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Gloeostereum incarnatum has edible and medicinal value and was first cultivated and domesticated in China. We sequenced the G. incarnatum monokaryotic strain GiC-126 on an Illumina HiSeq X Ten system and obtained a 34.52-Mb genome assembly sequence that encoded 16,895 predicted genes. We combined the GiC-126 genome with the published genome of G. incarnatum strain CCMJ2665 to construct a genetic linkage map (GiC-126 genome) that had 10 linkage groups (LGs), and the 15 assembly sequences of CCMJ2665 were integrated into 8 LGs. We identified 1912 simple sequence repeat (SSR) loci and detected 700 genes containing 768 SSRs in the genome; 65 and 100 of them were annotated with gene ontology (GO) terms and KEGG pathways, respectively. Carbohydrate-active enzymes (CAZymes) were identified in 20 fungal genomes and annotated; among them, 144 CAZymes were annotated in the GiC-126 genome. The A mating-type locus (MAT-A) of G. incarnatum was located on scaffold885 at 38.9 cM of LG1 and was flanked by two homeodomain (HD1) genes, mip and beta-fg. Fourteen segregation distortion markers were detected in the genetic linkage map, all of which were skewed toward the parent GiC-126. They formed three segregation distortion regions (SDR1–SDR3), and 22 predictive genes were found in scaffold1920 where three segregation distortion markers were located in SDR1. In this study, we corrected and updated the genomic information of G. incarnatum. Our results will provide a theoretical basis for fine gene mapping, functional gene cloning, and genetic breeding the follow-up of G. incarnatum.

Auricularia cornea, jelly mushroom, is a popular ingredient of traditional Chinese cuisine. This study aimed at evaluating the growth, yield, biological efficiency, total phenolic and flavonoid contents, the antioxidant activity, elemental composition, and molecular structure of the wild and domesticated strain Ac24 and the commercially cultivated edible mushroom A. cornea strains Ac1, Ac3 and Ac15. Based on the weight of the fresh fruiting bodies of A. cornea strains, the maximum yield was obtained from commercial strain Ac1 (237.10 g), followed by Ac3 (224.47 g), Ac15 (158 g) and Ac24 (132.37 g), while the biological efficiency range of A. cornea strains was 52.94–94.84%, with significant differences among the A. cornea strains. Our results revealed that Ac24 contained the highest phenolic content (20.10 mg GAE · g−1), while the highest flavonoid content was found in Ac1 (35.13 mg CE · g−1). The maximum mineral contents and the strains were as follows: copper (7.2 mg · kg−1) and zinc (310 mg · kg−1) in Ac1, manganese (788 mg · kg−1) in Ac3 and iron (310 mg · kg−1) in Ac24. DPPH assay found maximum antioxidant activity in Ac24 (IC50 0.233 mg TX · mL−1), FRAP (591 mg TX · g−1) in Ac15, and erythrocyte haemolysis in Ac24. SEM-EDX and FTIR analyses verified the differences among A. cornea strains. The results revealed that wild, domesticated A. cornea strain Ac24 is a promising dietary source of natural antioxidants and is of high nutritional value, compared to commercially cultivated strains.

Background This study aimed to evaluate the possibility of cotton waste enrichment with glycine betaine (GB) for production of two strains (P9, P10) of king oyster (Pleurotus eryngii). Cotton waste was used as (100%) control (T0 = cotton waste) and augmented with various combinations of GB, (T1 = 2 mmol L-1 , T2 = 4 mmol L-1 , T3 = 6 mmol L-1 , T4 = 8 mmol L-1 and T5 = 10 mmol L-1 ). The response of king oyster to GB was evaluated by earliness, yield, biological efficiency (BE), minerals (nitrogen, phosphorus, potassium, zinc (Zn), copper (Cu), magnesium (Mg), manganese (Mn), iron (Fe), sodium (Na), calcium (Ca)), total sugars, total soluble solids, reducing sugars, non-reducing sugars, ascorbic acid, proximate (crude protein, carbohydrates, crude fibers, ash, fats) content of fruiting body and Fourier-transform infrared (FTIR) spectroscopy analysis compared with the control substrate (cotton waste). Results The earliness, yield, and BE were higher as compared to control substrate and increased with an augmentation in the concentration of GB within the cotton waste. Two strains showed (on dry weight basis) 33.9-54.9 mg g-1 nitrogen, 6.8-12.5 mg g-1 phosphorus, 16.9-25.1 mg g-1 potassium, 40.5-64.2 mg kg-1 Zn, 17.1-37.3 mg kg-1 Cu, 1174-1325 mg kg-1 Mg, 20.1-29.1 mg kg-1 Mn, 129-265 mg kg-1 Fe, 779-835 mg kg-1 Ca), 6.3%-11.3% total sugars, 7.3-14.9 °Brix total soluble solids, 2.1-7.3% reducing sugars, 10.4-18.1% crude protein, 3.6-4.4% crude fiber and 5.6-16.7 mg (100 g)-1 on various concentration of GB enrich cotton waste. Cotton waste enriched with GB significantly affected nutritional profile of king oyster mushroom. Conclusion The results revealed that GB enriched cotton waste can be used as an innovative substrate to enhance the yield and quality of king oyster mushroom. © 2019 Society of Chemical Industry.

Gloeostereum incarnatum is an edible medicinal mushroom widely grown in China. Using the whole genome of G. incarnatum, simple sequence repeat (SSR) markers were developed and synthetic primers were designed to construct its first genetic linkage map. The 1,048.6 cm map is composed of 10 linkage groups and contains 183 SSR markers. In total, 112 genome assembly sequences were anchored, representing 16.43 Mb and covering 46.41% of the genome. Selfing populations were used for quantitative trait loci (QTL) targeting, and the composite interval mapping method was used to co-localize the mycelium growth rate (potato dextrose agar and sawdust), growth period, yield and fruiting body length, and width and thickness. The 14 QTLs of agronomic traits had LOD values of 3.20-6.51 and contribution rates of 2.22-13.18%. No linkage relationship was found between the mycelium growth rate and the growth period, but a linkage relationship was observed among the length, width and thickness of the fruiting bodies. Using NCBI's BLAST alignment, the genomic sequences corresponding to the QTL regions were compared, and a TPR-like protein candidate gene was selected. Using whole-genome data, 138 candidate genes were found in four sequence fragments of two SSR markers located in the same scaffold. The genetic map and QTLs established in this study will aid in developing selective markers for agronomic traits and identifying corresponding genes, thereby providing a scientific basis for the further gene mapping of quantitative traits and the marker-assisted selection of functional genes in G. incarnatum breeding programs.

The fruiting body pattern is an important agronomic trait of the edible fungus Auricularia auricula-judae, and an important breeding target. There are two types of fruiting body pattern: the cluster type and the chrysanthemum type. We identified the fruiting body pattern of 26 test strains, and then constructed two different near-isogenic pools. Then, we developed sequence characterized amplified region (SCAR) molecular markers associated with the fruiting body pattern based on sequence-related amplified polymorphism (SRAP) markers. Ten different bands (189–522 bp) were amplified using 153 pairs of SRAP primers. The SCAR marker “SCL-18” consisted of a single 522-bp band amplified from the cluster-type strains, but not the chrysanthemum strains. This SCAR marker was closely associated with the cluster-type fruiting body trait of A. auricula-judae. These results lay the foundation for further research to locate and clone genes controlling the fruiting body pattern of A. auricula-judae.

Auricularia heimuer is one of the most popular edible fungi in China. It has high economic and medicinal value. The complete mitochondrial genome of A. heimuer is 40586 bp. It contains 48 genes, including 25 protein-coding genes, 22 tRNA genes, and 1 gene coding RNase P RNA. The G + C content is 37.92%. The phylogenetic relationships were constructed on the Bayesian inference method. It showed that A. heimuer was in distance to other species of Russulales, Polyporales, and Agaricales. The complete genome sequence of A. heimuer will provide a useful resource for the genetic and systematics studies.

Color is an important quality attribute of fungi, and a useful marker for classification, genetic, and molecular research. However, there is much debate over which enzymes play key regulatory roles in pigment synthesis pathways among different fungi and even within the same species. Auricularia cornea is the most widely cultivated mushroom in the genus Auricularia; 1.834 million tons of this mushroom were produced in 2016 in China. Thus, systematic studies on its color inheritance and the genes encoding key enzymes for pigment synthesis have high scientific and economic value. In this study, the white strain ACW001 and the purple strain ACP004 of A. cornea were used as dikaryotic parents. Selfing populations of ACW001 and ACP004 were constructed with their monokaryotic strains. The fruiting body color of the two populations was consistent with that of their parents, confirming that the two parents were color homozygotes. All strains in the hybrid population of the two parents produced purple fruiting bodies. A robust hybrid strain (ACW001-33×ACP004-33) was selected from the hybrid population, and 87 monokaryotic strains of ACW001-33×ACP004-33 were obtained as a mapping population. Finally, a testcross population was constructed by crossing the mapping population with the test strain ACW001-9. The color genotype of each monokaryotic strain in the mapping population was identified by a fruiting test. The genomes of the two monokaryotic strains ACW001-33 and ACP004-33 were sequenced, and then simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) molecular marker primers were developed. Then, 88 pairs of primers that could distinguish the genotypes of the mapping population were used to construct a genetic linkage map. The genetic linkage map consisted of 12 linkage groups (LGs) spanning 1315.2 cM. The color control locus was preliminarily located at 24.5 cM of the 11th LG. Fine-mapping primers were designed based on sequence differences between ACW001-33 and ACP004-33 in the primary location region. Four color control candidate genes were located in an 8.2-kb region of ACW001-33_contig733 and a 9.2-kb region of ACP004-33_contig802. Homologous alignment and prediction of conserved domain analyses indicated that two of the color control candidate genes encoded proteins with unknown function, and the other two, ACP004_g11815 and ACP004_g11816, encoded glutamyl aminotransferases. These two genes were consecutively arranged on ACP004-33_contig802, and were likely to encode key enzymes in the γ-glutamine-4-hydroxy-benzoate (GHB) pigment synthesis pathway. Primers were designed from the flanking sequences of the two genes and used to analyze the testcross population. Products were amplified only from the 30 testcross strains with purple fruiting bodies, confirming the accuracy of the localization results. We discuss the deficiencies and advantages of map-based cloning in fungi vs. plants, and summarize the steps and requirements of the map-based cloning method for fungi. This study has provided novel ideas and methods for locating functional genes in fungi.

Auricularia heimuer is one of the most popular edible fungi in China. In this study, the whole genome of A. heimuer was sequenced on the Illumina HiSeq X system and compared with other mushrooms genomes. As a wood-rotting fungus, a total of 509 carbohydrate-active enzymes (CAZymes) were annotated in order to explore its potential capabilities on wood degradation. The glycoside hydrolases (GH) family genes in the A. heimuer genome were more abundant than the genes in the other 11 mushrooms genomes. The A. heimuer genome contained 102 genes encoding class III, IV, and V ethanol dehydrogenases. Evolutionary analysis based on 562 orthologous single-copy genes from 15 mushrooms showed that Auricularia formed an early independent branch of Agaricomycetes. The mating-type locus of A. heimuer was located on linkage group 8 by genetic linkage analysis. By combining the genome sequence analysis with the genetic linkage map, the mating-type locus of A. heimuer was located on scaffold45 and consisted of two subunits, &alpha, and &beta, Each subunit consisted of a pair of homeodomain mating-type protein genes HD1 and HD2. The mapping revealed conserved synteny at the whole mating-type loci and mirror symmetry relations near the &beta, subunit between A. heimuer and Exidia glandulosa. This study proposed the potential for the bioethanol production by consolidated bioprocessing of A. heimuer. It will promote understanding of the lignocellulose degradation system and facilitate more efficient conversion of the agricultural wastes used for mushroom cultivation. It also will advance the research on the fruiting body development and evolution of A. heimuer.

Auricularia auricula-judae is a traditional edible fungus that is cultivated widely in China. In this study, a genetic linkage map for A. auricula-judae was constructed using a mapping population consisting of 138 monokaryons derived from a hybrid strain (A119-5). The monokaryotic parent strains A14-5 and A18-119 were derived from two cultivated varieties, A14 (Qihei No. 1) and A18 (Qihei No. 2), respectively. In total, 130 simple sequence repeat markers were mapped. These markers were developed using the whole genome sequence of A. auricula-judae and amplified in A14-5, A18- 119, and the mapping population. The map consisted of 11 linkage groups (LGs) spanning 854 cM, with an average interval length of 6.57 cM. A testcross population was derived from crossing between the monokaryon A184-57 (from the wild strain A184 as a tester strain) and the mapping population. Important agronomic trait-related QTLs, including mycelium growth rate on potato dextrose agar for the mapping population, mycelium growth rate on potato dextrose agar and sawdust for the testcross population, growth period (days from inoculation to fruiting body harvesting), and yield for the testcross population, were identified using the composite interval mapping method. Six mycelium growth raterelated QTLs were identified on LG1 and LG4, two growth period-related QTLs were identified on LG2, and three yieldrelated QTLs were identified on LG2 and LG6. The results showed no linkage relationship between mycelium growth rate and growth period. The present study provides a foundation for locating genes for important agronomic characteristics in A. auricula-judae in the future.