Whole genome and global gene expression analyses of the model mushroom Flammulina velutipes reveal a high capacity for lignocellulose degradation.
Flammulina velutipes is a fungus with health and medicinal benefits that has been used for consumption and cultivation in East Asia. F. velutipes is also known to degrade lignocellulose and produce ethanol. The overlapping interests of mushroom production and wood bioconversion make F. velutipes an attractive new model for fungal wood related studies. Here, we present the complete sequence of the F. velutipes genome. This is the first sequenced genome for a commercially produced edible mushroom that also degrades wood. The 35.6-Mb genome contained 12,218 predicted protein-encoding genes and 287 tRNA genes assembled into 11 scaffolds corresponding with the 11 chromosomes of strain KACC42780. The 88.4-kb mitochondrial genome contained 35 genes. Well-developed wood degrading machinery with strong potential for lignin degradation (69 auxiliary activities, formerly FOLymes) and carbohydrate degradation (392 CAZymes), along with 58 alcohol dehydrogenase genes were highly expressed in the mycelium, demonstrating the potential application of this organism to bioethanol production. Thus, the newly uncovered wood degrading capacity and sequential nature of this process in F. velutipes, offer interesting possibilities for more detailed studies on either lignin or (hemi-) cellulose degradation in complex wood substrates. The mutual interest in wood degradation by the mushroom industry and (ligno-)cellulose biomass related industries further increase the significance of F. velutipes as a new model.
Department of Biomedical Chemistry, Konkuk University, Chung-Ju, Republic of Korea.
Young-Jin
YJ
Park
Macrogen Inc., Seoul, Republic of Korea.
Jeong Hun
JH
Baek
Macrogen Inc., Seoul, Republic of Korea.
Seonwook
S
Lee
Macrogen Inc., Seoul, Republic of Korea.
Changhoon
C
Kim
Macrogen Inc., Seoul, Republic of Korea.
Hwanseok
H
Rhee
Macrogen Inc., Seoul, Republic of Korea.
Hyungtae
H
Kim
Macrogen Inc., Seoul, Republic of Korea; Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul, Republic of Korea.
Jeong-Sun
JS
Seo
Department of Biomedical Chemistry, Konkuk University, Chung-Ju, Republic of Korea.
Hae-Ran
HR
Park
Department of Biomedical Chemistry, Konkuk University, Chung-Ju, Republic of Korea.
Dae-Eun
DE
Yoon
Department of Biomedical Chemistry, Konkuk University, Chung-Ju, Republic of Korea.
Jae-Young
JY
Nam
Department of Biomedical Chemistry, Konkuk University, Chung-Ju, Republic of Korea.
Hong-Il
HI
Kim
Department of Life Sciences and Biotechnology, Kyungpook National University, Daegu, Republic of Korea.
Jong-Guk
JG
Kim
Department of Life Sciences and Biotechnology, Kyungpook National University, Daegu, Republic of Korea.
Hyeokjun
H
Yoon
Graduate School of Biotechnology and Information Technology, Hankyong National University, Ansung, Republic of Korea.
Hee-Wan
HW
Kang
Department of Pharmaceutical Engineering, Sangji University, Wonju, Republic of Korea.
Jae-Yong
JY
Cho
National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea.
Eun-Sung
ES
Song
Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumsung, Republic of Korea.
Gi-Ho
GH
Sung
Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumsung, Republic of Korea.
Young-Bok
YB
Yoo
Department of Biomedical Chemistry, Konkuk University, Chung-Ju, Republic of Korea.
Chang-Soo
CS
Lee
National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea.
Byoung-Moo
BM
Lee
Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumsung, Republic of Korea.
Won-Sik
WS
Kong
D000426:Alcohol Dehydrogenase / Q000235:genetics / Q000378:metabolism; D004271:DNA, Fungal / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D055393:Flammulina / Q000235:genetics* / Q000378:metabolism; D005656:Fungal Proteins / Q000235:genetics* / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D008031:Lignin / Q000235:genetics / Q000378:metabolism*
D004271:DNA, Fungal; D004272:DNA, Mitochondrial; D005656:Fungal Proteins; C036909:lignocellulose; D008031:Lignin; D000426:Alcohol Dehydrogenase