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Research Articles

Analysis of the Genome Sequence of Strain GiC-126 of Gloeostereum incarnatum with Genetic Linkage Map

, ORCID Icon, , , , , , , , , , & show all
Pages 406-420 | Received 29 Mar 2021, Accepted 07 Jul 2021, Published online: 12 Aug 2021

References

  • Li YT, Song H, Li YQ, et al. Study on antioxidant properties of alcohol extract of Gleoeostereum incarnatum fermentation. J Fungal Res. 2010;8:90–92.
  • Zhang ZF, Lv GY, Jiang X, et al. Extraction optimization and biological properties of a polysaccharide isolated from Gleoestereum incarnatum. Carbohydr Polym. 2015;117:185–191.
  • Wang D, Li Q, Qu YD, et al. The investigation of immunomodulatory activities of Gloeostereum incaratum polysaccharides in cyclophosphamide-induced immunosuppression mice. Exp Ther Med. 2018;15(4):3633–3638.
  • Li X, Liu X, Zhang YF, et al. Protective effect of Gloeostereum incarnatum on ulcerative colitis via modulation of Nrf2/NF-κB signaling in C57BL/6 mice. Mol Med Rep. 2020;22(4):3418–3428.
  • Yu Y, Yao FJ, Sun ML, et al. A new Gloeostereum incarnatum cultivar ‘Qirou 1. Acta Horticulturae Sin. 2013;40:15–15.
  • Yu Y, Yao FJ, Zhang YM. A new Gloeostereum incarnatum cultivar ‘Jirou 1. Acta Horticulturae Sin. 2016;43:1013–1014.
  • Gao YL, He D, Wei YY, et al. Research progress on fungal genetic methods. J Fungal Res. 2019;17:173–179.
  • Zhang Y, Huang CY, Gao W. Research advances on molecular mushroom breeding. J Fungal Res. 2019;17:229–239.
  • Wang DD, Li LQ, Ma LY, et al. Progress in development and applications of SSR molecular marker in macrofungi. Microbiology. 2013;40:646–654.
  • Cao Y, Zhang YZ, Cheng SJ, et al. Genome-wide distributional and comparative analysis of SSR loci in Trametes versicolor. Mycosystema. 2017;36:1524–1542.
  • Lu LX, Yao FJ, Wang P, et al. Construction of a genetic linkage map and QTL mapping of agronomic traits in Auricularia auricula-judae. J Microbiol. 2017;55(10):792–799.
  • Wang P, Yao FJ, Lu LX, et al. Map-based cloning of genes encoding key enzymes for pigment synthesis in Auricularia cornea. Fungal Biol. 2019;123(11):843–853.
  • Yao FJ, Lu LX, Wang P, et al. Development of a molecular marker for fruiting body pattern in Auricularia auricula-judae. Mycobiology. 2018;49:72–78.
  • Wang XX, Peng JY, Sun L, et al. Genome sequencing illustrates the genetic basis of the pharmacological properties of Gloeostereum incarnatum. Genes. 2019;10(3):188.
  • Chen SL, Xu J, Liu C, et al. Genome sequence of the model medicinal mushroom Ganoderma lucidum. Nat Commun. 2012;3:913.
  • Bao DP, Gong M, Zheng HJ, et al. Sequencing and comparative analysis of the straw mushroom (Volvariella volvacea) genome. PLOS One. 2013;8(3):e58294.
  • Bau T, Lu T. Advance of macro-fungal genomes Ssquencing. J Fungal Res. 2017;15:151–165.
  • Au CH, Wong MC, Qin J, et al. Genome sequence and genetic linkage analysis of Shiitake mushroom Lentinula edodes. Nat Prec. 2012. DOI:https://doi.org/10.1038/npre.2012.6855.1
  • Park YJ, Baek JH, Lee S, et al. Whole genome and global gene expression analyses of the model mushroom Flammulina velutipes reveal a high capacity for lignocellulose degradation. PLoS One. 2014;9(4):e93560.
  • Eid J, Fehr A, Gray J, et al. Real-time DNA sequencing from single polymerase molecules. Science. 2009;323(5910):133–138.
  • Sonnenberg AS, Gao W, Lavrijssen B, et al. A detailed analysis of the recombination landscape of the button mushroom Agaricus bisporus var. bisporus. Fungal Genet Biol. 2016;93:35–45.
  • Yuan Y, Wu F, Si J, et al. Whole genome sequence of Auricularia heimuer (Basidiomycota, Fungi), the third most important cultivated mushroom worldwide. Genomics. 2019;111:50–58.
  • Song H, Yao FJ, Tang J, et al. Research overview of Gloeostereum incarnatum. Chin Edible Fungi. 2008;27:3–4.
  • Yu Y, Yao FJ, Sun ML, et al. Spring and autumn cultivation management technology of Gloeostereum incarnatum. Northern Horticulture. 2013;10:145–146.
  • Choi YW, Hyde KD, Ho WWH. Single spore isolation of fungi. Fungal Divers. 1999;3:29–38.
  • Jiang WZ, Yao FJ, Lu LX, et al. Genetic linkage map construction and quantitative trait loci mapping of agronomic traits in Gloeostereum incarnatum. J Microbiol. 2021;59(1):41–50.
  • Watanabe M, Lee K, Goto K, et al. Rapid and effective DNA extraction method with bead grinding for a large amount of fungal DNA. J Food Prot. 2010;73(6):1077–1084.
  • Borodovsky M, Lomsadze A. Eukaryotic gene prediction using GeneMark.hmm-E and GeneMark-ES. Curr Protocols Bioinform. 2011;4:1–10.
  • Boeckmann B, Bairoch AM, Apweiler R, et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 2003;31(1):365–370.
  • Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. Nat Genet. 2000;25(1):25–29.
  • Kanehisa M, Goto S, Kawashima S, et al. The KEGG resource for deciphering the genome. Nucleic Acids Res. 2004;32(90001):277D–2280.
  • Kanehisa M, Goto S, Hattori M, et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 2006;34(90001):D354–D357.
  • Murat C, Riccioni C, Belfiori B, et al. Distribution and localization of microsatellites in the Perigord black truffle genome and identification of new molecular markers. Fungal Genet Biol. 2011;48(6):592–601.
  • Untergasser A, Cutcutache I, Koressaar T, et al. Primer3-new capabilities and interfaces. Nucleic Acids Res. 2012;40(15):e115–e115.
  • Zhang H, Yohe T, Huang L, et al. dbCAN2: A meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2018;46(W1):W95–W101.
  • Van Ooijen J, Voorrips R. JoinMap 4.0: Software for the calculation of genetic linkage maps in experimental populations. 2006; Kyazma BV, Wageningen.
  • Floudas D, Binder D, Riley R, et al. The paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science. 2012;336(6089):1715–1719.
  • Fang M, Wang XE, Chen Y, et al. Genome sequence analysis of Auricularia heimuer combined with genetic linkage map. J Fungi. 2020;6(1):37.
  • Liu DB, Gong J, Dai WK, et al. The genome of Ganderma lucidum provide insights into triterpense biosynthesis and wood degradation. PLos One. 2012;7(5):e36146.
  • Chen BZ, Gui F, Xie BG, et al. Composition and expression of genes encoding carbohydrate-active enzymes in the straw-degrading mushroom Volvariella volvacea. PLos One. 2013;8(3):e58780.
  • Qian J, Xu HB, Song JY, et al. Genome-wide analysis of simple sequence repeats in the model medicinal mushroom Ganoderma lucidum. Gene. 2013;512(2):331–336.
  • Wang Y, Chen MJ, Wang H, et al. Microsatellites in the genome of the edible mushroom, Volvariella volvacea. BioMed Res Int. 2014;2014:28912.
  • Qu JB, Huang CY, Zhang JX. Genome-wide functional analysis of SSR for an edible mushroom Pleurotus ostreatus. Gene. 2016;575(2 Pt 2):524–530.
  • Lombard V, Golaconda Ramulu H, Drula E, et al. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014;42:D490–D495.
  • Riley R, Salamov AA, Brown DW, et al. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. Proc Natl Acad Sci USA. 2014;111(27):9923–9928.
  • James TY, Srivilai P, Kües U, Vilgalys, et al. Evolution of the bipolar mating system of the mushroom Coprinellus disseminatus from its tetrapolar ancestors involves loss of mating-type-specific pheromone receptor function. Genetics. 2006;172(3):1877–1891.
  • Yi R, Tachikawa T, Mukaiyama H, Mochida, et al. DNA-mediated transformation system in a bipolar basidiomycete, Pholiota microspora (P. nameko). Mycoscience. 2009;50(2):123–129.
  • James TY, Lee M, van Diepen LTA. A Single Mating-Type Locus Composed of Homeodomain genes promotes nuclear migration and heterokaryosis in the white-rot fungus Phanerochaete chrysosporium. Eukaryot Cell. 2011;10(2):249–261.
  • Van Peer AF, Park SY, Shin PG, et al. Comparative genomics of the mating-type loci of the mushroom Flammulina velutipes reveals widespread synteny and recent inversions. PLoS One. 2011;6(7):e22249.
  • Bakkeren G, Kronstad JW. Linkage of mating-type loci distinguishes bipolar from tetrapolar mating in basidiomycetous smut fungi. Proc Natl Acad Sci USA. 1994;91(15):7085–7089.
  • Au CH, Wong MC, Bao DP, et al. The genetic structure of the A mating-type locus of Lentinula edodes. Gene. 2014;535(2):184–190.
  • Casselton LA, Asante-Owusu RN, Banham AH, et al. Mating type control of sexual development in Coprinus cinereus. Can J Bot. 1995;73(S1):266–272.
  • Specht CA, Stankis MM, Giasson L, et al. Functional analysis of the homeodomain related proteins of the A alpha locus of Schizophyllum commune. Proc Natl Acad Sci USA. 1992;89(15):7174–7178.
  • Liu HY, Cui JT, Gao YM. Progress of segregation distortion. J Plant Genet Res. 2009;10:613–617.
  • Liu ZF, Zhu ZP, Huang DR, et al. Genetic analysis on segregation distortion of molecular markers in F2 population of C. Moschata Duch. Mol Plant Breed. 2019;17:3993–3999.