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22 December 2019, Volume 38 Issue 12
    

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  • Da-Peng BAO
    MYCOSYSTEMA. 2019, 38(12): 2061-2077. https://doi.org/10.13346/j.mycosystema.190265
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    Most of the cultivated macrofungi belong to basidiomycetes and have complex mating systems usually involving two types of mating genes, A mating genes encoding two types of homeodomain transcription factors and B mating genes encoding lipopeptide pheromones and pheromone receptors. The mating system has been studied for hundred years. In recent years, with the development of high-throughput sequencing technology, many cultivated mushrooms have completed the sequencing of the whole genome, so that we can make a more detailed analysis of the molecular genetics of different mating type systems. This paper generally introduces the sexual reproductive system and the molecular characteristics of mating genes of basidiomycetes, and summarized and analyzed the molecular genetic structure of mating type loci of some cultivated mushrooms including Lentinula edodes, Flammulina velutipes, Ganoderma lucidum, Pleurotus ostreatus, P. eryngii, P. tuoliensis, Schizophyllum commune, Agaricus bisporus, Volvariella volvacea, Coprinopsis cinerea and Lentinus tigrinus. It is found that the molecular genetic structure of mating type loci of the cultivated mushrooms is diverse, and the mating type loci of different species have different characteristics. The number and location of mating genes of different strains within species are also varied. The understanding of the mating type loci of cultivated mushrooms at level of molecular genetics will help us to clarify the regulation of mating type genes in the development of fruiting bodies and thereby to solve the scientific problems in the production of mushrooms. At present, there are still many gaps in the research on mating type loci and genes of mushrooms, which need to be further deepened and expanded.

  • Hong-You LIU, Liu-Long CHEN, Jiang-Tao GAO
    MYCOSYSTEMA. 2019, 38(12): 2078-2086. https://doi.org/10.13346/j.mycosystema.190240
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    Metabolomics is a discipline that uses modern analytical chemistry to characterize and quantify small molecule metabolites (primary and secondary metabolites) in a given environment, thereby revealing life phenomena and their inherent laws. Relative to the genome, transcriptome and proteome, the metabolome is a collection of final metabolites after completion of biological processes under certain conditions, and thus is the closest phenotype of omics in various omics studies, and can directly and dynamically reflects the physiological and biochemical processes of the cells, so that specific biochemical pathways can be effectively detected and discovered, thereby accurately explaining physiological or pathological phenomena. Metabolomics is one of the current research hotspots as an extension and complement of the three major omics of genomics, transcriptomics and proteomics in system biology. At present, the research of metabolomics in the field of fungi has been extensively developed. This paper briefly describes the development of metabolomics in fungal research in seven aspects: fungal classification, biofilm research, metabolic pathway, metabolic engineering, natural product discovery and fungi-plant interaction.

  • Hong LUO
    MYCOSYSTEMA. 2019, 38(12): 2087-2098. https://doi.org/10.13346/j.mycosystema.190250
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    Poisonous mushrooms seem to constitute a perpetual topic due to that, on one hand, they inflict a considerable number of human poisonings and fatal incidents yearly, and on the other, the values of these once “evil” mushrooms are being increasingly recognized, e.g., the exploration of mycotoxins for curing human diseases including cancers. Lately, genomics and other omics studies on poisonous mushrooms have been moving forward rapidly, which greatly promote the research on these fungi. The biosynthesis of some toxins has been elucidated, and the histories of a few toxin biosynthetic pathways have been outlined with increasing clarity. In this review, recent advances in the fields of genomics, transcriptomics and proteomics of poisonous mushrooms are discussed, with summaries towards prominent directions for future researches.

  • Research papers
  • Li-Gang XIANG, Han-Cheng WANG, Zhen-Ni GUO, Hong-Lian XIE, Liu-Ti CAI, Zhi-He YU
    MYCOSYSTEMA. 2019, 38(12): 2099-2111. https://doi.org/10.13346/j.mycosystema.190362
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    Black shank disease of tobacco is soil-borne and caused by Phytophthora parasitica var. nicotianae, which can cause huge economic losses to tobacco production. The changes of fungal community structure and diversity in rhizosphere soil and stem of tobacco plants infected by black shank disease were investigated by using PCR amplification of the ITS1 region. The amplified fragments were sequenced using Illumina Miseq high-throughput sequencing technique. A total of 755 599 high-quality sequence fragments were obtained from 20 sequencing samples. The shortest sequence is 200bp, and the longest 356bp, and the average sequence length is 248bp. It was showed that the dominant fungi in rhizosphere soil of healthy and diseased tobacco plants were Ascomycota, Zygomycota and Basidiomycota, while those in stem were Ascomycota and Basidiomycota. The fungal genera with relative abundance of more than 1% in rhizosphere soil samples of healthy and diseased plants were Fusarium, Mortierella, Cryptococcus, Alternaria and Gibberella, of which Fusarium (39.35%) and Mortierella (14.19%) were dominant in rhizosphere soil of healthy plants. The relative abundance of Fusarium and Mortierella in rhizosphere soil of diseased plants was 40.26% and 20.77%, respectively. The dominant genera in healthy stem were Cryptococcus (31.12%), Alternaria (18.28%), Fusarium (15.67%) and Rhodotorula (13.34%). Fusarium (41.36%), Cryptococcus (28.15%) and Alternaria (22.32%) were dominant in symptomatic-asymptomatic junction of stem. Cryptococcus (62.14%) and Alternaria (27.75%) were dominant in diseased stem. The dominant genera in rhizosphere soil and stem of infected plants did not change significantly as compared with the healthy plants, but the relative abundance of the genera changed significantly. The Sobs, Chao1 and Shannon indices of the fungal communities in rhizosphere soil and stem of diseased plants were lower than those of healthy plants, while Simpson index was higher, indicating that the richness and diversity of fungal communities in rhizosphere soil and stem tissue decreased in tobacco plants infected with black shank disease.

  • Yuan YUAN, Hai-Chen HUANG, Li-Yun YE, Jun-Sheng FU, Xiao-Ping WU
    MYCOSYSTEMA. 2019, 38(12): 2112-2121. https://doi.org/10.13346/j.mycosystema.190316
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    ITS1 amplicon sequencing of the soil fungi in uncropped wild soil (GL0) adjacent to cropping soil, and 1 year cropping soil (GL1), 2 year cropping soil (GL2), and 4 year cropping soil (GL4) of Ganoderma lingzhi was performed by Illumina MiSeq platform to analyze the changes of fungus communities in the continuous cropping soil, for the purpose of exploring the possible obstacle of G. lingzhi continuous cropping. A total of 349 642 valid sequences was obtained from 12 G. lingzhi cropping soil samples, and 2 426 OTUs was obtained by clustering, affiliated to 8 phyla, 28 classes, 64 orders, 127 families, 233 genera and 449 species. At the level of phylum, with the increase of continuous cropping years, the diversity of fungi in G. lingzhi cropping soil is gradually reduced. In GL4 experimental group, Basidiomycota, Ascomycota and Mortierellomycota are dominant, accounting for 85.03%, 14.77% and 0.20% of the total taxa respectively. The relative abundance of basidiomycetes increased significantly with the increase of continuous cropping years, while that of ascomycotes significantly reduced. There was no significant difference in the relative abundance of Mortierellomycota. At the genus level, the relative abundance of Ganoderma increased significantly with the increase of continuous cropping years. The relative abundance of Penicillium in ascomycetes decreased in the beginning and then increased, whose relative abundance in GL4 increased by 57.92% as compared with that in GL0, indicating Penicillium may be a key factor obstructing continuous cultivation of G. lingzhi.

  • Fang-Jie YAO, Cheng-Yuan HUANG, Xiang-Hui KONG, Peng WANG, Li-Xin LU, Ming FANG, You-Min ZHANG
    MYCOSYSTEMA. 2019, 38(12): 2122-2132. https://doi.org/10.13346/j.mycosystema.190139
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    The genetic diversity of 27 strains of Auricularia cornea (14 wild strains, 13 cultivated strains) was analyzed by using the SSR markers developed based on whole genome sequence. Using the DNA of 3 strains randomly selected (2 wild strains and 1 cultivated strain) as template, 24 pairs of primers with clear amplification bands, strong stability and rich polymorphism were screened from 144 pairs of SSR primers. In total, 116 alleles were detected by 24 pairs of SSR primers. The number of alleles amplified by each pair of primer ranged from 3 to 7. The average detection efficiency was 4.83 alleles/primer. Shannon’s genetic diversity index was 0.866-1.885, and the polymorphic locus ratio was 100%. The genetic similarity coefficient (GS) of the tested strains ranged from 0.618 to 0.971, suggesting that the germplasm resources of A. cornea were rich in genetic diversity. The average GS of wild strains and cultivated strains were 0.746 and 0.779, respectively, indicating that the genetic diversity of wild strains was more abundant. Cluster analysis showed that the tested strains were divided into colorless (white) group I and colored (light yellow to reddish brown) group II when GS was 0.680. When GS was 0.704, the cultivated strains and wild strains could be clearly distinguished (14 wild strains were in group II-2, and 13 cultivated strains were in group I and group II-1). This study demonstrated that SSR markers based on the whole genome could reveal the genetic differences among strains at molecular level, facilitating breeding and genetic studies of A. cornea.

  • Li-Ning WANG, Meng-Ran ZHAO, Xiang-Li WU, Chen-Yang HUANG, Ji-Bin QU
    MYCOSYSTEMA. 2019, 38(12): 2133-2143. https://doi.org/10.13346/j.mycosystema.190237
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    With the completion of genome sequencing of Pleurotus ostreatus, deep exploration and utilization of genomic data have become the research focuses. In this study, intraspecific comparative genomic analysis was carried out based on high quality genomic assemblies of P. ostreatus strains CCMSSC00389-1 and CCMSSC03989-1. The 11 chromosome sequences of CCMSSC00389-1 and CCMSSC03989-1 showed good collinearity and contained 89.92% and 91.68% conserved genes respectively. GO enrichment analysis of the strain-specific genes indicated that each strain had some unique regulatory functions or pathways. There were 931 542 SNPs, 231 65 In/Dels and 9 221 SVs between genomes of CCMSSC00389-1 and CCMSSC03989-1. GO enrichment analysis of genetic variation-overlapped genes revealed that genes related to carbohydrate degradation were prone to have SNPs, genes related to transportation/catalysis of substances were prone to have In/Dels, and genes related to regulation/protein activity were prone to have SVs. A 50.326kb deletion with double strand break repair (DSB) signatures in its two breakpoints was identified in CCMSSC00389-1, and DSB was predicted to mediate the 50.326kb deletion.

  • Yong-Xin TAO, Jin-Chao CHE, Han-Bing SONG, Zi-Yan LI, Jing-Yi DUAN, Mukhtar Irum, Bao-Gui XIE
    MYCOSYSTEMA. 2019, 38(12): 2144-2160. https://doi.org/10.13346/j.mycosystema.190263
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    Basidiomycete edible fungi have high value and large yield. The upgrade and development of edible fungal industry requires in-depth analysis of biological issues involved in growth and development of edible fungi. At present, several edible fungi have completed the whole genome sequencing; however, the lack of systematic genome-wide research of the orthologous genes between non-model edible fungi and model filamentous fungi limits in-depth study of their molecular biology to some extent. In this study, straw mushroom Volvariella volvacea as the reference species was used to analyze the orthologous genes of straw mushroom and other several edible fungi and model filamentous fungi, and the functional enrichment of different types of orthologous genes was performed multispecifically. The results showed that the one-to-one orthologous genes were more enriched in the basic and conserved functional categories including gene replication, transcription, translation, modification and processing. The non one-to-one orthologous genes mainly belonged to gene family, and also included over 65% of the whole transcription factors, being enriched in the transport and metabolic pathways of carbohydrates, lipids, amino acids, secondary metabolites and exogenous substances. Non orthologous genes were enriched in the functional categories involved in gene recombination, repair, signal transduction, specific transcription factors and predicted genes with unknown functions. The results provide valuable information for further in-depth study of molecular biology in edible fungi.

  • Yuan-Ping LU, Zhong-Jie GUO, Zhi-Xin CAI, Mei-Yuan CHEN, Jian-Hua LIAO
    MYCOSYSTEMA. 2019, 38(12): 2161-2173. https://doi.org/10.13346/j.mycosystema.190267
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    In order to investigate the gene transcript pattern at different developmental stages of Agaricus blazei fruiting bodies (primordial stage, harvest stage and pileus opening stage), transcriptome analysis was carried out and genome sequence of sterile monospore strain JA-15036 obtained previously in our laboratory was used as reference genome. The gene ontology classification showed that the differentially expressed genes (DEGs) were mainly enriched in transmembrane transport, carbohydrate metabolism pathway and membrane components, and the coordinated regulation of these genes could provide a stable internal environment for the growth and development of fruiting bodies. KEGG pathway analysis showed that the DEGs were mainly enriched in ribosome, DNA replication, carbohydrate metabolism, fatty acid degradation and amino acid metabolism. Of these, most genes related to ribosome and DNA replication were up-regulated at primordial stage, indicating that the cell metabolism was more active in primordia, which could be prepare for protein synthesis. The up-regulated DEGs at harvested stage and pileus opening stage were mainly enriched in carbohydrate metabolism, fatty acid degradation and amino acid metabolism, implying that these genes have an important role in providing nutrition and energy for A. blazei during fruiting body development process.

  • Xiao LI, Wen-Jia LI, Fen WANG, Ling TANG, Zheng-Ming QIAN, Cai-Hong DONG
    MYCOSYSTEMA. 2019, 38(12): 2174-2182. https://doi.org/10.13346/j.mycosystema.190273
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    The MYB family of transcription factors is widely distributed in all eukaryotic organisms, which have been shown to play an important role in the growth and development of fungi. In this study, genome-wide identification and bioinformatics analysis of MYB transcription factor family were performed, and the expression patterns of MYB family members at different development stages and different parts of fruiting body of the caterpillar fungus Ophiocordyceps sinensis were studied. The results showed that there were three 1R-MYBs and three 2R-MYBs in the genome of O. sinensis. They also contained nearly 50 conserved amino acid sequences giving rise to a helix-turn-helix (HTH) secondary structure. The relative expression levels of MYB transcription factors at different development stages (MYB-1-6) and different parts (MYB-1, 3, 6) of the fruiting body were studied. MYB-1 expressed constitutively during the whole growth and development stages; MYB-3 may regulate the maturation of perithecia and ascospores; MYB-6 may play role in the elongation of fruiting body.

  • Yan-Jiao SONG, Long-Ji LIN, Li-Zhi YANG, Xiao-Ping WU, Yu-Ji JIANG, Rui-Guang MING, You-Jin DENG
    MYCOSYSTEMA. 2019, 38(12): 2183-2194. https://doi.org/10.13346/j.mycosystema.190307
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    Genetic transformation is one of the important methods for gene function analysis. However, some unexpected mutations occur during transformation, making results unreliable. Six knock-out like Annulohypoxylon stygium strains with TJAS01-V10012900 gene were used as experimental strains, of which 12900-5 showed obvious differences in morphology. PCR tests, genome sequencing, and RNA-seq were employed to analyze the cause of morphological variation of 12900-5 strain. The obtained results showed similarity between 12900-5 and 12900-6 at knock-out region and copy number of hygromycin resistance gene. However, 12900-5 strain had two additional SNPs within different genes. One SNP was within the gene related to the control of cell cycle at S phase, and another was within the gene related to vesicle transport, both putatively affect mycelial growth. The results suggested that morphological variations of 12900-5 might be due to the SNP mutations in the genome. Gene expression related to metabolic pathways, translation processes and other metabolic and signaling pathways were down-regulated in 12900-5 strain as compared to those in 12900-6 strain. This result is an example that non-target point mutations occurred during gene-deletion transformation. The exact mechanism responsible for this kind of point mutations remains to be determined.

  • Wei LIU, Qian-Qian ZHANG, Fang SHU, Ying-Li CAI, Xiao-Long MA, Yin-Bing BIAN
    MYCOSYSTEMA. 2019, 38(12): 2195-2204. https://doi.org/10.13346/j.mycosystema.190148
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    Based on two monosporic genome sequencing data, the genome-wide SNP/Indel variants’ calling was carried out of Morchella importuna. A total of 18 438 variant loci was identified, with an average of 361 variant loci per M base. The main variant loci were single nucleotide polymorphic (SNPs) with a total of 17 104 and variation rate of 335SNPs/Mbp. 1 334 insertion-deletion polymorphic loci (Indel) were identified, of which 2-10bp were dominant. 73.4% of SNP/Indels were located in the intergenic region, and 3 042 variant loci were detected in the exon region accounting for 16.50%. There were 1 088 frame-shift mutations (5.90%) and 916 missense mutations (4.97%) that have a definite effect on gene function. The SNP/Indel mutation rates on different Scaffolds were different, and Scaffold80 with the largest variation rate contained an average of 2 856 SNPs per M base, and Scaffold60 and Scaffold75 with the lowest mutation rates 16 and 30SNPs/Mbp, respectively. 75 polymorphic indel markers with the mutation loci ≥11bp were successfully developed by exploiting and polymorphic population analysis. Based on protoplast homokaryotic technology, two compatible strains M04P01 and M04P40 of parent strain M04 of Morchella importuna were obtained, together with 58 monospore populations from M04 ascocarp as mapping populations, twelve linkage groups with the total length of 273.7cM were preliminarily constructed containing 75 indel markers and a mating type gene of M. importuna.

  • Bing-Zhi CHEN, Ming-Meng QIU, Li-Yun YE, Tian-Ci CHEN, Xin LU, Yu-Ji JIANG, Xiao-Ping WU
    MYCOSYSTEMA. 2019, 38(12): 2205-2213. https://doi.org/10.13346/j.mycosystema.190266
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    Pleurotus pulmonarius is a tetrapolarity heterothallic fungus, but the structure of its mating loci has not yet been resolved, causing troubles in breeding of the fungus. In this study, the genome of P. pulmonarius was sequenced by second generation sequencing technology, and mating type loci of progeny of the wild variety X1 were searched by bioinformatics method. The results showed that A mating loci of P. pulmonarius were specific and the structure of A mating loci in two protoplast mononucleated strains (X1-1 and X1-15) was quite different. X1-1 contained a pair of conservative HD1 and HD2 genes, while X1-15 contained two additional HD2 genes and one HD1 gene in addition to a pair of HD1 and HD2 genes. The B mating type locus of P. pulmonarius is similar to that of other basidiomycetes, containing eight pheromone receptor genes and one pheromone precursor gene. The specific mating-locus structure of P. pulmonarius revealed in this paper provides a theoretical basis for later genetic study and breeding of the fungus.

  • Bing-Yu LI, You-Jin DENG, Rong‐Mei HUANG, Chen ZHAO, Zhi-Hua WEN, Wei‐Nan XU, Bao‐Gui XIE
    MYCOSYSTEMA. 2019, 38(12): 2214-2220. https://doi.org/10.13346/j.mycosystema.190320
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    ITS in rDNA sequences is widely used as a DNA barcode for phylogeny and auxiliary species identification of fungi, and IGS is used to identify different strains within-species level. There are rare reports on complete rDNA sequence in edible fungi. In this study, the third-generation sequencing of the Auricularia cornea mononuclear strain B02 were performed. The assembled sequencing data of the third-generation sequencing was corrected by the data of the next-generation sequencing, and a set of well assembled genome data was obtained. The complete sequence of the rDNA repeat unit was obtained by comparing rDNA sequence of Fibroporia vaillantii with that of A. cornea. Each repeat unit contained ETS, 18S rDNA, ITS1, 5.8S rDNA, ITS2, 28S rDNA, IGS1, 5S rDNA and IGS2, and the length was 398bp, 1 790bp, 156bp, 156bp, 206bp, 3 432bp, 2 247bp, 121bp and 2 135bp respectively, with a total length of 10 641bp. Both transcriptome and phylogenetic analysis supported this result. There were 310 tandem repeat units in the rDNA region. Unlike the other reported edible fungi, the IGS1 and IGS2 sequences of Auricularia cornea were highly conserved, and the 1 400-2 200bp region of IGS1 had no polymorphism between strains, and there was a higher frequency of SNPs between strains. This IGS1 fragment is expected to identify varities of the fungus.

  • XIE Fan, SONG Yan-Jiao, CHENG Bing, MENG Guo-Liang, HAO Jin-Bin, YE Li-Yun, WU Xiao-Ping
    Mycosystema. 2019, 38(12): 2221-2231. https://doi.org/10.13346/j.mycosystema.190270
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  • Sen YAO, Yuan-Yuan LIU, Chen ZHAO, Jun-Jie YAN, Bao-Gui XIE
    MYCOSYSTEMA. 2019, 38(12): 2232-2240. https://doi.org/10.13346/j.mycosystema.190269
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    Stipe is a key indicator for evaluation of the qualities of Flammulina filiformis product. The part of 0.6-1.5cm below the cap is the stipe elongation zone, and other parts are not elongate. To study the regulation mechanism of stipe elongation, LC-MS/MS was used to detect the metabolites accumulated in the elongate, transitional and non-elongate segments of the stipes, and the differential metabolites were analyzed by using statistical method such as HCA and t test. Metabolite enrichment was analyzed by KEGG. The results showed that 69 metabolites were found to be gradationally different in elongate, transitional and non-elongate segments, and the content of 52 differential metabolites was gradually reduced, and that of 17 metabolites gradually increased. The differential metabolites include organic acids, fatty acids, lipids and nucleotides, and fatty acids predominate. The content of oleic acid, arachidonic acid and adrenic acid was significantly higher in elongate part than that in other parts. It was inferred that the unsaturated fatty acids and their derivatives might take part in regulating the elongation growth of stipe of Flammulina filiforms.

  • Xing HAN, Yi-Ning LI, Chen ZHAO, Yuan-Yuan LIU, Mu-Yun DU, Qian-Hui HUANG, Wei-Nan XU, Bao-Gui XIE
    MYCOSYSTEMA. 2019, 38(12): 2241-2248. https://doi.org/10.13346/j.mycosystema.190292
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    The genome-sequenced Flammualia filiformis monokaryon strains “6-3” and “6-21” were used as parental strains, and the paired hybrid was cultivated to produce fruiting body. 90 strains obtained from individual basidospores were constituted as mapping group. Genome sequencing of each strain in the mapping group was performed by NGS and the mycelial growth rate on PDA plates was determined. The analysis of SNPs of both the parental strains resulted in 68 914 SNPs with high quality for constructing 14 genetic linkage groups. The total length, the average length and the average genetic distance between genetic markers were 744.32cM, 53.17cM and 1.88cM, respectively. QTL analysis showed a locus qMGRP1-LG7 controlling the mycelium growth rate, which contained 134 genes, enriching in pathways and genes related to metabolism.

  • Yuan-Yuan LIU, Zong-Jun TONG, Yi-Ning LI, Jun-Jie YAN, Chen ZHAO, Sen YAO, Bing-Yu LI, Bao-Gui XIE
    MYCOSYSTEMA. 2019, 38(12): 2249-2257. https://doi.org/10.13346/j.mycosystema.190272
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    The growth of the caps of cultivated Flammulina filiformis can be inhibited by increasing environmental CO2 concentration to improve product quality. Carbonic anhydrases (CAs) regulate the intracellular balance of CO2/HCO3 -. It is speculated that CAs probably are key enzymes in response to CO2 stress. In the study, the completed genome data of Flammulina filiformis were utilized. Using genes of Laccaria bicolor CA family as reference, 7 putative CA genes, named CA-1, CA-2, CA-3, CA-4, CA-5, CA-6 and CA-7, were obtained from Flammulina filiformis genome. Gene structure, conserved domain and phylogenetic analyses revealed that the 7 putative CAs belonged to the carbonic anhydrase family. As a result of treatment of high concentration of CO2 for 12 hours, the expression level of CA-1 and CA-2 in Flammulina filiformis fruiting body showed positive correlation with CO2 concentration, however, the expression level of CA-5 showed negatively correlative, and that of CA-3, CA-4 and CA-6 unchanged, while that of CA-7 irregular. Thus, it could be speculated that CA-1, CA-2 and CA-5 might be the key genes in response to CO2 stress in Flammulina filiformis, participating in the regulation of cap growth and development.