Zheng Wang - Academia.edu (original) (raw)

Papers by Zheng Wang

Research paper thumbnail of Future Perspectives and Challenges of Fungal Systematics in the Age of Big Data

Fungal Biology, 2016

Mycological research, especially research on fungal evolution and ecology, requires a robust and ... more Mycological research, especially research on fungal evolution and ecology, requires a robust and detailed fungal classification and phylogeny to facilitate efficient and informative communication among mycologists as well as for comparative biology relevant to the larger bioscience community. The field of fungal systematics has undergone numerous revisions recently, from early morphological classifications to an integrative taxonomy that is increasingly reliant on molecular phylogeny. These revisions have taken place at a range of taxonomic ranks, fueled by advances surmounting two major challenges, namely, adequate and balanced sampling of genetic markers and taxa and reinterpretation of phylogenetic informativeness of numerous morphological and ecological characters. The Assembling the Fungal Tree of Life (AFTOL) projects reflected a corresponding surge of collaborative effort in fungal molecular phylogeny using PCR and Sanger sequencing. Here we review recent progress in fungal systematics after AFTOL, in the post-Sanger age, and discuss the future fungal systematics that is emerging as a result of the extraordinary volume of data being gathered by high-throughput sequencing. We examine how environmental DNA surveys, sequence-based classification, and phylogenomics and phylotranscriptomics can impact fungal systematics and point out that sequenced fungal genomes could significantly improve multi-marker phylogenetic inference at a range of levels of fungal systematics by facilitating application of phylogenetically informative experimental design. We argue that it is time to integrate fungal systematics, genome-enabled mycology, and other dimensions of fungal research within the framework of evolutionary biology.

Research paper thumbnail of Another Fossil Agaric from Dominican Amber

Research paper thumbnail of Evolution of helotialean fungi (Leotiomycetes, Pezizomycotina): a nuclear rDNA phylogeny

Molecular phylogenetics and evolution, 2006

The highly divergent characters of morphology, ecology, and biology in the Helotiales make it one... more The highly divergent characters of morphology, ecology, and biology in the Helotiales make it one of the most problematic groups in traditional classification and molecular phylogeny. Sequences of three rDNA regions, SSU, LSU, and 5.8S rDNA, were generated for 50 helotialean fungi, representing 11 out of 13 families in the current classification. Data sets with different compositions were assembled, and parsimony and Bayesian analyses were performed. The phylogenetic distribution of lifestyle and ecological factors was assessed. Plant endophytism is distributed across multiple clades in the Leotiomycetes. Our results suggest that (1) the inclusion of LSU rDNA and a wider taxon sampling greatly improves resolution of the Helotiales phylogeny, however, the usefulness of rDNA in resolving the deep relationships within the Leotiomycetes is limited; (2) a new class Geoglossomycetes, including Geoglossum, Trichoglossum, and Sarcoleotia, is the basal lineage of the Leotiomyceta; (3) the Le...

Research paper thumbnail of Mycology: An International Journal on Fungal Biology

Research paper thumbnail of <I>Geoglossomycetes</I> cl. nov., <I>Geoglossales</I> ord. nov. and taxa above class rank in the <I>Ascomycota</I> Tree of Life

Persoonia - Molecular Phylogeny and Evolution of Fungi, 2009

Research paper thumbnail of Reconstructing the early evolution of Fungi using a six-gene phylogeny

Research paper thumbnail of Phylogeny and a new species of Sparassis (Polyporales, Basidiomycota): evidence from mitochondrial atp6, nuclear rDNA and rpb2 genes

Research paper thumbnail of A New Species of Cudonia Based on Morphological and Molecular Data

Research paper thumbnail of Phylogenetic Relationships of Sparassis Inferred from Nuclear and Mitochondrial Ribosomal DNA and RNA Polymerase Sequences

Research paper thumbnail of Sparassis cystidiosa sp. nov. from Thailand Is Described Using Morphological and Molecular Data

Research paper thumbnail of Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi)

Molecular Phylogenetics and Evolution, 2007

Research paper thumbnail of Northern species of earth tongue genus Thuemenidium revisited, considering morphology, ecology and molecular phylogeny

Mycologia

Thuemenidium is a small earth tongue genus with three recognized white-spored species. Within Thu... more Thuemenidium is a small earth tongue genus with three recognized white-spored species. Within Thuemenidium, T. atropurpureum and T. arenarium have been reported only from the northern hemisphere while T. berteroi is known solely in the southern hemisphere. We reviewed the ecology, examined the morphology and inferred the systematic positions of northern species of Thuemenidium from LSU-rDNA gene phylogeny of 48 taxa in Pezizomycotina including recent collections. Our results suggest that Thuemenidium in its current sense is polyphyletic and that T. atropurpureum, closely related to Microglossum and Leotia species, is a member of Leotiaceae (Helotiales, Leotiomycetes). Our phylogeny placed the other northern species, T. arenarium, in Geoglossaceae (Geoglossales, Geoglossomycetes), retaining genus Thuemenidium, pending further investigation.

Research paper thumbnail of Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data

PloS one, Jan 21, 2011

An abundance of novel fungal lineages have been indicated by DNA sequencing of the nuclear riboso... more An abundance of novel fungal lineages have been indicated by DNA sequencing of the nuclear ribosomal ITS region from environmental samples such as soil and wood. Although phylogenetic analysis of these novel lineages is a key component of unveiling the structure and diversity of complex communities, such analyses are rare for environmental ITS data due to the difficulties of aligning this locus across significantly divergent taxa. One potential approach to this issue is simultaneous alignment and tree estimation. We targeted divergent ITS sequences of the earth tongue fungi (Geoglossomycetes), a basal class in the Ascomycota, to assess the performance of SATé, recent software that combines progressive alignment and tree building. We found that SATé performed well in generating high-quality alignments and in accurately estimating the phylogeny of earth tongue fungi. Drawing from a data set of 300 sequences of earth tongues and progressively more distant fungal lineages, 30 insufficie...

Research paper thumbnail of A new Sparassis species from Spain described using morphological and molecular data

Mycological Research, 2006

Research paper thumbnail of A higher-level phylogenetic classification of the Fungi

Mycological Research, 2007

Research paper thumbnail of Multi-targeted priming for genome-wide gene expression assays

BMC Genomics, 2010

Background Complementary approaches to assaying global gene expression are needed to assess gene ... more Background Complementary approaches to assaying global gene expression are needed to assess gene expression in regions that are poorly assayed by current methodologies. A key component of nearly all gene expression assays is the reverse transcription of transcribed sequences that has traditionally been performed by priming the poly-A tails on many of the transcribed genes in eukaryotes with oligo-dT, or by priming RNA indiscriminately with random hexamers. We designed an algorithm to find common sequence motifs that were present within most protein-coding genes of Saccharomyces cerevisiae and of Neurospora crassa, but that were not present within their ribosomal RNA or transfer RNA genes. We then experimentally tested whether degenerately priming these motifs with multi-targeted primers improved the accuracy and completeness of transcriptomic assays. Results We discovered two multi-targeted primers that would prime a preponderance of genes in the genomes of Saccharomyces cerevisiae ...

Research paper thumbnail of Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets

Antonie van Leeuwenhoek, 2011

Research paper thumbnail of Evolutionary relationships of Mycaureola dilseae (Agaricales), a basidiomycete pathogen of a subtidal rhodophyte

American Journal of Botany, 2006

Research paper thumbnail of Life history and systematics of the aquatic discomycete Mitrula (Helotiales, Ascomycota) based on cultural, morphological, and molecular studies

American Journal of Botany, 2005

Research paper thumbnail of The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits

Systematic biology, 2009

We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum o... more We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive...

Research paper thumbnail of Future Perspectives and Challenges of Fungal Systematics in the Age of Big Data

Fungal Biology, 2016

Mycological research, especially research on fungal evolution and ecology, requires a robust and ... more Mycological research, especially research on fungal evolution and ecology, requires a robust and detailed fungal classification and phylogeny to facilitate efficient and informative communication among mycologists as well as for comparative biology relevant to the larger bioscience community. The field of fungal systematics has undergone numerous revisions recently, from early morphological classifications to an integrative taxonomy that is increasingly reliant on molecular phylogeny. These revisions have taken place at a range of taxonomic ranks, fueled by advances surmounting two major challenges, namely, adequate and balanced sampling of genetic markers and taxa and reinterpretation of phylogenetic informativeness of numerous morphological and ecological characters. The Assembling the Fungal Tree of Life (AFTOL) projects reflected a corresponding surge of collaborative effort in fungal molecular phylogeny using PCR and Sanger sequencing. Here we review recent progress in fungal systematics after AFTOL, in the post-Sanger age, and discuss the future fungal systematics that is emerging as a result of the extraordinary volume of data being gathered by high-throughput sequencing. We examine how environmental DNA surveys, sequence-based classification, and phylogenomics and phylotranscriptomics can impact fungal systematics and point out that sequenced fungal genomes could significantly improve multi-marker phylogenetic inference at a range of levels of fungal systematics by facilitating application of phylogenetically informative experimental design. We argue that it is time to integrate fungal systematics, genome-enabled mycology, and other dimensions of fungal research within the framework of evolutionary biology.

Research paper thumbnail of Another Fossil Agaric from Dominican Amber

Research paper thumbnail of Evolution of helotialean fungi (Leotiomycetes, Pezizomycotina): a nuclear rDNA phylogeny

Molecular phylogenetics and evolution, 2006

The highly divergent characters of morphology, ecology, and biology in the Helotiales make it one... more The highly divergent characters of morphology, ecology, and biology in the Helotiales make it one of the most problematic groups in traditional classification and molecular phylogeny. Sequences of three rDNA regions, SSU, LSU, and 5.8S rDNA, were generated for 50 helotialean fungi, representing 11 out of 13 families in the current classification. Data sets with different compositions were assembled, and parsimony and Bayesian analyses were performed. The phylogenetic distribution of lifestyle and ecological factors was assessed. Plant endophytism is distributed across multiple clades in the Leotiomycetes. Our results suggest that (1) the inclusion of LSU rDNA and a wider taxon sampling greatly improves resolution of the Helotiales phylogeny, however, the usefulness of rDNA in resolving the deep relationships within the Leotiomycetes is limited; (2) a new class Geoglossomycetes, including Geoglossum, Trichoglossum, and Sarcoleotia, is the basal lineage of the Leotiomyceta; (3) the Le...

Research paper thumbnail of Mycology: An International Journal on Fungal Biology

Research paper thumbnail of <I>Geoglossomycetes</I> cl. nov., <I>Geoglossales</I> ord. nov. and taxa above class rank in the <I>Ascomycota</I> Tree of Life

Persoonia - Molecular Phylogeny and Evolution of Fungi, 2009

Research paper thumbnail of Reconstructing the early evolution of Fungi using a six-gene phylogeny

Research paper thumbnail of Phylogeny and a new species of Sparassis (Polyporales, Basidiomycota): evidence from mitochondrial atp6, nuclear rDNA and rpb2 genes

Research paper thumbnail of A New Species of Cudonia Based on Morphological and Molecular Data

Research paper thumbnail of Phylogenetic Relationships of Sparassis Inferred from Nuclear and Mitochondrial Ribosomal DNA and RNA Polymerase Sequences

Research paper thumbnail of Sparassis cystidiosa sp. nov. from Thailand Is Described Using Morphological and Molecular Data

Research paper thumbnail of Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi)

Molecular Phylogenetics and Evolution, 2007

Research paper thumbnail of Northern species of earth tongue genus Thuemenidium revisited, considering morphology, ecology and molecular phylogeny

Mycologia

Thuemenidium is a small earth tongue genus with three recognized white-spored species. Within Thu... more Thuemenidium is a small earth tongue genus with three recognized white-spored species. Within Thuemenidium, T. atropurpureum and T. arenarium have been reported only from the northern hemisphere while T. berteroi is known solely in the southern hemisphere. We reviewed the ecology, examined the morphology and inferred the systematic positions of northern species of Thuemenidium from LSU-rDNA gene phylogeny of 48 taxa in Pezizomycotina including recent collections. Our results suggest that Thuemenidium in its current sense is polyphyletic and that T. atropurpureum, closely related to Microglossum and Leotia species, is a member of Leotiaceae (Helotiales, Leotiomycetes). Our phylogeny placed the other northern species, T. arenarium, in Geoglossaceae (Geoglossales, Geoglossomycetes), retaining genus Thuemenidium, pending further investigation.

Research paper thumbnail of Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data

PloS one, Jan 21, 2011

An abundance of novel fungal lineages have been indicated by DNA sequencing of the nuclear riboso... more An abundance of novel fungal lineages have been indicated by DNA sequencing of the nuclear ribosomal ITS region from environmental samples such as soil and wood. Although phylogenetic analysis of these novel lineages is a key component of unveiling the structure and diversity of complex communities, such analyses are rare for environmental ITS data due to the difficulties of aligning this locus across significantly divergent taxa. One potential approach to this issue is simultaneous alignment and tree estimation. We targeted divergent ITS sequences of the earth tongue fungi (Geoglossomycetes), a basal class in the Ascomycota, to assess the performance of SATé, recent software that combines progressive alignment and tree building. We found that SATé performed well in generating high-quality alignments and in accurately estimating the phylogeny of earth tongue fungi. Drawing from a data set of 300 sequences of earth tongues and progressively more distant fungal lineages, 30 insufficie...

Research paper thumbnail of A new Sparassis species from Spain described using morphological and molecular data

Mycological Research, 2006

Research paper thumbnail of A higher-level phylogenetic classification of the Fungi

Mycological Research, 2007

Research paper thumbnail of Multi-targeted priming for genome-wide gene expression assays

BMC Genomics, 2010

Background Complementary approaches to assaying global gene expression are needed to assess gene ... more Background Complementary approaches to assaying global gene expression are needed to assess gene expression in regions that are poorly assayed by current methodologies. A key component of nearly all gene expression assays is the reverse transcription of transcribed sequences that has traditionally been performed by priming the poly-A tails on many of the transcribed genes in eukaryotes with oligo-dT, or by priming RNA indiscriminately with random hexamers. We designed an algorithm to find common sequence motifs that were present within most protein-coding genes of Saccharomyces cerevisiae and of Neurospora crassa, but that were not present within their ribosomal RNA or transfer RNA genes. We then experimentally tested whether degenerately priming these motifs with multi-targeted primers improved the accuracy and completeness of transcriptomic assays. Results We discovered two multi-targeted primers that would prime a preponderance of genes in the genomes of Saccharomyces cerevisiae ...

Research paper thumbnail of Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets

Antonie van Leeuwenhoek, 2011

Research paper thumbnail of Evolutionary relationships of Mycaureola dilseae (Agaricales), a basidiomycete pathogen of a subtidal rhodophyte

American Journal of Botany, 2006

Research paper thumbnail of Life history and systematics of the aquatic discomycete Mitrula (Helotiales, Ascomycota) based on cultural, morphological, and molecular studies

American Journal of Botany, 2005

Research paper thumbnail of The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits

Systematic biology, 2009

We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum o... more We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive...