Volume 13 - 2022 - Issue 2 (SI Fungal Evolution)


1. On the evolution of ectomycorrhizal fungi

Authors: Ryberg M, Kalsoom Khan F, Sánchez-García M

Recieved: 04 April 2022, Accepted: 09 June 2022, Published: 24 June 2022

Ectomycorrhiza is a symbiosis between plants and fungi. It is the type of mycorrhiza that involves the highest number of fungal species and it involves many stand forming tree species. As the ectomycorrhizal trees include the majority of all the worlds tree stems, it has a huge impact on the nutrient and carbon cycles. Here, we review the evolution of ectomycorrhiza within fungi. It has evolved many times in different clades. The rate of evolution has not varied much through time, but has varied between clades. Thus, no time period seems to have been more important than others for the evolution of new ectomycorrhizal lineages. It seems like once becoming ectomycorrhizal the probability of becoming saprotrophic again is very low. Despite the large change in nutritional strategy, it does not seem like becoming ectomycorrhizal is a key innovation that by itself gives a high rate of speciation and/or adaptive radiations. Genomic studies have shown little commonality in the evolution of ectomycorrhiza except for the loss of decay genes, expansions of transposable elements, and expansions of Mycorrhiza-induced Small Secreted Proteins. Although this fits with a biotrophic lifestyle and possibly an elevated rate of genome evolution, it does not hint at any other functional similarity. As ectomycorrhizal lineages have evolved many times during the evolutionary history of fungi, and it is not unlikely that there are ectomycorrhizal lineages that have gone extinct, the available functions provided by ectomycorrhiza to plants may have varied over time.

Keywords: Evolutionary analysis – Evolutionary transition – Genome evolution – Key innovation – Symbiosis

 

2. Phylogenetic diversity and affiliation of tropical African ectomycorrhizal fungi

Authors: Houdanon RD, Furneaux B, Yorou NS, Ryberg M

Recieved: 01 April 2022, Accepted: 16 June 2022, Published: 06 July 2022

Ectomycorrhizal fungi form a mutualistic symbiosis with plant roots, and are key for nutrient cycling in many ecosystems. Here we study the ectomycorrhizal fungal communities in the Ouémé Supérieur reserve forest in Benin (West Africa). We use phylogenetic methods to test if the species from the study site are closer to other tropical African species than to species from other regions. The Ouémé Supérieur community was represented by nine Operational Taxonomic Units in Amanitaceae, one in Boletaceae, one in Cantharellaceae, one in Cortinariaceae, two in Inocybaceae, fourteen in Russulaceae and three in Sclerodermataceae. Of these thirty-one Operational Taxonomic Units, twenty had no record in other areas, and unique Operational Taxonomic Units were found in all families except Boletaceae and Sclerodermataceae. The added phylogenetic diversity from these unique Operational Taxonomic Units tended to be higher than expected by chance in all families but Cantharellaceae. The Operational Taxonomic Units are generally fairly distinct and contribute proportionally to the phylogenetic diversity, reflecting that they do not only represent recently diverging species, but also more divergent lineages. Our analyses of the different families show that the communities of Amanitaceae, Inocybaceae, and Russulaceae are more closely related to the general Afrotropic community than expected by chance, at least measured as the nearest taxon distance. The lack of significant patterns in the other families may be due to lack of power, but the wide distribution of many Operational Taxonomic Units suggests that there are not likely to be strong patterns. It is only for Russulaceae that there is a significant pattern in the Ouémé Supérieur ectomycorrhizal fungal communities at a regional scale, with the Operational Taxonomic Units being less closely related than expected. At a global scale the patterns seem to reflect the overall distribution of the Afrotropic ectomycorrhizal fungal community. The phylogenetic patterns in the Afrotropic communities differ between families, from clustered to no clear pattern to over-dispersed measured as mean average phylogenetic distance. Each family seems to have its own biogeographic history, and there is no clear pattern for the ectomycorrhizal fungal community at large. Despite the lack of comprehensive taxonomic work to identify fungi in a region, it is still possible to draw some conclusions on their diversity using molecular phylogenetic methods. However, limited success in getting good sequence data from specimens, probably due to preservation issues in the field, and the lack of well annotated molecular data from many regions limit the power of these inferences.

Keywords: community assemblage – mycorrhizal fungi – Operational Taxonomic Units – phylogeny – west Africa

 

3. Evolutionary relationship and a novel method of efficient identification of Lentinula edodes cultivars in China

Authors: Ling YY, Zhang MZ, Ling ZL, Cao B, Wu XP, Peng H, Wang ZR, Zhao RL

Recieved: 24 February 2022, Accepted: 18 July 2022, Published: 24 August 2022

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 industrial development and germplasm innovation process. In this study, we developed and illustrated a methodological and technical system for the identification of L. edodes cultivars and for detecting their evolutionary relationship based on the multiple nucleotide polymorphism marker (MNP) sequences. Specifically, 501 universal MNP markers were screened based on the whole-genome resequencing data of 188 L. edodes strains mainly from China (25 of which were self-tested). The following analysis of detection rate, repeatability rate and accuracy rate showed those MNP markers are satisfactory with 94.4%, 99.92%, and 99.96% respectively. This method of multiplex PCR amplification and high-sequencing resulted in the construction of an MNP sequence library of L. edodes. On this basis, 187 MNP markers were further screened as core MNP markers. An ML phylogenetic tree of 162 wild strains and 78 cultivars was generated by using core MNP sequences, revealing all cultivars can be separated into 24 distinct evolutionary pedigrees. The genetic similarity (GS) value between different pedigrees and all cultivars tested showed that a broad library of pedigrees had GS values less than or equal to 94%, and the different cultivars within the same pedigrees had GS values range of 94-99.5%. The combination of all results indicated that most cultivars of L. edodes were originally from the Northeast Asia except the only cultivar L. edodes from south China, but there has a serious homogenization of L. edodes germplasms in China. In this study, we established a genealogical map of L. edodes cultivars in China, a standard library of MNP markers, and a rapid experimental procedure for genealogical and cultivar identification, which lays out a highly reliable platform for encouraging original innovation and modified cultivar innovation. Finally, a brief prospect for MNP markers identification of mushroom cultivars is addressed.

Keywords: edible mushroom – evolution – molecular marker – multiple nucleotide polymorphism – shiitake

 

4. Large-scale genome investigations reveal insights into domestication of cultivated mushrooms

Authors: Fu YP, Dai YT, Chethana KWT, Li ZH, Sun L, Li CT, Yu HL, Yang RH, Tan Q, Bao DP, Deng YJ, Wang SX, Wang YF, Tian FH, Qi LL, Shu LL, Jia PS, Chen LC, Chen MY, Hu QX, Tan H, Song TT, Zhang ZW, Bonito G, Zervakis GI, Xiao SJ, Hyde KD, Li Y, Yuan XH

Recieved: 22 April 2022, Accepted: 19 August 2022, Published: 21 September 2022

Domestication and cultivation of edible and medicinal mushrooms are ongoing ~1,400-year-old evolutionary experiments. There are roughly 55 commercially cultivated mushrooms worldwide; however, genomes for many species are lacking, as is our understanding of mushroom domestication. In this work, 22 high-quality reference genomes, along with 63 transcriptome and 381 re-sequencing data, were reported for the first time. Combined with public genome resources, an integrated omics database (MushDB, http://mushroomomics.com) were constructed including 50 reference genomes, 265 transcriptome and 621 whole-genome re-sequencing data, covering ~90% of the worldwide commercially cultivated mushroom species. Using multi-omics data in MushDB, whole-genome variations of the representative wild and cultivated populations were used for selective sweep analysis to identify putative functional genes contributing to the mushroom domestication. Key genes in the starch and sucrose metabolism and mitogen-activated protein kinase signaling pathway, such as chb1, cdc24 and hog1, were putatively selected in Auricularia cornea, Lentinula edodes, Pleurotus eryngii and Pleurotus tuoliensis, indicating those genes might play important roles during mushroom domestications. The function of hog1 in the low temperature stimulation adaptation and short growth period in cultivation environment, which could facilitate the successful domestication, was validated using CRISPR/Cas9 system. Our work offers valuable and abundant omics open resource for wide research communities and lays solid foundations for multi-purposes in mushroom evolution, genetics, and breeding studies.

Keywords: database – domestication – genome – multi-omics – mushroom

 

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Mycosphere publishes reviews, research articles, methodology papers, taxonomic works such as monographs, which are relevant to fungal biology, including lichens. The official journal language is English.

 

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