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Title: Genomics and Development of Lentinus tigrinus : A White-Rot Wood-Decaying Mushroom with Dimorphic Fruiting Bodies

Abstract

Lentinus tigrinus is a species of wood-decaying fungi (Polyporales) that has an agaricoid form (a gilled mushroom) and a secotioid form (puffball-like, with enclosed spore-bearing structures). Previous studies suggested that the secotioid form is conferred by a recessive allele of a single locus. We sequenced the genomes of one agaricoid (Aga) strain and one secotioid (Sec) strain (39.53-39.88 Mb, with 15,581-15,380 genes, respectively). We mated the Sec and Aga monokaryons, genotyped the progeny, and performed bulked segregant analysis (BSA). We also fruited three Sec/Sec and three Aga/Aga dikaryons, and sampled transcriptomes at four developmental stages. Using BSA, we identified 105 top candidate genes with nonsynonymous SNPs that cosegregate with fruiting body phenotype. Transcriptome analyses of Sec/Sec versus Aga/Aga dikaryons identified 907 differentially expressed genes (DEGs) along four developmental stages. On the basis of BSA and DEGs, the top 25 candidate genes related to fruiting body development span 1.5 Mb (4% of the genome), possibly on a single chromosome, although the precise locus that controls the secotioid phenotype is unresolved. The top candidates include genes encoding a cytochrome P450 and an ATP-dependent RNA helicase, which may play a role in development, based on studies in other fungi.

Authors:
 [1];  [2];  [1];  [1];  [2];  [1];  [3];  [3];  [3];  [3];  [3];  [4];  [5];  [6];  [7];  [1];  [1]
  1. Clark Univ., Worcester, MA (United States). Biology Dept.
  2. Huazhong Agricultural Univ., Wuhan (China). Institute of Applied Mycology
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Clark Univ., Worcester, MA (United States). Biology Dept.; Tokyo University of Agriculture and Technology, Tokyo (Japan). Department of Environmental and Natural Resource Science
  5. Univ. of Utrecht (Netherlands). Dept. of Biology
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States). Department of Plant and Microbial Biology
  7. Institute of Biochemistry, Szeged (Hungary). Synthetic and Systems Biology Unit
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1546629
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Genome Biology and Evolution
Additional Journal Information:
Journal Volume: 10; Journal Issue: 12; Journal ID: ISSN 1759-6653
Publisher:
Society for Molecular Biology and Evolution
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; basidiomycetes; bulked segregant analysis; development; fungi; gasteromycetes; transcriptome

Citation Formats

Wu, Baojun, Xu, Zhangyi, Knudson, Alicia, Carlson, Alexis, Chen, Naiyao, Kovaka, Sam, LaButti, Kurt, Lipzen, Anna, Pennachio, Christa, Riley, Robert, Schakwitz, Wendy, Umezawa, Kiwamu, Ohm, Robin A., Grigoriev, Igor V., Nagy, László G., Gibbons, John, and Hibbett, David. Genomics and Development of Lentinus tigrinus : A White-Rot Wood-Decaying Mushroom with Dimorphic Fruiting Bodies. United States: N. p., 2018. Web. doi:10.1093/gbe/evy246.
Wu, Baojun, Xu, Zhangyi, Knudson, Alicia, Carlson, Alexis, Chen, Naiyao, Kovaka, Sam, LaButti, Kurt, Lipzen, Anna, Pennachio, Christa, Riley, Robert, Schakwitz, Wendy, Umezawa, Kiwamu, Ohm, Robin A., Grigoriev, Igor V., Nagy, László G., Gibbons, John, & Hibbett, David. Genomics and Development of Lentinus tigrinus : A White-Rot Wood-Decaying Mushroom with Dimorphic Fruiting Bodies. United States. doi:10.1093/gbe/evy246.
Wu, Baojun, Xu, Zhangyi, Knudson, Alicia, Carlson, Alexis, Chen, Naiyao, Kovaka, Sam, LaButti, Kurt, Lipzen, Anna, Pennachio, Christa, Riley, Robert, Schakwitz, Wendy, Umezawa, Kiwamu, Ohm, Robin A., Grigoriev, Igor V., Nagy, László G., Gibbons, John, and Hibbett, David. Tue . "Genomics and Development of Lentinus tigrinus : A White-Rot Wood-Decaying Mushroom with Dimorphic Fruiting Bodies". United States. doi:10.1093/gbe/evy246. https://www.osti.gov/servlets/purl/1546629.
@article{osti_1546629,
title = {Genomics and Development of Lentinus tigrinus : A White-Rot Wood-Decaying Mushroom with Dimorphic Fruiting Bodies},
author = {Wu, Baojun and Xu, Zhangyi and Knudson, Alicia and Carlson, Alexis and Chen, Naiyao and Kovaka, Sam and LaButti, Kurt and Lipzen, Anna and Pennachio, Christa and Riley, Robert and Schakwitz, Wendy and Umezawa, Kiwamu and Ohm, Robin A. and Grigoriev, Igor V. and Nagy, László G. and Gibbons, John and Hibbett, David},
abstractNote = {Lentinus tigrinus is a species of wood-decaying fungi (Polyporales) that has an agaricoid form (a gilled mushroom) and a secotioid form (puffball-like, with enclosed spore-bearing structures). Previous studies suggested that the secotioid form is conferred by a recessive allele of a single locus. We sequenced the genomes of one agaricoid (Aga) strain and one secotioid (Sec) strain (39.53-39.88 Mb, with 15,581-15,380 genes, respectively). We mated the Sec and Aga monokaryons, genotyped the progeny, and performed bulked segregant analysis (BSA). We also fruited three Sec/Sec and three Aga/Aga dikaryons, and sampled transcriptomes at four developmental stages. Using BSA, we identified 105 top candidate genes with nonsynonymous SNPs that cosegregate with fruiting body phenotype. Transcriptome analyses of Sec/Sec versus Aga/Aga dikaryons identified 907 differentially expressed genes (DEGs) along four developmental stages. On the basis of BSA and DEGs, the top 25 candidate genes related to fruiting body development span 1.5 Mb (4% of the genome), possibly on a single chromosome, although the precise locus that controls the secotioid phenotype is unresolved. The top candidates include genes encoding a cytochrome P450 and an ATP-dependent RNA helicase, which may play a role in development, based on studies in other fungi.},
doi = {10.1093/gbe/evy246},
journal = {Genome Biology and Evolution},
number = 12,
volume = 10,
place = {United States},
year = {2018},
month = {11}
}

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