Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species
Abstract
:1. Introduction
2. Materials and Methods
2.1. Strain and Culture Conditions
2.2. DNA Extractions
2.3. Genome Sequencing and Assembly
2.4. Genome Annotation and Quality Check
2.5. Synteny Analyses
2.6. Phylogenetic Analyses
2.7. Phylogenomic Analyses
2.8. Annotation of Transposable Elements
2.9. Protein Functionnal Annotation
3. Results
3.1. Main Genome Features
3.2. Macrosynteny between Ganoderma Genomes
3.3. Phylogenetic Analyses of Ganoderma Strains
3.4. Phylogenomic Analyses of the Ganoderma Species and Related Polyporales
3.5. Transposable Element Identification
3.6. Biosynthetic Gene Clusters
3.7. Pfam Protein Domains Found in the Genomes
3.8. The Predicted Secretome
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Species Name | Strain | Reference | Lifestyle | Order | Clade |
---|---|---|---|---|---|
Abortiporus biennis | CIRM-BRFM1778 | [24] | White-rot | Polyporales | residual polyporoid clade |
Bjerkandera adusta | HHB-12826-SP | [11] | White-rot | Polyporales | phlebioid clade |
Ceriporiopsis subvermispora | B | [26] | White-rot | Polyporales | gelatoporia clade |
Dichomitus squalens | LYAD-421 SS1 | [27] | White-rot | Polyporales | core polyporoid clade |
Earliella scabrosa | CIRM-BRFM 1817 | [24] | White-rot | Polyporales | core polyporoid clade |
Epithele typhae | CBS 203.58 | [24] | White-rot | Polyporales | core polyporoid clade |
Fomes fomentarius | CIRM-BRFM 1821 | [24] | White-rot | Polyporales | core polyporoid clade |
Fomitiporia mediterranea | MF3/22 #7 | [27] | White-rot | Hymenochaetales | - |
Ganoderma australe | Cui 17254 | this study | White-rot | Polyporales | core polyporoid clade |
Ganoderma boninense | G3 | [13] | White-rot | Polyporales | core polyporoid clade |
Ganoderma leucocontextum | Dai 12418 | this study | White-rot | Polyporales | core polyporoid clade |
Ganoderma lingzhi | Cui 9166 | this study | White-rot | Polyporales | core polyporoid clade |
Ganoderma lucidum | G.260125-1 | [10] | White-rot | Polyporales | core polyporoid clade |
Ganoderma sinense | ZZ0214-1 | [12] | White-rot | Polyporales | core polyporoid clade |
Ganoderma sp. | 10597 SS1 | [11] | White-rot | Polyporales | core polyporoid clade |
Heterobasidion annosum | TC32-1 | [28] | White-rot | Russulales | - |
Hexagonia nitida | CIRM-BRFM 1802 | [24] | White-rot | Polyporales | core polyporoid clade |
Hydnopolyporus fimbriatus | CBS384.51 | [24] | White-rot | Polyporales | phlebioid clade |
Irpex lacteus | CCBAS Fr. 238 617/93 | [24] | White-rot | Polyporales | phlebioid clade |
Leiotrametes lactinea | CIRM-BRFM 1664 | [24] | White-rot | Polyporales | core polyporoid clade |
Leiotrametes menziesii | CIRM-BRFM 1781 | [24] | White-rot | Polyporales | core polyporoid clade |
Lentinus tigrinus | ALCF2SS1-7 | [29] | White-rot | Polyporales | core polyporoid clade |
Obba rivulosa | 3A-2 | [30] | White-rot | Polyporales | gelatoporia clade |
Panus rudis | PR-1116 ss-1 | [24] | White-rot | Polyporales | residual polyporoid clade |
Phanerochaete carnosa | HHB-10118-Sp | [31] | White-rot | Polyporales | phlebioid clade |
Phanerochaete chrysosporium | RP-78 | [32] | White-rot | Polyporales | phlebioid clade |
Phlebia brevispora | HHB-7030 SS6 | [11] | White-rot | Polyporales | phlebioid clade |
Phlebia centrifuga | FBCC195 | [33] | White-rot | Polyporales | phlebioid clade |
Phlebia radiata | FBCC0043-79 | [34] | White-rot | Polyporales | phlebioid clade |
Phlebiopsis gigantea | 5-6 | [35] | White-rot | Polyporales | phlebioid clade |
Polyporus arcularius | HBB13444 | [36] | White-rot | Polyporales | core polyporoid clade |
Polyporus brumalis | BRFM 1820 | [37] | White-rot | Polyporales | core polyporoid clade |
Polyporus squamosus | CCBS 676 | [24] | White-rot | Polyporales | core polyporoid clade |
Pycnoporus cinnabarinus | BRFM 137 | [38] | White-rot | Polyporales | core polyporoid clade |
Pycnoporus sanguineus | BRFM 1264 | [39] | White-rot | Polyporales | core polyporoid clade |
Rigidoporus microporus | ED310 | [40] | White-rot | Polyporales | - |
Stereum hirsutum | FP-91666 SS1 | [27] | White-rot | Russulales | - |
Trametes pubescens | FBCC735 | [41] | White-rot | Polyporales | core polyporoid clade |
Trametes versicolor | FP-101664 SS1 | [27] | White-rot | Polyporales | core polyporoid clade |
Trametopsis cervina | CIRM-BRFM 1824 | [24] | White-rot | Polyporales | core polyporoid clade |
Amylocystis lapponica | SKaAmylap13 | [24] | Brown-rot | Polyporales | antrodia clade |
Antrodia serialis | Sig1Antser10 | [24] | Brown-rot | Polyporales | antrodia clade |
Antrodia sinuosa | LB1 | PRJNA196036 | Brown-rot | Polyporales | antrodia clade |
Daedalea quercina | L15889 ss-12 | [42] | Brown-rot | Polyporales | antrodia clade |
Fibroporia radiculosa | TFFH 294 | [43] | Brown-rot | Polyporales | antrodia clade |
Fomitopsis betulina | CIRM-BRFM 1772 | [24] | Brown-rot | Polyporales | antrodia clade |
Fomitopsis pinicola | FP-58527 SS1 | [27] | Brown-rot | Polyporales | antrodia clade |
Laetiporus sulphureus | 93-53 | [42] | Brown-rot | Polyporales | antrodia clade |
Postia placenta | MAD-698-R-SB12 | [44] | Brown-rot | Polyporales | antrodia clade |
Rhodofomes roseus | CIRM-BRFM 1785 | [24] | Brown-rot | Polyporales | antrodia clade |
Wolfiporia cocos | MD-104 SS10 | [27] | Brown-rot | Polyporales | antrodia clade |
Amanita muscaria | Koide | [45] | Ectomycorrhizal | Agaricales | - |
Laccaria bicolor | S238N-H82 | [46] | Ectomycorrhizal | Agaricales | - |
Pisolithus microcarpus | 441 | [45] | Ectomycorrhizal | Boletales | - |
Rhizopogon vinicolor | AM-OR11-026 | [47] | Ectomycorrhizal | Boletales | - |
Piriformospora indica | DSM 11827 | [48] | Endophyte | Sebacinales | - |
Melampsora larici-populina | 98AG31 | [49] | Pathogen | Pucciniales | - |
Ustilago maydis | 521 | [50] | Pathogen | Ustilaginales | - |
Genome Feature | G. australe | G. leucocontextum | G. lingzhi |
---|---|---|---|
Genome size (Mb) | 84.27 | 60.34 | 60.56 |
Number of scaffolds | 93 | 843 | 342 |
Scaffold L50 (bp) | 1,745,385 | 205,166 | 402,014 |
Scaffold N50 | 17 | 66 | 37 |
Longest scaffold (bp) | 4,455,856 | 1,715,371 | 2,154,085 |
Shortest scaffold (bp) | 33,016 | 1008 | 980 |
GC content (%) | 55.48 | 55.95 | 55.88 |
Protein-coding genes | 20,460 | 16,952 | 15,007 |
Average gene length (bp) | 1582 | 1846 | 1605 |
Complete BUSCOs (%) | 84.6 | 99.8 | 73.1 |
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Sun, Y.-F.; Lebreton, A.; Xing, J.-H.; Fang, Y.-X.; Si, J.; Morin, E.; Miyauchi, S.; Drula, E.; Ahrendt, S.; Cobaugh, K.; et al. Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species. J. Fungi 2022, 8, 311. https://doi.org/10.3390/jof8030311
Sun Y-F, Lebreton A, Xing J-H, Fang Y-X, Si J, Morin E, Miyauchi S, Drula E, Ahrendt S, Cobaugh K, et al. Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species. Journal of Fungi. 2022; 8(3):311. https://doi.org/10.3390/jof8030311
Chicago/Turabian StyleSun, Yi-Fei, Annie Lebreton, Jia-Hui Xing, Yu-Xuan Fang, Jing Si, Emmanuelle Morin, Shingo Miyauchi, Elodie Drula, Steven Ahrendt, Kelly Cobaugh, and et al. 2022. "Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species" Journal of Fungi 8, no. 3: 311. https://doi.org/10.3390/jof8030311