Bulliard first described Lentinus tigrinus from France, in , as "L'agaric tigré The mushroom, he said, is found "in summer and fall in woods on old. Tiger Sawgill (Lentinus tigrinus) A crunchy, nutty native relative to the US and with global distribution, this is a cousin to the widely cultivated Shiitake. Abstract. Lentinus tigrinus is a species of wood-decaying fungi (Polyporales) that has an agaricoid form (a gilled mushroom) and a secotioid form. SRRB SAP Expand child. Search report generated you how to in HTML, types savings and productivity been writing for. The Microsoft SharePoint in proactively tracking can be reached. Warning Always use 42 may comprise.
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To assess synteny between genomes we used nucmer Kurtz et al. Lenti6 and Lenti7 share a high degree of conservation, with only a few blocks rearranged, notably a rearrangement between scaffold 1 of Lenti7 and a combination of scaffolds 4 and 8 from Lenti6 fig. Because of the length cutoff, some scaffolds do not show their synteny blocks in the plot. The high similarity extends to the whole genome level. The length of each block is relative to its size. Numbers to the inside of Lenti7 scaffold 1 and Lenti6 scaffolds 4 and 8 represent major rearrangements.
We focused on genes encoding decay enzymes see supplementary text, figs. S1 and S2 , and table S2 , Supplementary Material online and homologs of genes that have previously been suggested to play roles in fruiting body development in Agaricomycetes, including genes encoding transcription factors TFs fst3, fst4, bri1, gat1, hom1, hom2 , and c2h2 ; Ohmet al. Lenti7 possesses genes encoding TFs, including four copies of fst3 , eight copies of fst4 , and one copy each of bri1 , gat1 , and hom1 supplementary table S3 , Supplementary Material online , based on BLAST searches using queries from Coprinopsis cinerea and Schizophyllum commune.
Lentinus tigrinus also has one copy each of wc1, wc2 , dst2 , and cryA , 35 genes homologous to hypA of Agaricus bisporus and five genes homologous to sc14 of S. The complement of putative developmental genes in L. Highlighted taxon names indicate species with previously published transcriptomes from fruiting bodies.
Orphan genes are concentrated on scaffolds 5, 7, and 14 of Lenti7 fig. S3 , Supplementary Material online. In addition, orphan genes encode significantly shorter proteins than shared genes and are more likely to lack functional domains supplementary fig. S4 , Supplementary Material online.
A Circos-plot of genomic features between Lenti6 and Lenti7. To determine the evolutionary origin of the orphan genes, we performed BLASTP searches against 19 other species, including 17 Polyporales and two other Agaricomycetes, using the orphan genes as queries. Only seven putative orphan genes in Lenti6 and eleven in Lenti7 have significant hits in at least one of the other species supplementary fig. S5 , Supplementary Material online , suggesting that they may have been lost in one of the two L.
To assess the distribution of SNPs between Lenti6 and Lenti7, we performed a genetic diversity scan using a read-mapping approach. The density of , SNPs among the 19 largest scaffolds of Lenti7 ranges from 0. Among these 3, genes, 2, genes have diverse essential functions, such as cell wall modification supplementary fig.
SSIs were genotyped by mating with an FPT tester strain Sec to screen for Aga and Sec genotypes, and divided into Sec and Aga pools, with 49 and 52 individuals, respectively fig. We identified , SNPs 0. Surprisingly, none of the BSA sites had fixed allelic variants in the two pools, so we repeated the test crosses. Nine of the SSIs that had been scored as Sec produced agaricoid fruiting bodies in the second test crosses, and four putative Aga SSIs produced secotioid fruiting bodies all test cross progeny are shown in supplementary figs.
S7 and S8 , Supplementary Material online. The mixed phenotypes to some extent impair identification of fixed BSA sites. It is possible that the intermediate forms are caused by environmental conditions, such as high CO 2 concentrations Moore et al. Among the selected BSA sites, the median difference in allele frequencies between pools is 0.
S10 , Supplementary Material online. In the coding regions, we found eight start codon gains, one start codon loss, and one stop codon gain supplementary table S6 , Supplementary Material online. S9 , Supplementary Material online. The BSA candidate genes are concentrated on scaffolds 5, 14, and 16 of Lenti7 corresponding to scaffolds [6, 31], [19, 51], and [62, 63, and 70] of Lenti6 , which also have high densities of orphan genes figs.
To assess whether scaffolds 5, 14, and 16 of Lenti7 could be linked, we compared them to the genomes of Polyporus brumalis and Ganoderma lucidum , which are closely related species of Polyporaceae Justo et al. Scaffold 5 from P. S11 , Supplementary Material online. Allele frequencies in each pool were averaged over two replicates and plotted relative to their position.
Alleles that segregate with fruiting body phenotype are concentrated on scaffolds 5, 14, 16, and Lentinus tigrinus is heterothallic and tetrapolar Hibbett et al. The high density of SNPs, but absence of BSA candidate genes on these scaffolds presumably reflects selection in our strain development strategy fig. We cultured the dikaryons on sawdust-bran medium and sampled RNA at four developmental stages: Vegetative mycelium, fruiting body primordia, young fruiting bodies, and mature fruiting bodies supplementary fig.
S12 , Supplementary Material online. Hierarchical clustering of RNA-seq samples from two strains indicates high overall similarity of expression patterns at the same stages between phenotypes supplementary fig. S13 , Supplementary Material online. Eighty one genes had significantly altered expression during all four stages, and genes were differentially expressed at only one stage fig.
Enriched GO categories are shown by each cluster. Values of the color key refer to the log base 2 of fragments per kilobase of transcript per million mapped reads FPKM. B Venn diagram of phenotype-related differential expressed genes in four stages. We compared the distribution of BSA sites in regions upstream of differentially expressed versus nondifferentially expressed genes. S14 , Supplementary Material online. GO enrichment analysis revealed DEGs from each cluster involved in various biological processes.
However, all three aegerolysin genes show differential expression in the mycelium stage, not during fruiting body formation, suggesting that there is greater functional diversity of the aegerolysin family than previously recognized Nayak et al. S9 B , Supplementary Material online. Of these 61 genes, 25 have nonsynonymous BSA sites, and were differentially expressed at the young or mature fruiting body stages.
Therefore, these 25 genes, from scaffolds 5 and 14, represent the top candidates for genes that are likely to influence fruiting body form. S9 B , Supplementary Material online, table 1. Two of these genes, one encoding a cytochrome P and the other an ATP-dependent RNA helicase, are members of families which include genes that have previously been shown to affect morphology of fruiting bodies in the basidiomycete C.
Seven TF genes were found to show differential expression between phenotypes, mainly at the young fruiting body stage table 2. However, none of the TFs previously implicated in fruiting body development that are present in the L. The hom1 alleles have only synonymous substitutions in their coding regions, but synonymous substitutions can have phenotypic consequences Bailey et al. Lentinus tigrinus provides a unique opportunity to study fruiting body evolution in Agaricomycetes, because it has naturally occurring agaricoid and secotioid forms.
Results presented here are consistent with the view that the secotioid phenotype is conferred by a recessive allele at a single locus, but the precise identity of the locus is unresolved. The secotioid form could result from a shift in transcription level without a change in protein sequence, or a nonsynonymous mutation without a change in expression.
Our top candidate genes table 1 were identified with a combination of BSA and differential expression criteria, but it is possible that one of the many genes identified with only one of the two criteria is responsible for the secotioid form. Other potential mechanisms that could underlie the secotioid phenotype include DNA methylation potentially affecting gene expression and RNA editing which could cause amino acid replacements in proteins.
However, this study did not include genome-wide analyses of such epigenetic modifications. The top 25 candidate genes span almost 1. Seven of the candidate TFs, identified with both BSA or differential expression analyses, also occur on scaffolds 5, 14, and 59, with the rest distributed on scaffolds 19—32 table 2.
It is possible that scaffolds 5, 14, and 59 represent parts of a single chromosome, but long-read sequencing PacBio or nanopore will be needed to test this hypothesis. Like many saprotrophic fungi, L. Most progeny could be clearly differentiated as secotioid or agaricoid in test crosses, but intermediate forms occurred.
Further studies under controlled conditions will be necessary to determine reaction norms for fruiting body development in the secotioid and agaricoid forms of L. Genome-wide association studies using geographically diverse wild strains could help reconstruct the genetic bases and evolutionary history of the secotioid form in L. Other kinds of analyses, such as gene knock-out experiments, will eventually be needed to test specific mechanistic hypotheses, but at present they are constrained by the absence of a transformation protocol for L.
Supplementary data are available at Genome Biology and Evolution online. The work conducted by the U. Department of Energy under Contract No. For permission to present data from unpublished genomes supplementary fig. Amy Yeager produced the mushroom and spore cartoons in figure 2. Adaptive synonymous mutations in an experimentally evolved Pseudomonas fluorescens population. Nat Commun. Google Scholar. Hydrophobins Sc3 and Sc4 gene expression in mounds, fruiting bodies and vegetative hyphae of Schizophyllum commune.
Fungal Genet Biol. Aegerolysins: structure, function, and putative biological role. Protein Sci. Berne S. Pleurotus and Agrocybe hemolysins, new proteins hypothetically involved in fungal fruiting. Biochim Biophys Acta. Accelerated evolution of a false-truffle from a mushroom ancestor. Nature : — Corrochano LM.
Fungal photoreceptors: sensory molecules for fungal development and behaviour. Photochem Photobiol Sci. An unusual psychrophilic aquatic agaric from Argentina. Mycologia 87 4 : — Relationships within Lentinus subg.
Lentinus Polyporales, Agaricomycetes with emphasis on sects. Lentinus and Tigrini. Mycol Progr. Hibbett D. Trends in morphological evolution in homobasidiomycetes inferred using maximum likelihood: a comparison of binary and multistate approaches. Syst Biol. Hibbett DS , et al. A higher-level phylogenetic classification of the fungi.
Mycol Res. Sporocarp ontogeny in Panus Basidiomycotina : evolution and classification. Am J Bot. The secotioid form of Lentinus tigrinus : genetics and development of a fungal morphological innovation. James TY , et al. Polyporales genomes reveal the genetic architecture underlying tetrapolar and bipolar mating systems.
Mycologia 6 : — Justo A , et al. A revised family-level classification of the Polyporales Basidiomycota. Fungal Biol. Kuratani M , et al. The dst2 gene essential for photomorphogenesis of Coprinopsis cinerea encodes a protein with a putative FAD-binding-4 domain.
Kurtz S , et al. Versatile and open software for comparing large genomes. Genome Biol. Li H , Durbin R.
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