Data from: Lepidostroma vilgalysii, a new basidiolichen from the New World

The lichenized basidiomycete Lepidostroma vilgalysii is described from Mexico based on morphological analyses. The species is only the second representative of the family Lepidostromataceae documented from the New World, and is one of the few described lichens with an inverted morphology, with the algae in a layer at the base of the thallus. Molecular sequence data from the nuclear ribosomal LSU locus are used to confirm the placement of the holotype in Lepidostroma and to evaluate the molecular distinctiveness of the species from all other described species in the family and genus

Lepidostroma_RAxML_analyses

Input and output files for backbone-constrained topological and bootstrap searches performed with RAxML

Lepidostroma_LSU

Full nuclear ribosomal LSU alignment for the data matrix that was analyzed phylogenetically, including exclusion sets, the backbone constraint tree, and the best RAxML tree resulting from the ML analyses

sequence_renamer

A Perl script written primarily to take fasta files downloaded from GenBank and transform the complex sequence identifiers to a standardized format as follows: Genus_species_GenBankAccNum_GenInfoI

The ectomycorrhizal fungal community in a neotropical forest dominated by the endemic dipterocarp Pakaraimaea dipterocarpacea.

Ectomycorrhizal (ECM) plants and fungi can be diverse and abundant in certain tropical ecosystems. For example, the primarily paleotropical ECM plant family Dipterocarpaceae is one of the most speciose and ecologically important tree families in Southeast Asia. Pakaraimaea dipterocarpacea is one of two species of dipterocarp known from the Neotropics, and is also the only known member of the monotypic Dipterocarpaceae subfamily Pakaraimoideae. This Guiana Shield endemic is only known from the sandstone highlands of Guyana and Venezuela. Despite its unique phylogenetic position and unusual geographical distribution, the ECM fungal associations of P. dipterocarpacea are understudied throughout the tree's range. In December 2010 we sampled ECM fungi on roots of P. dipterocarpacea and the co-occurring ECM tree Dicymbe jenmanii (Fabaceae subfamily Caesalpinioideae) in the Upper Mazaruni River Basin of Guyana. Based on ITS rDNA sequencing we documented 52 ECM species from 11 independent fungal lineages. Due to the phylogenetic distance between the two host tree species, we hypothesized that P. dipterocarpacea would harbor unique ECM fungi not found on the roots of D. jenmanii. Although statistical tests suggested that several ECM fungal species did exhibit host preferences for either P. dipterocarpacea or D. jenmanii, most of the ECM fungi were multi-host generalists. We also detected several ECM fungi that have never been found in long-term studies of nearby rainforests dominated by other Dicymbe species. One particular mushroom-forming fungus appears to be unique and may represent a new ECM lineage of Agaricales that is endemic to the Neotropics

Genome-based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles

Ribosomal DNA (rDNA) copy number variation (CNV) has major physiological implications for all organisms, but how it varies for fungi, an ecologically ubiquitous and important group of microorganisms, has yet to be systemically investigated.Here, we examine rDNA CNV using an in silico read depth approach for 91 fungal taxa with sequenced genomes and assess copy number conservation across phylogenetic scales and ecological lifestyles. rDNA copy number varied considerably across fungi, ranging from an estimated 14 to 1,442 copies (mean = 113, median = 82), and copy number similarity was inversely correlated with phylogenetic distance.No correlations were found between rDNA CNV and fungal trophic mode, ecological guild or genome size.Taken together, these results show that like other microorganisms, fungi exhibit substantial variation in rDNA copy number, which is linked to their phylogeny in a scale-dependent manner

Ectomycorrhizal fungi detected on the roots of <i>Pakaraimaea dipterocarpacea</i> and <i>Dicymbe jenmanii</i> in this study.

<p>Species-level operational taxonomic units (OTUs) are defined as sequences that are ≥97% similar across the ITS rDNA sequence region. Taxa labeled with Latin binomials or voucher numbers (TH, MCA) were identified based on ITS matches with sporocarps. Species with ECM numbers are known only from sequences obtained from ECM roots. All species are assigned to the ECM lineages defined in Tedersoo et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055160#pone.0055160-Tedersoo4" target="_blank">[36]</a>. The numbers shown in the columns labeled <i>Pakaraimaea dipterocarpacea</i> and <i>Dicymbe jenmanii</i> designate the number of occurrences of each fungal OTU per host species. In cases where a particular fungal OTU was detected on more than one root tip from an individual tree this was not counted as a separate occurrence. The column on the far right indicates whether or not an OTU has been found previously on ECM roots or as sporocarps at other sites in Guyana.</p

Frequency of occurrence of the 17 most common ectomycorrhizal (ECM) fungi on the roots of host trees <i>Pakaraimaea dipterocarpacea</i> (white bars) and <i>Dicymbe jenmanii</i> (black bars) at the Pegaima savanna site, Upper Mazaruni Basin, Guyana.

<p>Each of these common fungal species occurred on three or more individual trees; 20 trees were sampled for each of the host tree species. Species that showed a significantly different distribution on the two host plants (as assessed by Fischer’s Exact test) are indicated by asterisks. Fungal species that have never been found in previous ECM sporocarp or root surveys in nearby rainforest sites are designated by black circles. All other ECM fungal species have been found previously in association with species of <i>Dicymbe</i> and <i>Aldina</i> at other locations. Named fungal species are indicated by a genus and species binomial whereas species with TH or MCA numbers were matched to voucher specimens of undescribed species identified to genus. The ECM numbers correspond to fungal species known only from ECM root sequences.</p

Cantharellaceae of guyana ii. new species of craterellus, new south american distribution records for cantharellus guyanensis and craterellus excelsus, and a key to the neotropical taxa

International audienceCraterellus olivaceoluteus sp. nov. and Craterellus cinereofimbriatus sp. nov. are described as new to science. These fungi were collected from Guyana in association with ectomycorrhizal host trees in the genera Dicymbe (Fabaceae subfam. Caesalpinioideae) and Pakaraimaea (Dipterocarpaceae). Cantharellus guyanensis Mont., originally described from French Guiana, is redescribed from recent collections from Guyana, with additional range extensions for the species provided based on material examined from French Guiana, Venezuela, and north central, northeastern and southern Brazil, circumscribing nearly the entire Guiana Shield region and beyond. A new distribution record from French Guiana is provided for Craterellus excelsus T.W. Henkel & Aime. Macromorphological, micromorphological and habitat data are provided for the new species and C. guyanensis as well as DNA sequence data from the nuclear ribosomal regions of the internal transcribed spacer (ITS) and 28S large subunit (LSU); additional sequence data is provided for C. guyanensis and C. excelsus specimens collected outside Guyana. The relationships of these taxa within the Cantharellaceae were evaluated with phylogenetic analyses of ITS and LSU sequence data. This work brings the total number of Cantharellaceae species known from Guyana to eight. A key to the Cantharellus and Craterellus species known from the lowland Neotropics and extralimital montane Central and South America is provided