Whole-Genome Sequencing and Comparative Genomics Analysis of the Wild Edible Mushroom (Gomphus purpuraceus) Provide Insights into Its Potential Food Application and Artificial Domestication
Abstract
:1. Introduction
2. Materials and Methods
2.1. Fungal Strains
2.2. Library Construction, Sequencing and Assembly
2.3. Genomic Prediction and Genome Annotation
2.4. Comparative Genomics Analysis
2.5. Optimization of Culture Medium for G. purpuraceus
3. Results
3.1. Analysis of the Genome Assembly and Gene Prediction
3.2. Gene General Annotation
3.3. Gene Special Annotation
3.4. Comparative Genomics Analysis
3.4.1. Gene Family Analysis
3.4.2. Phylogenetic Relationship of G. purpuraceus
3.4.3. Comparative Analysis of CAZymes
3.4.4. Comparative Analysis of Secondary Metabolisms
3.5. Optimization of Culture Medium
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Parameter | Value |
---|---|
Gene assembly | |
Contigs number | 50 |
GC content (%) | 47.74 |
N50 (bp) | 2,068,469 |
N90 (bp) | 391,632 |
Gene prediction and analysis | |
Genome size (bp) | 40,153,731 |
Number of protein-coding genes | 8705 |
Gene total length (bp) | 18,498,255 |
Gene average length (bp) | 2125.01 |
CDSs total length (bp) | 12,578,619 |
CDSs number | 62,798 |
Exon length (bp) | 14,695,320 |
Intron length (bp) | 3,802,935 |
Repeated sequence percentage (%) | 38.52 |
Non-coding RNA number | 107 |
rRNA number | 11 |
tRNA number | 78 |
Pseudo gene number | 119 |
Species | Total Gene Number | Total Gene Family Number | Cluster Gene Number |
---|---|---|---|
L. edodes | 9804 | 6136 | 7776 |
F. velutipes | 14,460 | 7393 | 12,308 |
P. ostreatus | 11,693 | 7333 | 10,130 |
M. importuna | 11,971 | 6237 | 7649 |
P. portentosus | 9899 | 6537 | 9104 |
T. melanosporum | 7496 | 5503 | 5812 |
B. edulis | 18,718 | 8153 | 15,426 |
L. hatsudake | 16,831 | 8553 | 13,716 |
L. deliciosus | 18,193 | 8772 | 14,583 |
L. bicolor | 18,215 | 7721 | 13,863 |
R. virescens | 20,499 | 7121 | 17,450 |
R. griseocarnosa | 17,754 | 6593 | 15,618 |
G. bonarii | 29,452 | 6309 | 25,493 |
G. purpuraceus | 8705 | 6590 | 7875 |
Secondary Metabolisms | Terpenes | NRPS and NRPS-like | PKS and PKS-like | DMAT | Siderophore | Hybrid | Other | Total |
---|---|---|---|---|---|---|---|---|
G. purpuraceus | 9 | 6 | 5 | 1 | 1 | 22 | ||
G. bonarii | 14 | 3 | 2 | 19 | ||||
R. griseocarnosa | 8 | 1 | 1 | 10 | ||||
R. virescens | 9 | 1 | 2 | 12 | ||||
L. bicolor | 9 | 4 | 3 | 1 | 17 | |||
L. deliciosus | 18 | 2 | 2 | 22 | ||||
L. hatsudake | 14 | 2 | 2 | 18 | ||||
B. edulis | 8 | 9 | 2 | 1 | 20 | |||
T. melanosporum | 0 | 4 | 4 | 8 | ||||
P. portentosus | 7 | 7 | 3 | 3 | 20 | |||
M. importuna | 1 | 6 | 3 | 10 | ||||
P. ostreatus | 10 | 9 | 2 | 21 | ||||
F. velutipes | 12 | 3 | 1 | 2 | 2 | 20 | ||
L. edodes | 7 | 10 | 5 | 22 |
Symbol and Definition | EC No. | KO Term | Gene ID |
---|---|---|---|
ACAT, acetyl-CoA C-acetyltransferase | EC:2.3.1.9 | K00626 | EVM0002057.1 |
HMGCS, hydroxymethylglutaryl-CoA synthase | EC:2.3.3.10 | K01641 | EVM0008435.1 |
HMGCR, hydroxymethylglutaryl-CoA reductase (NADPH) | EC:1.1.1.34 | K00021 | EVM0004540.1 |
mvaK2, phosphomevalonate kinase | EC:2.7.4.2 | K00938 | EVM0000866.1 |
mvaD, diphosphomevalonate decarboxylase | EC:4.1.1.33 | K01597 | EVM0000734.1 |
IDI, isopentenyl-diphosphate Delta-isomerase | EC:5.3.3.2 | K01823 | EVM0005424.1 |
FDPS, farnesyl diphosphate synthase | EC:2.5.1.1 2.5.1.10 | K00787 | EVM0002481.1 |
GGPS1, geranylgeranyl diphosphate synthase, type III | EC:2.5.1.1 2.5.1.10 2.5.1.29 | K00804 | EVM0001739.1 |
PCYOX1, prenylcysteine oxidase/farnesylcysteine lyase | EC:1.8.3.5 1.8.3.6 | K05906 | EVM0005178.1 |
ICMT, protein-S-isoprenylcysteine O-methyltransferase | EC:2.1.1.100 | K00587 | EVM0004818.1 |
STE24, STE24 endopeptidase | EC:3.4.24.84 | K06013 | EVM0003020.1 |
RCE1, prenyl protein peptidase | EC:3.4.22.- | K08658 | EVM0006143.2 |
FNTB, protein farnesyltransferase subunit β | EC:2.5.1.58 | K05954 | EVM0000741.3 |
FNTA, protein farnesyltransferase/geranylgeranyltransferase type-1 subunit α | EC:2.5.1.58 2.5.1.59 | K05955 | EVM0000039.3 |
DHDDS, ditrans, polycis-polyprenyl diphosphate synthase | EC:2.5.1.87 | K11778 | EVM0004045.1 |
hexPS, hexaprenyl-diphosphate synthase | EC:2.5.1.82 2.5.1.83 | K05355 | EVM0005717.4 |
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Geng, Y.; Zhang, S.; Yang, N.; Qin, L. Whole-Genome Sequencing and Comparative Genomics Analysis of the Wild Edible Mushroom (Gomphus purpuraceus) Provide Insights into Its Potential Food Application and Artificial Domestication. Genes 2022, 13, 1628. https://doi.org/10.3390/genes13091628
Geng Y, Zhang S, Yang N, Qin L. Whole-Genome Sequencing and Comparative Genomics Analysis of the Wild Edible Mushroom (Gomphus purpuraceus) Provide Insights into Its Potential Food Application and Artificial Domestication. Genes. 2022; 13(9):1628. https://doi.org/10.3390/genes13091628
Chicago/Turabian StyleGeng, Yangyang, Shixin Zhang, Ningxian Yang, and Likang Qin. 2022. "Whole-Genome Sequencing and Comparative Genomics Analysis of the Wild Edible Mushroom (Gomphus purpuraceus) Provide Insights into Its Potential Food Application and Artificial Domestication" Genes 13, no. 9: 1628. https://doi.org/10.3390/genes13091628
APA StyleGeng, Y., Zhang, S., Yang, N., & Qin, L. (2022). Whole-Genome Sequencing and Comparative Genomics Analysis of the Wild Edible Mushroom (Gomphus purpuraceus) Provide Insights into Its Potential Food Application and Artificial Domestication. Genes, 13(9), 1628. https://doi.org/10.3390/genes13091628