Global status of tospovirus epidemics in diverse cropping systems: successes achieved and challenges ahead.

The Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.

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Notes, outline and divergence times of Basidiomycota

The grapevine (Vitis spp.) undoubtedly represents one of the woody crops most widely grown in temperate climates, and a highly valuable agricultural commodity. As most of the vegetatively propagated crops, grapevines are exposed to the attacks of a variety of pests and pathogens among which infectious intracellular agents (viruses, viroids, phloem‑ and xylem‑limited prokaryotes) play a major role, causing heavy losses, shortening the productive life of vineyars, and endangering the survival itself of affected vines. The importance of the grapevine industry and the magnitude of the problems caused by these pathogens has generated wide interest which, in turn, has fostered intensive research which has been especially active at the international scale from the late 1950’s onwards.

Directory of virus and virus-like diseases of the grapevine and their agents

Grapevine leafroll-associated virus 2 (GLRaV-2) was recognized in 1984, but its nomenclature was settled only in 1995. It is one of the five viruses involved in grapevine leafroll disease. It is also associated with graft incompatibility disorders. Because of peculiar genome structure and evolutionary history, GLRaV-2 belongs to the genus Closterovirus in the family Closteroviridae. The GLRaV-2 genome is a single-stranded, positive-sense RNA of ca. 16,500 nucleotides that is presumably capped at the 5′ terminus but lacks a poly(A) tail at the 3′ end. The nine ORFs encoded by GLRaV-2 comprise three functional modules, including the replication module, the quintuple gene block module, and the module for RNA silencing suppressors. The translation product of ORF1a lacks an AlkB domain, unlike all members of the genus Ampelovirus that infect the grapevine. The genetic diversity of GLRaV-2 is very high, with six lineages that are characterized by up to 25% nucleotide divergence and different biological behavior on plant hosts. All Vitis vinifera, rootstocks, and interspecific hybrids are susceptible to GLRaV-2. The identification of GLRaV-2 in wild Vitis spp. native to the American continent supports the hypothesis that the virus originated from North America. The virus is restricted to the phloem tissue, and infected cells are characterized by a massive presence of membranous vesicles that are typical of infection by members of the genus Closterovirus. No arthropod vector is known for GLRaV-2, but the virus is graft transmissible and mechanically transmissible to some herbaceous hosts, unlike other GLRaVs. Management of GLRaV-2 is through the use of virus-tested, clean propagation materials. The recent development of infectious GLRaV-2 clones sets the foundation for studies on gene function, virus replication, pathological properties, as well as virus-host interactions.

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Grapevine leafroll-associated virus 3

Genome annotation is the process of identifying the location and function of a genome's encoded features. Improving the biological accuracy of annotation is a complex and iterative process requiring researchers to review and incorporate multiple sources of information such as transcriptome alignments, predictive models based on sequence profiles, and comparisons to features found in related organisms. Because rapidly decreasing costs are enabling an ever-growing number of scientists to incorporate sequencing as a routine laboratory technique, there is widespread demand for tools that can assist in the deliberative analytical review of genomic information. To this end, we present Apollo, an open source software package that enables researchers to efficiently inspect and refine the precise structure and role of genomic features in a graphical browser-based platform. Some of Apollo's newer user interface features include support for real-time collaboration, allowing distributed users to simultaneously edit the same encoded features while also instantly seeing the updates made by other researchers on the same region in a manner similar to Google Docs. Its technical architecture enables Apollo to be integrated into multiple existing genomic analysis pipelines and heterogeneous laboratory workflow platforms. Finally, we consider the implications that Apollo and related applications may have on how the results of genome research are published and made accessible.

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Apollo: Democratizing genome annotation

Lentinula edodes, one of the most popular, edible mushroom species with a high content of proteins and polysaccharides as well as unique aroma, is widely cultivated in many Asian countries, especially in China, Japan and Korea. As a white rot fungus with lignocellulose degradation ability, L. edodes has the potential for application in the utilization of agriculture straw resources. Here, we report its 41.8-Mb genome, encoding 14,889 predicted genes. Through a phylogenetic analysis with model species of fungi, the evolutionary divergence time of L. edodes and Gymnopus luxurians was estimated to be 39 MYA. The carbohydrate-active enzyme genes in L. edodes were compared with those of the other 25 fungal species, and 101 lignocellulolytic enzymes were identified in L. edodes, similar to other white rot fungi. Transcriptome analysis showed that the expression of genes encoding two cellulases and 16 transcription factor was up-regulated when mycelia were cultivated for 120 minutes in cellulose medium versus glucose medium. Our results will foster a better understanding of the molecular mechanism of lignocellulose degradation and provide the basis for partial replacement of wood sawdust with agricultural wastes in L. edodes cultivation.

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Genome sequence of the edible cultivated mushroom Lentinula edodes (shiitake) reveals insights into lignocellulose degradation

Efficacy of virus elimination from in vitro-cultured sand pear (Pyrus pyrifolia) by chemotherapy combined with thermotherapy

Background/aims Heat stress could cause huge losses for Lentinula edodes in China and other Asian cultivation areas. Yet our understanding of mechanism how to defend to heat stress is incomplete. Methods Using heat-tolerant and heat-sensitive strains of L. edodes, we reported a combined proteome and transcriptome analysis of L. edodes response to 40 °C heat stress for 24 h. Meanwhile, the effect of LeDnaJ on the thermotolerance and IAA (indoleacetic acid) biosynthesis in L. edodes was analyzed via the over-expression method. Results The proteome results revealed that HSPs (heat shock proteins) such as Hsp40 (DnaJ), Hsp70, Hsp90 and key enzymes involved in tryptophan and IAA metabolism process LeTrpE, LeTrpD, LeTam-1, LeYUCCA were more highly expressed in S606 than in YS3357, demonstrating that HSPs and tryptophan as well as IAA metabolism pathway should play an important role in thermotolerance. Over-expression of LeDnaJ gene in S606 strains showed better tolerance to heat stress. It was also documented that intracellular IAA accumulation of S606 (8-fold up) was more than YS3357 (2-fold up), and exogenous IAA enhanced L. edodes tolerance to heat stress. Conclusion Our data support the interest of LeTrpE, LeDnaJ, tryptophan and IAA could play a pivotal role in enhancing organism thermotolerance.

/pdf/proteome-and-transcriptome-reveal-involvement-of-heat-shock-27th99yrnp.pdf

Proteome and Transcriptome Reveal Involvement of Heat Shock Proteins and Indoleacetic Acid Metabolism Process in Lentinula Edodes Thermotolerance.

Lentinula edodes, one of the most important edible mushrooms in China, is affected heavily by the infection of green mold that overgrows mushroom mycelia. We collected the diseased samples from main L. edodes cultivation regions in China to characterize the pathogen and to study the effect of Trichoderma spp. on L. edodes species. We identified six Trichoderma species, that is, T. harzianum, T. atroviride, T. viride, T. pleuroticola, T. longibrachiatum, and T. oblongisporum based on the internal transcribed spacer or tef1-α sequences and morphology characteristics. In confrontation cultures on Petri plates or in tubes, and in L. edodes cultures in a medium containing Trichoderma metabolites, L. edodes mycelia were not only distorted and swollen, but also inhibited by Trichoderma isolates. It is not possible that adjusting pH value or temperature is used for controlling L. edodes green disease, because the growth of most of Trichoderma isolates and L. edodes shared similar pH and temperature conditions.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/mbo3.364

Diversity and effect of Trichoderma spp. associated with green mold disease on Lentinula edodes in China.

A new strain of Capsicum chlorosis virus (CaCV) from peanut (Arachis hypogaea L.) in China, designated CaCV-CP, was characterized. CaCV-CP causes yellow spots and necrosis on the leaves of affected peanut plants. Of 31 plant species inoculated mechanically, 24 were susceptible to this strain. Quasi-spherical virions were present in ultrathin section of diseased leaves. The complete sequence of S RNA of CaCV-CP consisted of 3399 nucleotides (nts). The NSs and N genes of the virus contained 1320 nts and 828 nts, respectively; these two open reading frames were in an ambisense arrangement. The N gene of CaCV-CP shared 84.7-86.4% and 92.4-93.1% identity, with that of CaCV strains from Thailand and Australia at nt and amino acid levels, respectively (the GenBank accession number of the sequence reported in this study is DQ355974).

G. P. Wang

Papers

Genome sequence of the edible cultivated mushroom Lentinula edodes (shiitake) reveals insights into lignocellulose degradation

Efficacy of virus elimination from in vitro-cultured sand pear (Pyrus pyrifolia) by chemotherapy combined with thermotherapy

Proteome and Transcriptome Reveal Involvement of Heat Shock Proteins and Indoleacetic Acid Metabolism Process in Lentinula Edodes Thermotolerance.

Diversity and effect of Trichoderma spp. associated with green mold disease on Lentinula edodes in China.

Characterization of a New Strain of Capsicum chlorosis virus from Peanut (Arachis hypogaea L.) in China