Ustilago-Sporisorium-Macalpinomyces complex are defined explicitly. The genera Sporisorium and Anthracocystis are emended to reflect morphological synapomorphies. Three new genera, Langdonia, Stollia and Triodiomyces are described based on soral synapomorphies and host classification. The new classification of the Ustilago-Sporisorium-Macalpinomyces complex incorporates 142 new taxonomic combinations.

Published
2012
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139. Development of an immunomagnetic capture-reverse transcriptase-PCR assay for three pineapple ampeloviruses.

Author

Gambley CF, Geering AD, and Thomas JE

Subjects
Closteroviridae genetics, Plant Leaves virology, RNA, Viral analysis, Sensitivity and Specificity, Ananas virology, Closteroviridae immunology, Closteroviridae isolation & purification, Immunomagnetic Separation methods, Plant Diseases virology, Reverse Transcriptase Polymerase Chain Reaction methods
Abstract

A semi-automated, immunomagnetic capture-reverse transcription PCR (IMC-RT-PCR) assay for the detection of three pineapple-infecting ampeloviruses, Pineapple mealybug wilt-associated virus-1, -2 and -3, is described. The assay was equivalent in sensitivity but more rapid than conventional immunocapture RT-PCR. The assay can be used either as a one- or two-step RT-PCR and allows detection of the viruses separately or together in a triplex assay from fresh, frozen or freeze-dried pineapple leaf tissue. This IMC-RT-PCR assay could be used for high throughput screening of pineapple planting propagules and could easily be modified for the detection of other RNA viruses in a range of plant species, provided suitable antibodies are available.

Published
2009
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