The Genome Sequences of 90 Mushrooms

Li, Huiying; Wu, Surui; Ma, Xiao; Chen, Wei; Zhang, Jing; Duan, Shengchang; Gao, Yun; Kui, Ling; Huang, Wenli; Wu, Peng; Shi, Ruoyu; Li, Yifan; Wang, Yuanzhong; Li, Jieqing; Guo, Xiang; Luo, Xiaofeng; Li, Qiang; Xiong, Chuan; Liu, Honggao; Gui, Mingying; Sheng, Jun; Dong, Yang

doi:10.1038/s41598-018-28303-2

Cited by 83 publications

(91 citation statements)

References 34 publications

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“…The genome size of the assembled P. pulmonarius is ~39.2 Mb for ss2 and ~39.9 Mb for ss5 (Table 1). These sizes are consistent with genome sizes observed in other related Pleurotus species: for example, P. ostreatus with about 35 Mb (Riley et al 2014;Qu et al 2016;Wang et al 2018) and P. eryngii with 49.9 Mb (Zhang et al 2018). Both of our genomes are distributed in 23 scaffolds ranging in size from 5.55 Mb to 11 kb (in ss2) and 5.06 Mb to 21 kb (in ss5), and with N50 values of 3.2 Mb and 3.4 Mb (respectively), showing high contiguity.…”

Section: High Quality Genome Assemblies Of P Pulmonariussupporting

confidence: 86%

“…Both of our genomes are distributed in 23 scaffolds ranging in size from 5.55 Mb to 11 kb (in ss2) and 5.06 Mb to 21 kb (in ss5), and with N50 values of 3.2 Mb and 3.4 Mb (respectively), showing high contiguity. These N50 values are higher than those of four other available Pleurotus assemblies: P. platypus (N50 = 62 kb); P. citrinopileatus (N50 = 9.7 kb) (Li et al 2018); P. tuoliensis (N50 = 1.17 Mb); and P. eryngii (N50 = 563 kb) (Zhang et al…”

Section: High Quality Genome Assemblies Of P Pulmonariusmentioning

confidence: 86%

“…Only the latest assemblies of P. ostreatus (Riley et al 2014;Qu et al 2016;Wang et al 2018) show the overall quality and contiguity necessary for more comprehensive genetic analyses of these mushrooms. In contrast most of the Pleurotus genomes are very fragmented, including P. eryngii, P. tuoliensis (Zhang et al 2018), P. platypus and P.…”

Section: Introductionmentioning

confidence: 99%

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Genomic analyses of two Italian oyster mushroomPleurotus pulmonariusstrains

Ulzurrun

Lee

Stajich

et al. 2020

Preprint

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Pleurotus mushrooms are among the most cultivated fungi in the world and are highly valuable for food, medicine and biotechnology industries. Furthermore, Pleurotus species are carnivorous fungi; they can rapidly paralyze and kill nematodes when nutrient-deprived. The predator-prey interactions between Pleurotus and nematodes are still widely unexplored. Moreover, the molecular mechanisms and the genes involved in the carnivorous behavior of Pleurotus mushrooms remain a mystery. We are attempting to understand the interactions between Pleurotus mushrooms and their nematode prey through genetic and genomic analyses. Two single spores (ss2 and ss5) isolated from a fruiting body of Pleurotus pulmonarius exhibited significant differences in growth and toxicity against nematodes. Thus, using PacBio long reads, we assembled and annotated two high-quality genomes for these two isolates of Pleurotus pulmonarius. Each of these assemblies contains 23 scaffolds, including 6 (ss2) and 8 (ss5) telomere-to-telomere scaffolds, and they are among the most complete assembled genomes of the Pleurotus species. Comparative analyses identified the genomic differences between the two P. pulmonarius strains. In sum, this work provides a genomic resource that will be invaluable for better understanding the Italian oyster mushroom P. pulmonarius.

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Section: High Quality Genome Assemblies Of P Pulmonariussupporting

confidence: 86%

Section: High Quality Genome Assemblies Of P Pulmonariusmentioning

confidence: 86%

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Genomic analyses of two Italian oyster mushroomPleurotus pulmonariusstrains

Ulzurrun

Lee

Stajich

et al. 2020

Preprint

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show abstract

“…When investigating the amount of fungi, the number of cells was not estimated due www.nature.com/scientificreports www.nature.com/scientificreports/ to the biases that could have been introduced by different ploidy between species. However, an average amount of fungal genomes was estimated based on the information reported in 49 , with the average size for ascomycetes and basidiomycetes estimated at 13 and 42 Mb respectively. Accordingly, since members of both phyla were retrieved, 27.5 Mb was used as the average size for genomes.…”

Section: Discussionmentioning

confidence: 99%

Seasonal epiphytic microbial dynamics on grapevine leaves under biocontrol and copper fungicide treatments

Gobbi

Kyrkou

Filippi

et al. 2020

Sci Rep

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Winemakers have long used copper as a conventional fungicide treatment on grapevine and only recently, the use of biocontrol agents depicted a promising alternative. Most of the studies that investigate the impact of fungicide treatments, focus on specific pathogenic microbes. In the present work instead, a field experiment conducted in South Africa shows the seasonal microbial change occurring on grapevine leaves, periodically treated with two different fungicide treatments: copper sulphate and Lactobacillus plantarum MW-1. In this work, NGS data were combined with strain-specific and community qpcRs to reveal the shift of the microbial communities throughout the growing season and highlight the impact of fungicides on the microbiota. Only the family of Lactobacillaceae systematically changed between treatments, while the bacterial community remained relatively stable over time. MW-1 was exclusively detected on biocontrol-sprayed leaves. Conversely, the fungal community was largely shaped by sampling time, underlining the succession of different dominant taxa over the months. Between treatments, only a few fungal taxa appeared to change significantly and the fungal load was also comparable. Monitoring the dynamics of the microbial community under different fungicide treatments may advise the best timing to apply treatments to the plants, toward the realization of more sustainable agricultural practices.

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“…When investigating the amount of fungi, the number of cells was not estimated due to the biases that could have been introduced by different ploidy between species. However, an average amount of fungal genomes was estimated based on the information reported in Li et al (2018), with the average size for ascomycetes and basidiomycetes estimated at 13 and 42 Mb respectively. Accordingly, since members of both phyla were retrieved, 27.5 Mb was used as the average size for genomes.…”

Section: Discussionmentioning

confidence: 99%

Seasonal microbial dynamics on grapevine leaves under biocontrol and copper fungicide treatments

Gobbi

Kyrkou

Filippi

et al. 2019

Preprint

View full text Add to dashboard Cite

11Winemakers have long used copper as a fungicide on grapevine. However, the potential of copper to 12 accumulate on soil and affect the biota poses a challenge to achieving sustainable agriculture. One 13 recently developed option is the use of biocontrol agents to replace or complement traditional methods. 14 In the present study, a field experiment was conducted in South Africa in which the leaves in two blocks 15 of a vineyard were periodically treated with either copper sulphate or sprayed with Lactobacillus 16 plantarum MW-1 as a biocontrol agent. This study evaluated the impact of the two treatments on the 17 bacterial and fungal communities as they changed during the growing season. To do this, NGS was 18 combined with quantitative strain-specific and community qPCRs. The results revealed the progression 19 of the microbial communities throughout the season and how the different treatments affected the 20 microbiota. Bacteria appeared to be relatively stable at the different time points, with the only taxa that 21 systematically changed between treatments being Lactobacillaceae, which included reads from the 22 biocontrol agent. Cells of Lactobacillus plantarum MW-1 were only detected on treated leaves using 23 strain-specific qPCR, with its amount spanning from 10 3 to 10 5 cells/leaves. Conversely the fungal 24 community was largely shaped by a succession of different dominant taxa over the months. Between 25

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The Genome Sequences of 90 Mushrooms

Cited by 83 publications

References 34 publications

Genomic analyses of two Italian oyster mushroomPleurotus pulmonariusstrains

Genomic analyses of two Italian oyster mushroomPleurotus pulmonariusstrains

Seasonal epiphytic microbial dynamics on grapevine leaves under biocontrol and copper fungicide treatments

Seasonal microbial dynamics on grapevine leaves under biocontrol and copper fungicide treatments

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