Dataset Information

Taxonomy and phylogeny of Resinicium sensu lato from Asia-Pacific revealing a new genus and five new species (Hymenochaetales, Basidiomycota).

ABSTRACT: Resinicium, belonging to Hymenochaetales, Agaricomycetes, is a worldwide genus of corticioid wood-inhabiting fungi. To improve the knowledge of species diversity within the Hymenochaetales, two dozen specimens from Asia-Pacific preliminarily identified to be members of Resinicium sensu lato were carefully studied from morphological and phylogenetic perspectives. From these specimens, a new monotypic genus Skvortzoviella, and five new species, viz. Resinicium austroasianum, R. lateastrocystidium, Skvortzovia dabieshanensis, S. qilianensis and Skvortzoviella lenis are described; moreover, a new basal lineage of Resinicium represented by a Vietnam specimen and three Chinese specimens of S. pinicola are identified. The six newly proposed taxa are morphologically compared with related genera and species, while the family positions of Resinicium, Skvortzovia, and Skvortzoviella within the Hymenochaetales are still ambiguous. In addition, the ancestral geographic origin of Resinicium, even though inconclusive, is now thought to be Asia-Pacific instead of tropical America as previously assumed.

SUBMITTER: Yu J

PROVIDER: S-EPMC8287719 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Taxonomy and phylogeny of Resinicium sensu lato from Asia-Pacific revealing a new genus and five new species (Hymenochaetales, Basidiomycota).

Yu Jia J Wang Xue-Wei XW Liu Shi-Liang SL Shen Shan S Zhou Li-Wei LW

IMA fungus 20210719 1

Resinicium, belonging to Hymenochaetales, Agaricomycetes, is a worldwide genus of corticioid wood-inhabiting fungi. To improve the knowledge of species diversity within the Hymenochaetales, two dozen specimens from Asia-Pacific preliminarily identified to be members of Resinicium sensu lato were carefully studied from morphological and phylogenetic perspectives. From these specimens, a new monotypic genus Skvortzoviella, and five new species, viz. Resinicium austroasianum, R. lateastrocystidium, ...[more]

PMID: 34275495

Similar Datasets

Project description:Five new wood-inhabiting fungi, Lyomycesalbopulverulentus, L.yunnanensis, Xylodondaweishanensis, X.fissuratus, and X.puerensisspp. nov., are proposed based on a combination of morphological features and molecular evidence. Lyomycesalbopulverulentus is characterized by brittle basidiomata, pruinose hymenophore with a white hymenial surface, a monomitic hyphal system with clamped generative hyphae, and ellipsoid basidiospores. Lyomycesyunnanensis is characterized by a grandinioid hymenial surface, the presence of capitate cystidia, and ellipsoid basidiospores. Xylodondaweishanensis is characterized by an odontioid hymenial surface, a monomitic hyphal system with clamped generative hyphae, and broad ellipsoid-to-subglobose basidiospores. Xylodonfissuratus is characterized by a cracking basidiomata with a grandinioid hymenial surface, and ellipsoid basidiospores. Xylodonpuerensis is characterized by a poroid hymenophore with an angular or slightly daedaleoid configuration, and ellipsoid-to-broad-ellipsoid basidiospores. Sequences of ITS and nLSU rRNA markers of the studied samples were generated and phylogenetic analyses were performed with the maximum likelihood, maximum parsimony, and Bayesian inference methods. The phylogram based on the ITS+nLSU rDNA gene regions (Fig. 1) included six genera within the families Chaetoporellaceae, Hyphodontiaceae, Hymenochaetaceae, and Schizoporaceae (Hymenochaetales)-Fasciodontia, Hastodontia, Hyphodontia, Kneifiella, Lyomyces, and Xylodon-in which the five new species were grouped into genera Lyomyces and Xylodon. The phylogenetic tree inferred from the ITS sequences highlighted that Lyomycesalbopulverulentus formed a monophyletic lineage and was then grouped closely with L.bambusinus, L.orientalis, and L.sambuci; additionally, L.yunnanensis was sister to L.niveus with strong supports. The topology, based on the ITS sequences, revealed that Xylodondaweishanensis was retrieved as a sister to X.hyphodontinus; X.fissuratus was grouped with the four taxa X.montanus, X.subclavatus, X.wenshanensis, and X.xinpingensis; and X.puerensis was clustered with X.flaviporus, X.ovisporus, X.subflaviporus, X.subtropicus, and X.taiwanianus.

Project description:Hyphodontia sensu lato, belonging to Hymenochaetales, accommodates corticioid wood-inhabiting basidiomycetous fungi with resupinate basidiocarps and diverse hymenophoral characters. Species diversity of Hyphodontia sensu lato has been extensively explored worldwide, but in previous studies the six accepted genera in Hyphodontia sensu lato, viz. Fasciodontia, Hastodontia, Hyphodontia, Kneiffiella, Lyomyces and Xylodon were not all strongly supported from a phylogenetic perspective. Moreover, the relationships among these six genera in Hyphodontia sensu lato and other lineages within Hymenochaetales are not clear. In this study, we performed comprehensive phylogenetic analyses on the basis of multiple loci. For the first time, the independence of each of the six genera receives strong phylogenetic support. The six genera are separated in four clades within Hymenochaetales: Fasciodontia, Lyomyces and Xylodon are accepted as members of a previously known family Schizoporaceae, Kneiffiella and Hyphodontia are, respectively, placed in two monotypic families, viz. a previous name Chaetoporellaceae and a newly introduced name Hyphodontiaceae, and Hastodontia is considered to be a genus with an uncertain taxonomic position at the family rank within Hymenochaetales. The three families emerged between 61.51 and 195.87 million years ago. Compared to other families in the Hymenochaetales, these ages are more or less similar to those of Coltriciaceae, Hymenochaetaceae and Oxyporaceae, but much older than those of the two families Neoantrodiellaceae and Nigrofomitaceae. In regard to species, two, one, three and 10 species are newly described from Hyphodontia, Kneiffiella, Lyomyces and Xylodon, respectively. The taxonomic status of additional 30 species names from these four genera is briefly discussed; an epitype is designated for X. australis. The resupinate habit and poroid hymenophoral configuration were evaluated as the ancestral state of basidiocarps within Hymenochaetales. The resupinate habit mainly remains, while the hymenophoral configuration mainly evolves to the grandinioid-odontioid state and also back to the poroid state at the family level. Generally, a taxonomic framework for Hymenochaetales with an emphasis on members belonging to Hyphodontia sensu lato is constructed, and trait evolution of basidiocarps within Hymenochaetales is revealed accordingly.

Project description:BackgroundBacillus cereus sensu lato (s. l.) is an ecologically diverse bacterial group of medical and agricultural significance. In this study, I use publicly available genomes and novel bioinformatic workflows to characterize the B. cereus s. l. pan-genome and perform the largest phylogenetic and population genetic analyses of this group to date in terms of the number of genes and taxa included. With these fundamental data in hand, I identify genes associated with particular phenotypic traits (i.e., "pan-GWAS" analysis), and quantify the degree to which taxa sharing common attributes are phylogenetically clustered.MethodsA rapid k-mer based approach (Mash) was used to create reduced representations of selected Bacillus genomes, and a fast distance-based phylogenetic analysis of this data (FastME) was performed to determine which species should be included in B. cereus s. l. The complete genomes of eight B. cereus s. l. species were annotated de novo with Prokka, and these annotations were used by Roary to produce the B. cereus s. l. pan-genome. Scoary was used to associate gene presence and absence patterns with various phenotypes. The orthologous protein sequence clusters produced by Roary were filtered and used to build HaMStR databases of gene models that were used in turn to construct phylogenetic data matrices. Phylogenetic analyses used RAxML, DendroPy, ClonalFrameML, PAUP*, and SplitsTree. Bayesian model-based population genetic analysis assigned taxa to clusters using hierBAPS. The genealogical sorting index was used to quantify the phylogenetic clustering of taxa sharing common attributes.ResultsThe B. cereus s. l. pan-genome currently consists of ≈60,000 genes, ≈600 of which are "core" (common to at least 99% of taxa sampled). Pan-GWAS analysis revealed genes associated with phenotypes such as isolation source, oxygen requirement, and ability to cause diseases such as anthrax or food poisoning. Extensive phylogenetic analyses using an unprecedented amount of data produced phylogenies that were largely concordant with each other and with previous studies. Phylogenetic support as measured by bootstrap probabilities increased markedly when all suitable pan-genome data was included in phylogenetic analyses, as opposed to when only core genes were used. Bayesian population genetic analysis recommended subdividing the three major clades of B. cereus s. l. into nine clusters. Taxa sharing common traits and species designations exhibited varying degrees of phylogenetic clustering.ConclusionsAll phylogenetic analyses recapitulated two previously used classification systems, and taxa were consistently assigned to the same major clade and group. By including accessory genes from the pan-genome in the phylogenetic analyses, I produced an exceptionally well-supported phylogeny of 114 complete B. cereus s. l. genomes. The best-performing methods were used to produce a phylogeny of all 498 publicly available B. cereus s. l. genomes, which was in turn used to compare three different classification systems and to test the monophyly status of various B. cereus s. l. species. The majority of the methodology used in this study is generic and could be leveraged to produce pan-genome estimates and similarly robust phylogenetic hypotheses for other bacterial groups.

Dataset Information

Taxonomy and phylogeny of Resinicium sensu lato from Asia-Pacific revealing a new genus and five new species (Hymenochaetales, Basidiomycota).

Publications

Taxonomy and phylogeny of Resinicium sensu lato from Asia-Pacific revealing a new genus and five new species (Hymenochaetales, Basidiomycota).

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets