
Rui-Lin ZhaoInstitute of Microbiology, Chinese Academy of Sciences
Rui-Lin Zhao
PhD
About
194
Publications
218,062
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
7,892
Citations
Introduction
My research team focus on:
Basidiomycota systematics (taxonomy); mushroom evolutionary genomics; evolutionary biology.
Publications
Publications (194)
The Qinghai-Xizang Plateau, known for its high altitude, geological history of plate collision, crustal uplift, and special ecology factors, provides an ideal environment for studying fungal biodiversity in extreme environmental conditions. Some species within the Conocybe, containing secondary metabolites such as psilocybin, phallotoxins, and amat...
Abstract: Novel species of fungi described in this study include those from various countries as follows: Antarctica, Leuconeurospora bharatiensis from accumulated snow sediment sample. Argentina, Pseudocercospora quetri on leaf spots of Luma apiculata. Australia, Polychaetomyces verrucosus on submerged decaying wood in sea water, Ustilaginoidea co...
Horizontal gene transfer (HGT) in fungi is less understood despite its significance in prokaryotes. In this study, we systematically searched for HGT events in 829 representative fungal genomes. Using a combination of sequence similarity and phylogeny-based approaches, we detected 20,093 prokaryotic-derived transferred genes across 750 fungal genom...
With the simultaneous growth in interest from the mycological community to discover fungal species and classify them, there is also an important need to assemble all taxonomic information onto common platforms. Fungal classification is facing a rapidly evolving landscape and organizing genera into an appropriate taxonomic hierarchy is central to be...
The members of Lycoperdaceae, commonly known as puffballs, are widely distributed as saprotrophic fungi. The current taxonomic system of this family has been extensively debated, primarily due to conflicts between morphological based system and the phylogenetics one. In this study, we reconstructed a comprehensive phylogeny of Lycoperdaceae, repres...
Fungi are one of the most diverse groups of organisms with an estimated number of species in the range of 2–3 million. The higher-level ranking of fungi has been discussed in the framework of molecular phylogenetics since Hibbett et al., and the definition and the higher ranks (e.g., phyla) of the ‘true fungi’ have been revised in several subsequen...
Guotao Chen Guohui Shi Yi Dai- [...]
Qi Wu
The “cost of domestication” hypothesis suggests that the domestication of wild species increases the number, frequency, and/or proportion of deleterious genetic variants, potentially reducing their fitness in the wild. While extensively studied in domesticated species, this phenomenon remains understudied in fungi. Here, we used Saccharomyces cerev...
Based on phylogenetic analysis, Candolleomyces (Psathyrellaceae, Agaricales) was established with Psathyrella candolleana as the type species. The basidiomes range from small to large and are typically terrestrial, lignicolous, and rarely fimicolous. We analysed the Candolleomyces species collected during five years in China, and based on morpholog...
The global diversity of fungi has been estimated between 2 to 11 million species, of which only about 155 000 have been named. Most fungi are
invisible to the unaided eye, but they represent a major component of biodiversity on our planet, and play essential ecological roles, supporting life as we
know it. Although approximately 20 000 fungal gener...
Basidiomycota is one of the major phyla in the fungal tree of life. The outline of Basidiomycota provides essential taxonomic information for researchers and workers in mycology. In this study, we present a time-framed phylogenomic tree with 487 species of Basidiomycota from 127 families, 47 orders, 14 classes and four subphyla; we update the outli...
The species of Gymnopilus (Hymenogastraceae, Agricales) are commonly recognized as wood-decaying fungi. Certain members of this genus have been identified as psilocybin-producing mushrooms. Gymnopilus exhibits a diverse range and has a global distribution. In this study, a total of seventy-eight specimens were gathered from ten provinces in China....
The Global Consortium for the Classification of Fungi and fungus-like taxa is an international initiative of more than 550 mycologists to develop an electronic structure for the classification of these organisms. The members of the Consortium originate from 55 countries/regions worldwide, from a wide range of disciplines, and include senior, mid-ca...
Russula is the largest genus in the Russulales and is widespread throughout the world. Almost all Russula species are known to be ectomycorrhizal with high ecological and edible values, and some are lethal poisonous. In this study, four new species belonging to the subgenus Russula crown clade are identified based on morphological and phylogenetic...
Cyclocybe encompasses 12 species which are distributed worldwide. In this study, two new species named C. suberebia and C. dinggyensis are introduced from China. Phylogenetic analyses based on nrITS, nrLSU, tef1-α, and rpb2 data show their placement within Cyclocybe in two distinct lineages. Cyclocybe suberebia is characterized by its dark brown to...
Macrofungi are well known as mushrooms, which belong mostly to Basidiomycota with a few from Ascomycota, and up to now, around 40,000 species have been described. In people’s lives, macrofungi are closely related to our economic activities, especially for food and medicine. “One meat, one vegetable and one mushroom” has become a healthy and fashion...
Agaricus bisporus (J.E. Lange) Imbach; Agaricus campestris L.; Agaricus xanthodermus Genev. - AGARICACEAE
. Yusufjon Gafforov, Mustafa Yamaç, Milena Rašeta, Sylvie Rapior, Mustafa Sevindik, Rui-Lin Zhao , Samantha Chandranath Karunarathna, Manzura Yarasheva et Soumya Ghosh.
Agaricus bisporus (J.E. Lange) Imbach; Agaricus campestris L.; Agaricus xa...
Helvella lacunosa and its allies are widely distributed in the Northern Hemisphere and perform important functions in ecosystems. A comprehensive study on 101 collections of Helvella lacunosa, including those deposited in four Chinese fungaria or collected recently from 10 provinces, was conducted based on morphological and molecular characteristic...
The Shaluli Mountains are located in the southeastern part of the Tibetan Plateau at an elevation of 2500-5000 m. They are characterized by a typical vertical distribution of climate and vegetation and are considered a global biodiversity hotspot. We selected ten vegetation types at different elevation gradients representing distinct forests in the...
Agaricus bisporus is the most widely cultivated edible mushroom in the world with a only around three hundred years known history of cultivation. Therefore, it represents an ideal organism not only to investigate the natural evolutionary history but also the understanding on the evolution going back to the early era of domestication. In this study,...
The species of Agrocybe (Strophariaceae, Agaricales, Agaricomycetes) are saprophytic and widely distributed in temperate regions. In this study, a new species named Agrocybe striatipes from China is described, which has been successfully cultivated in China recently. The phenotypic characteristics examination and molecular phylogenetic analyses usi...
The enoki mushroom (Flammulina filiformis) is one of the most important and popular edible mushrooms commercially in China. However, traditional mushroom cultivar identification is challenging due to poor accuracy, heavy workloads, and low reproducibility. To overcome this challenge, we developed a method for identifying F. filiformis strains using...
Animal meat is one of the major, high-quality protein sources in human food. The rapid economic development is accompanied by increasing demand for meat, which puts pressure on the global meat supply but also gives room for the development of the meat substitute market. Edible mushrooms are high in protein, rich in nutrients, and do not require lar...
Agaricus sinodeliciosus is a rare wild edible mushroom from northwest China, and grows naturally in mild saline-alkali soil, which is also unusual in mushrooms. A. sinodeliciosus represents a potential model organism for explaining saline-alkali tolerance mechanisms and revealing related physiological processes in mushrooms. Here, we provide a high...
Lentinula edodes (shiitake in Japanese, xiang-gu in Chinese) is the most productive mushroom in China, and there are more than 500 cultivars names. However, the traditional identification of mushroom cultivars can be challenging due to the problems of the heavy workload, insufficient accuracy and low reproducibility, which greatly affect the indust...
The shiitake mushroom ( Lentinus edodes ) is the second most popular edible mushroom globally due to its rich nutritional value and health benefits associated with consumption. However, the characteristics of growing at low temperatures limit the area and time of its cultivating. We selected a low-temperature cultivar as the original strain. We pro...
The genus Omphalina is an ideal genus for studying the evolutionary mechanism of lichenization. Based on molecular phylogeny using ITS and nuLSU sequences by means of Bayesian and maximum likelihood analyses and morphological examination, combining the existence of green algae in basidiomata stipe and a Botrydina-type vegetative thallus, we describ...
Mushrooms have long been considered as delicacies as well as used as important dietary supplements and food. However, there are major concerns with poisonous mushrooms as these pose threats to public health and safety. In this paper, we provide a review focusing on poisonous mushrooms, their toxins, symptoms and utilizations. In addition, this pape...
Taxonomy plays an important role in understanding the origin, evolution, and
ecological functionality of biodiversity. There are large number of unknown species yet to be described by taxonomists, which together with their ecosystem services cannot be effectively protected prior to description. Despite this, taxonomy has been increasingly underrat...
The Greater Mekong Sub-region (GMS) is a global biodiversity hotspot and habitat for many ecologically and economically important mushrooms species. The diversity of mushrooms in the GMS has been studied and published in different journals, and many have been documented from different countries in the GMS region but data remain mostly fragmented. A...
High‐throughput sequencing has substantially improved our understanding of fungal diversity. However, the short read (<500 bp) length of current second‐generation sequencing approaches provides limited taxonomic and phylogenetic resolution for species discrimination. Longer sequences containing more information are highly desired to provide greater...
Pleurotus placentodes, a fungus, belongs to the Pleurotaceae family. The aim of the present study was to characterize the structure of a novel polysaccharide from fruiting bodies of P. placentodes (PPp-W) and evaluate its anticoagulant activity in vitro. The high-performance liquid chromatography and GC–MS analysis indicated that PPp-W with a molec...
Fungi are eukaryotes that play essential roles in ecosystems. Among fungi, Basidiomycota is one of the major phyla with more than 40,000 described species. We review species diversity of Basidiomycota from five groups with different lifestyles or habitats: saprobic in grass/forest litter, wood-decaying, yeast-like, ectomycorrhizal, and plant parasi...
As an indispensable essential amino acid in the human body, lysine is extremely rich in edible mushrooms. The α-aminoadipic acid (AAA) pathway is regarded as the biosynthetic pathway of lysine in higher fungal species in Agaricomycetes. However, there is no deep understanding about the molecular evolutionary relationship between lysine biosynthesis...
Cystoderma comprises the species with heavily universal veil remnants on basidiomes, weakly to strongly amyloid basidiospores, evanescent floccose-scaly ring zone or persistent membranous ring, which were often encountered in forests and grassland. However, they were less studied than other mushroom groups mainly because of its unclearly phylogenet...
Edible mushrooms are important nutraceutical sources of foods and drugs, which can produce various nutritional ingredients including all essential amino acids. The method of rapid screening for the strains producing specific functional components is very indispensable. Homocitrate synthase is one of the key enzymes in the α-aminoadipate pathway for...
Basidiomycota constitute a major phylum of the kingdom Fungi, distributed in 4 subphyla, 18 classes, 68 orders and 241 families. Advances in molecular phylogeny over the past years have resulted in numerous changes to their classification at a rapid pace. Consequently, a vast amount of taxonomic information is available in many publications. The we...
Species delimitation is one of the most fundamental processes in biology. Biodiversity undertakings, for instance, require explicit species concepts and criteria for species delimitation in order to be relevant and translatable. However, a perfect species concept does not exist for Fungi. Here, we review the species concepts commonly used in Basidi...
Species diversity of Micropsalliota in China remains poorly known, especially in southwestern China, a hotspot of biodiversity. Based on morphological characteristics and molecular phylogenetic analyses using ITS and nrLSU sequences, three new species named Micropsalliota delicatula, M. dentatomarginata and M. digitatocystis are introduced from Chi...
Agaricus subgenus Spissicaules is widely distributed in the world. In this study, 114 specimens were included in multigene phylogenetic analyses that allowed a better circumscription of the four sections in A. subg. Spissicaules. Three new species from China, A. brunneovariabilis, A. beijingensis, and A. planiceps, are described and placed in diffe...
s
Basidiomycota is a major lineage of fungi embracing more than 40,000 species which takes nearly 1/3 fungal species. It comprises important groups like mushrooms, plant pathogenetic smut, rust and industrial important yeast. Species of Basidiomycota also play essential roles in ecosystem participating in the cycling of nutrients. Based on the adva...
Fungi have a worldwide distribution, however, less than 10% of the estimated species have
Agaricus sect. Arvenses includes numerous species that are potential candidates for cultivation, and some have high nutritional and medicinal interests. Between 2012 and 2017, 147 specimens of A. sect. Arvenses were collected in China. For this study, nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS), nuc 28S rDNA (28S), and translat...
A chemical investigation on the fruiting bodies of Fomitopsis pinicola led to the isolation and identification of twenty eight lanostane triterpenoids including eleven new compounds (1-11) and seventeen known analogues (12-28). Their structures were elucidated by extensive 1D, 2D NMR, and MS spectra. All isolates were tested for their anti-inflamma...
This article is the ninth in the series of Fungal Diversity Notes, where 107 taxa distributed in three phyla, nine classes, 31
orders and 57 families are described and illustrated. Taxa described in the present study include 12 new genera, 74 new
species, three new combinations, two reference specimens, a re-circumscription of the epitype, and 15 r...
Micropsalliota embraces approximately 70 species which are mainly distributed in tropical and subtropical areas. In this study, two new species named Micropsalliota albella and M. purpureobrunneola are introduced from northern Thailand. Phylogenetic analyses based on ITS and LSU data shows their placement in Micropsalliota in two distinct lineages....
Agaricus section Agaricus is generally recognized as a monophyletic group. In this study, 28 specimens of this section were collected from five provinces of China. Phylogenetic trees were produced based on the ITS sequences using Maximum Likelihood and Bayesian analyses. Based on this phylogenetic approach combined with their morphological examinat...
Chemical investigation on the peels of the cultivated edible mushroom Wolfiporia cocos led to the identification of 13 diterpenes and 4 steroids, including two new abietane diterpenes (1 and 2) and one new pregnane steroid (14). Structures of new compounds were determined by analysis of NMR, MS, and electronic circular dichroism (ECD) data. All com...
Two new meroterpenoid compounds (1 and 2) together with five known meroterpenoid derivatives (3–7) were isolated from solid culture of mushroom Panus lecomtei. The structures of new compounds were confirmed by the analysis of NMR and HR-ESI-MS spectroscopic data. The biosynthetic pathway of 1–7 was postulated. All isolated compounds were evaluated...
Two new meroterpenoid compounds (1 and 2) together with five known meroterpenoid derivatives (3-7) were isolated from solid culture of mushroom Panus lecomtei. The structures of new compounds were confirmed by the analysis of NMR and HRESIMS spectroscopic data. The biosynthetic pathway of 1-7 was postulated. All isolated compounds were evaluated fo...
This article provides an outline of the classification of the kingdom Fungi (including fossil fungi. i.e. dispersed spores, mycelia, sporophores, mycorrhizas). We treat 19 phyla of fungi. These are Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomoph...
This article provides an outline of the classification of the kingdom Fungi (including fossil fungi. i.e. dispersed spores, mycelia, sporophores, mycorrhizas). We treat 19 phyla of fungi. These are Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomoph...
Maintaining and updating databases and checklists of genera of fungi is an essential task for most fungal research. Advances in molecular techniques in the last 20 years have greatly influenced the fungal taxonomy and classification. Consequently, it is important to have access to all existing data and for these data to be continuously updated with...
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...
This article is the tenth series of the Fungal Diversity Notes, where 114 taxa distributed in three phyla, ten classes, 30 orders and 53 families are described and illustrated. Taxa described in the present study include one new family (viz. Pseudoberkleasmiaceae in Dothideomycetes), five new genera (Caatingomyces, Cryptoschizotrema, Neoacladium, P...
A chemical study on the peels of the cultivated edible mushroom Wolfiporia cocos led to the isolation and identification of 47 lanostane triterpenoids including 16 new compounds (1-16). The structures of new compounds were determined by analysis of the NMR, MS, and electronic circular dichroism (ECD) data. Compounds 1 and 2 represent new members of...
Agaricus sinodeliciosus is an edible wild mushroom known in northwest China. It belongs to Agaricus section Bivelares that includes several popular cultivated species, such as A. bisporus, the button mushroom. The life cycle of the latter species has been described as amphithallic because both homokaryotic (n) and heterokaryotic (n+n) spores are pr...
Morphology, phylogeny, and molecular clock analyses were carried out on Savoryellaceae in order to understand the placements of taxa in this family. Ascotaiwania and Neoascotaiwania formed a well-supported separate clade in the phylogeny of concatenated partial SSU, LSU, TEF, and RPB2 gene data. These two genera share similar morphological features...
We introduce three new Phylloporus species, P. pusillus, P. subbacillisporus and P. subrubeolus, from southwestern China and northern Thailand with macro- and micro-descriptions and illustrations. They are found mostly in forests dominated by Fagaceae or Dipterocarpaceae trees. A three-gene phylogenetic analysis of the new Phylloporus species along...
This article is the ninth in the series of Fungal Diversity Notes, where 107 taxa distributed in three phyla, nine classes, 31 orders and 57 families are described and illustrated. Taxa described in the present study include 12 new genera, 74 new species, three new combinations, two reference specimens, a re-circumscription of the epitype, and 15 r...
A large species diversity has recently been discovered in the genus Agaricus . Six subgenera and 23 sections are now recognised. In this study, three specimens collected from Thailand, formed a monophyletic clade in subgenus Pseudochitonia, based on analyses of ITS sequence data. Further analyses, based on multi-gene sequence data (ITS, LSU, tef1-α...
Russula is a worldwid genus which has a high species diversity . Aiming accurate and rapid species identification, candidate genes nLSU (28S), ITS, tef-1α, mtSSU, rpb1, and rpb2, were analysed as potential DNA barcodes. This analysis included 433 sequences from 38 well-circumscribed Russula species of eight subgenera. Two vital standards were analy...
Two new species of Russulaceae from China are herein described and illustrated based on their morphologies and phylogenies. A hypogeous gasteroid species, Lactarius sulphosmus sp. nov. and an agaricoid species, Russula vinosobrunneola sp. nov. are introduced. The latter is morphologically distinguished from R. sichuanensis, although the ITS-based p...