Analyses of transcriptomes and the first complete genome of Leucocalocybe mongolica provide new insights into phylogenetic relationships and conservation
Abstract
In this study, we report a de novo assembly of the first high-quality genome for a wild mushroom species Leucocalocybe mongolica (LM). We performed high-throughput transcriptome sequencing to analyze the genetic basis for the life history of LM. Our results show that the genome size of LM is 46.0 Mb, including 26 contigs with a contig N50 size of 3.6 Mb. In total, we predicted 11,599 protein-coding genes, of which 65.7% (7630) could be aligned with high confidence to annotated homologous genes in other species. We performed phylogenetic analyses using genes form 3269 single-copy gene families and showed support for distinguishing LM from the genus Tricholoma (L.) P.Kumm., in which it is sometimes circumscribed. We believe that one reason for limited wild occurrences of LM may be the loss of key metabolic genes, especially carbohydrate-active enzymes (CAZymes), based on comparisons with other closely related species. The results of our transcriptome analyses between vegetative (mycelia) and reproductive (fruiting bodies) organs indicated that changes in gene expression among some key CAZyme genes may help to determine the switch from asexual to sexual reproduction. Taken together, our genomic and transcriptome data for LM comprise a valuable resource for both understanding the evolutionary andmore »
- Authors:
-
- Jilin Agricultural Univ (China). Ministry of Agriculture and Rural Afairs. Key Lab. of Edible Fungi Resources and Utilization (North)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1816460
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Scientific Reports
- Additional Journal Information:
- Journal Volume: 11; Journal Issue: 1; Journal ID: ISSN 2045-2322
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES
Citation Formats
Duan, Mingzheng, Bao, Haiying, and Bau, Tolgor. Analyses of transcriptomes and the first complete genome of Leucocalocybe mongolica provide new insights into phylogenetic relationships and conservation. United States: N. p., 2021.
Web. doi:10.1038/s41598-021-81784-6.
Duan, Mingzheng, Bao, Haiying, & Bau, Tolgor. Analyses of transcriptomes and the first complete genome of Leucocalocybe mongolica provide new insights into phylogenetic relationships and conservation. United States. https://doi.org/10.1038/s41598-021-81784-6
Duan, Mingzheng, Bao, Haiying, and Bau, Tolgor. Wed .
"Analyses of transcriptomes and the first complete genome of Leucocalocybe mongolica provide new insights into phylogenetic relationships and conservation". United States. https://doi.org/10.1038/s41598-021-81784-6. https://www.osti.gov/servlets/purl/1816460.
@article{osti_1816460,
title = {Analyses of transcriptomes and the first complete genome of Leucocalocybe mongolica provide new insights into phylogenetic relationships and conservation},
author = {Duan, Mingzheng and Bao, Haiying and Bau, Tolgor},
abstractNote = {In this study, we report a de novo assembly of the first high-quality genome for a wild mushroom species Leucocalocybe mongolica (LM). We performed high-throughput transcriptome sequencing to analyze the genetic basis for the life history of LM. Our results show that the genome size of LM is 46.0 Mb, including 26 contigs with a contig N50 size of 3.6 Mb. In total, we predicted 11,599 protein-coding genes, of which 65.7% (7630) could be aligned with high confidence to annotated homologous genes in other species. We performed phylogenetic analyses using genes form 3269 single-copy gene families and showed support for distinguishing LM from the genus Tricholoma (L.) P.Kumm., in which it is sometimes circumscribed. We believe that one reason for limited wild occurrences of LM may be the loss of key metabolic genes, especially carbohydrate-active enzymes (CAZymes), based on comparisons with other closely related species. The results of our transcriptome analyses between vegetative (mycelia) and reproductive (fruiting bodies) organs indicated that changes in gene expression among some key CAZyme genes may help to determine the switch from asexual to sexual reproduction. Taken together, our genomic and transcriptome data for LM comprise a valuable resource for both understanding the evolutionary and life history of this species.},
doi = {10.1038/s41598-021-81784-6},
journal = {Scientific Reports},
number = 1,
volume = 11,
place = {United States},
year = {Wed Feb 03 00:00:00 EST 2021},
month = {Wed Feb 03 00:00:00 EST 2021}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
The genome sequence of the commercially cultivated mushroom Agrocybe aegerita reveals a conserved repertoire of fruiting-related genes and a versatile suite of biopolymer-degrading enzymes
journal, January 2018
- Gupta, Deepak K.; Rühl, Martin; Mishra, Bagdevi
- BMC Genomics, Vol. 19, Issue 1
Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea
journal, October 2015
- Muraguchi, Hajime; Umezawa, Kiwamu; Niikura, Mai
- PLOS ONE, Vol. 10, Issue 10
BLAST: at the core of a powerful and diverse set of sequence analysis tools
journal, July 2004
- McGinnis, S.; Madden, T. L.
- Nucleic Acids Research, Vol. 32, Issue Web Server
TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders
journal, May 2004
- Majoros, W. H.; Pertea, M.; Salzberg, S. L.
- Bioinformatics, Vol. 20, Issue 16
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation
journal, May 2018
- Zhang, Han; Yohe, Tanner; Huang, Le
- Nucleic Acids Research, Vol. 46, Issue W1
Whole genome sequence of an edible and medicinal mushroom, Hericium erinaceus (Basidiomycota, Fungi)
journal, May 2020
- Gong, Wenbing; Wang, Yahui; Xie, Chunliang
- Genomics, Vol. 112, Issue 3
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
journal, January 2013
- Kim, Daehwan; Pertea, Geo; Trapnell, Cole
- Genome Biology, Vol. 14, Issue 4
The immunomodulatory and antitumor activities of lectins from the mushroom Tricholoma mongolicum
journal, March 1996
- Wang, H. X.; Liu, W. K.; Ng, T. B.
- Immunopharmacology, Vol. 31, Issue 2-3
Whole genome sequence of Auricularia heimuer (Basidiomycota, Fungi), the third most important cultivated mushroom worldwide
journal, January 2019
- Yuan, Yuan; Wu, Fang; Si, Jing
- Genomics, Vol. 111, Issue 1
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
journal, June 2015
- Simão, Felipe A.; Waterhouse, Robert M.; Ioannidis, Panagiotis
- Bioinformatics, Vol. 31, Issue 19
OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species
journal, May 2019
- Xu, Ling; Dong, Zhaobin; Fang, Lu
- Nucleic Acids Research, Vol. 47, Issue W1
Gene Ontology: tool for the unification of biology
journal, May 2000
- Ashburner, Michael; Ball, Catherine A.; Blake, Judith A.
- Nature Genetics, Vol. 25, Issue 1
Genome sequence of the cauliflower mushroom Sparassis crispa (Hanabiratake) and its association with beneficial usage
journal, October 2018
- Kiyama, Ryoiti; Furutani, Yoshiyuki; Kawaguchi, Kayoko
- Scientific Reports, Vol. 8, Issue 1
Comparative transcriptomics of Pleurotus eryngii reveals blue-light regulation of carbohydrate-active enzymes (CAZymes) expression at primordium differentiated into fruiting body stage
journal, May 2018
- Xie, Chunliang; Gong, Wenbing; Zhu, Zuohua
- Genomics, Vol. 110, Issue 3
Transcriptome Analysis and Its Application in Identifying Genes Associated with Fruiting Body Development in Basidiomycete Hypsizygus marmoreus
journal, April 2015
- Zhang, Jinjing; Ren, Ang; Chen, Hui
- PLOS ONE, Vol. 10, Issue 4
OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs
journal, November 2018
- Kriventseva, Evgenia V.; Kuznetsov, Dmitry; Tegenfeldt, Fredrik
- Nucleic Acids Research, Vol. 47, Issue D1
From genomics to chemical genomics: new developments in KEGG
journal, January 2006
- Kanehisa, M.
- Nucleic Acids Research, Vol. 34, Issue 90001
The Pfam protein families database
journal, January 2004
- Bateman, Alex; Coin, Lachlan; Durbin, Richard
- Nucleic Acids Research, Vol. 32, Issue S1, p. D138-D141
The COG database: a tool for genome-scale analysis of protein functions and evolution
journal, January 2000
- Tatusov, R. L.
- Nucleic Acids Research, Vol. 28, Issue 1
Pleurotus eryngii Genomes Reveal Evolution and Adaptation to the Gobi Desert Environment
journal, September 2019
- Dai, Yueting; Sun, Lei; Yin, Xiaolei
- Frontiers in Microbiology, Vol. 10
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
journal, September 2003
- Li, L.
- Genome Research, Vol. 13, Issue 9
r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
journal, January 2003
- Sanderson, M. J.
- Bioinformatics, Vol. 19, Issue 2
AUGUSTUS: a web server for gene finding in eukaryotes
journal, July 2004
- Stanke, M.; Steinkamp, R.; Waack, S.
- Nucleic Acids Research, Vol. 32, Issue Web Server
Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes
journal, February 2019
- Yoo, Seung-il; Lee, Hwa-Yong; Markkandan, Kesavan
- BMC Genomics, Vol. 20, Issue 1
De novo assembly and characterization of the transcriptome of a wild edible mushroom Leucocalocybe mongolica and identification of SSR markers
journal, September 2017
- Lu, Tie; Bau, Tolgor
- Biotechnology & Biotechnological Equipment, Vol. 31, Issue 6
Physiological Study of the Wild Edible Mushroom Leucocalocybe mongolica
journal, January 2017
- Lu, Tie; Bau, Tolgor; Ohga, Shoji
- Journal of the Faculty of Agriculture, Kyushu University, Vol. 62, Issue 1
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory
journal, September 2012
- Chaisson, Mark J.; Tesler, Glenn
- BMC Bioinformatics, Vol. 13, Issue 1
Genome Assembly and Pathway Analysis of Edible Mushroom Agrocybe cylindracea
journal, June 2020
- Liang, Yuan; Lu, Dengxue; Wang, Sen
- Genomics, Proteomics & Bioinformatics, Vol. 18, Issue 3
Extraction, purification, and antioxidant activities of polysaccharides from Tricholoma mongolicum Imai
journal, January 2014
- You, Qinghong; Yin, Xiulian; Zhang, Shengnan
- Carbohydrate Polymers, Vol. 99
The evolution of genomic and epigenomic features in two Pleurotus fungi
journal, May 2018
- Zhang, Zhibin; Wen, Jiawei; Li, Juzuo
- Scientific Reports, Vol. 8, Issue 1
HTSeq--a Python framework to work with high-throughput sequencing data
journal, September 2014
- Anders, S.; Pyl, P. T.; Huber, W.
- Bioinformatics, Vol. 31, Issue 2
Comparative transcriptome analysis of dikaryotic mycelia and mature fruiting bodies in the edible mushroom Lentinula edodes
journal, June 2018
- Song, Ha-Yeon; Kim, Dae-Hyuk; Kim, Jung-Mi
- Scientific Reports, Vol. 8, Issue 1
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
journal, January 2008
- Haas, Brian J.; Salzberg, Steven L.; Zhu, Wei
- Genome Biology, Vol. 9, Issue 1
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
journal, September 2017
- Xiao, Chuan-Le; Chen, Ying; Xie, Shang-Qian
- Nature Methods, Vol. 14, Issue 11
Lectin from Tricholoma mongolicum S. Imai (Agaricomycetideae) Mycelia Stimulates Gene Expression of Immunomodulating Cytokines in Mouse Peritoneal Macrophages and Splenocytes
journal, January 2005
- Liu, Fang; Ng, Tzi Bun; Wang, Hexiang
- International Journal of Medicinal Mushrooms, Vol. 7, Issue 1-2
Hypotensive and Vasorelaxing Activities of a Lectin from the Edible Mushroom Tricholoma mongolicum
journal, December 1996
- Wang, H. X.; Ooi, V. E. C.; Ng, T. B.
- Pharmacology & Toxicology, Vol. 79, Issue 6
Optimization of polysaccharides extraction from Tricholoma mongolicum Imai and their antioxidant and antiproliferative activities
journal, October 2015
- Wang, Jin; Zhao, Yongming; Li, Wei
- Carbohydrate Polymers, Vol. 131
Transcriptome and Proteome Exploration to Provide a Resource for the Study of Agrocybe aegerita
journal, February 2013
- Wang, Man; Gu, Bianli; Huang, Jie
- PLoS ONE, Vol. 8, Issue 2
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
journal, January 2003
- Boeckmann, B.
- Nucleic Acids Research, Vol. 31, Issue 1
Genetic diversity and population structure of endemic mushroom Leucocalocybe mongolica in Mongolian Plateau uncovered by EST-SSR markers
journal, September 2018
- Lu, Tie; Bao, Haiying; Bau, Tolgor
- Biotechnology & Biotechnological Equipment, Vol. 32, Issue 5
Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes
journal, May 2018
- Lomsadze, Alexandre; Gemayel, Karl; Tang, Shiyuyun
- Genome Research, Vol. 28, Issue 7
An efficient algorithm for large-scale detection of protein families
journal, April 2002
- Enright, A. J.
- Nucleic Acids Research, Vol. 30, Issue 7
On an Edible Mongolian Fungus “Pai-mo-ku.”
journal, January 1937
- Imai, Sanshi
- Proceedings of the Imperial Academy, Vol. 13, Issue 7
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
journal, October 2003
- Haas, B. J.
- Nucleic Acids Research, Vol. 31, Issue 19
MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004
- Edgar, R. C.
- Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
PAML 4: Phylogenetic Analysis by Maximum Likelihood
journal, April 2007
- Yang, Z.
- Molecular Biology and Evolution, Vol. 24, Issue 8
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
journal, November 2014
- Walker, Bruce J.; Abeel, Thomas; Shea, Terrance
- PLoS ONE, Vol. 9, Issue 11
TimeTree: A Resource for Timelines, Timetrees, and Divergence Times
journal, April 2017
- Kumar, Sudhir; Stecher, Glen; Suleski, Michael
- Molecular Biology and Evolution, Vol. 34, Issue 7
HISAT: a fast spliced aligner with low memory requirements
journal, March 2015
- Kim, Daehwan; Langmead, Ben; Salzberg, Steven L.
- Nature Methods, Vol. 12, Issue 4
Non-Coding RNA Analysis Using the Rfam Database
journal, June 2018
- Kalvari, Ioanna; Nawrocki, Eric P.; Argasinska, Joanna
- Current Protocols in Bioinformatics, Vol. 62, Issue 1
Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes
journal, January 2013
- Levasseur, Anthony; Drula, Elodie; Lombard, Vincent
- Biotechnology for Biofuels, Vol. 6, Issue 1, Article No. 41