{Reference Type}: Journal Article
{Author}: Nagy, L. G.; Desjardin, D. E.; Vagvolgyi, C.; Kemp, R.; Papp, T.
{Year}: 2013
{Title}: Phylogenetic analyses of Coprinopsis sections Lanatuli and Atramentarii identify   multiple species within morphologically defined taxa
{URL}: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=23074175&query_hl=1
{Tag}: 0
{Star}: 0
{Journal}: Mycologia
{Volume}: 105
{Issue}: 1
{Pages}: 112-24
{DOI}: 10.3852/12-136
{Date Displayed}: 2013 Jan-Feb
{Date}: 2013-01-01
{Type of Work}: Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
{Accession Number}: 23074175
{Keywords}: Agaricales/*classification/genetics/growth & development/*isolation &
           purification; DNA, Fungal/genetics; DNA, Ribosomal Spacer/genetics; Molecular Sequence Data; *Phylogeny
{Abstract}: Sections Lanatuli and Atramentarii of the genus Coprinopsis contain some of the best known and most important agaric species, including C. cinerea and C. lagopus, yet a critical, phylogeny-based assessment of the species limits has not been carried out. Taxa have been characterized chiefly on the basis of morphological characters, which however show little discriminatory power and/or considerable overlap between several species pairs. We used ITS and LSU sequence   data of 29 described taxa in Coprinopsis sections Lanatuli and Atramentarii to infer species limits and the correspondence between morphological characters and   species lineages, as well as to examine the phylogenetic affinities of sections Lanatuli and Atramentarii. Our analyses recovered three large clades, implying a   paraphyly for section Lanatuli. Based on morphology and clade structure, we estimate ca. 38 species in the two sections, including several potentially new taxa, three of which are described herein. Coprinopsis pachyderma, C. lagopus var. vacillans, C. acuminata, C. spelaiophila, Coprinus citrinovelatus and Cop. brunneistrangulatus were found to be synonymous with other, earlier described species. Congruent with previous mating studies, our analyses recovered multiple, morphologically indistinguishable lineages within C. lagopus, which included C. lagopus var. vacillans, an ephemeral, developmental variant. Morphological traits supporting the inferred clade structure are discussed. Three new taxa (C. fusispora, C. babosiae, C. villosa), and one new combination (C. mitraespora) are proposed.
{Author Address}: Department of Microbiology, University of Szeged, Szeged, Hungary. cortinarius2000@yahoo.co.uk
{Language}: eng

{Reference Type}: Journal Article
{Author}: Ge, Zai-Wei; Smith, Matthew E.
{Year}: 2013
{Title}: Phylogenetic analysis of rDNA sequences indicates that the sequestrate Amogaster viridiglebus is derived from within the agaricoid genus Lepiota (Agaricaceae) - Springer
{Tag}: 0
{Star}: 0
{Journal}: Mycological Progress
{Volume}: Volume 12
{Issue}: Issue 1
{Pages}: pp 151-155
{DOI}: 10.1007/s11557-012-0841-y
{Date}: 2013-02-01
{Abstract}: The rare sequestrate fungus <em class="a-plus-plus">Amogaster viridiglebus</em> is known from only one collection in California where it was discovered among <em class="a-plus-plus">Populus</em> roots. Based on sporocarp coloration and spore morphology, this sequestrate taxon was putatively considered to be an ectomycorrhizal member of the <em class="a-plus-plus">Boletales</em>. However, no molecular data were previously available to definitively determine the closest relatives of this fungus. Here we revisit the morphology of <em class="a-plus-plus">Amogaster viridiglebus</em> and present a phylogenetic analysis based on ITS and 28S ribosomal DNA. Our phylogeny indicates that <em class="a-plus-plus">Amogaster viridiglebus</em> is nested in the genus <em class="a-plus-plus">Lepiota</em>, suggesting that this rare species has a saprobic trophic mode and does not form ectomycorrhizae with plants. A new combination, <em class="a-plus-plus">L. viridigleba,</em> is made based on these phylogenetic results.
{Subject}: Plant Sciences;Ecology;Microbiology

{Reference Type}: Journal Article
{Author}: Qian, J.; Xu, H.; Song, J.; Xu, J.; Zhu, Y.; Chen, S.
{Year}: 2013
{Title}: Genome-wide analysis of simple sequence repeats in the model medicinal mushroom Ganoderma lucidum
{URL}: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=23069850&query_hl=1
{Tag}: 0
{Star}: 0
{Journal}: Gene
{Volume}: 512
{Issue}: 2
{Pages}: 331-6
{DOI}: 10.1016/j.gene.2012.09.127
{Date Displayed}: 2013 Jan 10
{Date}: 2013-01-10
{Type of Work}: Journal Article; Research Support, Non-U.S. Gov't
{Original Publication}: Copyright (c) 2012 Elsevier B.V. All rights reserved.
{Accession Number}: 23069850
{Keywords}: Fungal Proteins/*genetics/metabolism; *Genes, Fungal; Genetic Markers; Genome-Wide Association Study; Introns/*genetics; *Microsatellite Repeats; Reishi/*genetics/metabolism
{Abstract}: Simple sequence repeats (SSRs) or microsatellites are one of the most popular sources of genetic markers and play a significant role in gene function and genome organization. We identified SSRs in the genome of Ganoderma lucidum and analyzed their frequency and distribution in different genomic regions. We also compared the SSRs in G. lucidum with six other Agaricomycetes genomes: Coprinopsis cinerea, Laccaria bicolor, Phanerochaete chrysosporium, Postia placenta, Schizophyllum commune and Serpula lacrymans. Based on our search criteria, the total number of SSRs found ranged from 1206 to 6104 and covered from 0.04% to 0.15% of the fungal genomes. The SSR abundance was not correlated with the genome size, and mono- to tri-nucleotide repeats outnumbered other SSR categories in all of the species examined. In G. lucidum, a repertoire of 2674 SSRs was detected, with mono-nucleotides being the most abundant. SSRs were found in all genomic regions and were more abundant in non-coding regions than coding regions. The highest SSR relative abundance was found in introns (108 SSRs/Mb), followed by intergenic regions (84 SSRs/Mb). A total of 684 SSRs were found in the protein-coding sequences (CDSs) of 588 gene models, with 81.4% of them being   tri- or hexa-nucleotides. After scanning for InterPro domains, 280 of these genes were successfully annotated, and 215 of them could be assigned to Gene Ontology (GO) terms. SSRs were also identified in 28 bioactive compound synthesis-related   gene models, including one 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), three polysaccharide biosynthesis genes and 24 cytochrome P450 monooxygenases (CYPs). Primers were designed for the identified SSR loci, providing the basis for the future development of SSR markers of this medicinal fungus.
{Author Address}: The National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, PR China.
{Language}: eng