Genomic Evidence of Recombination in the Basidiomycete Wallemia mellicola
Abstract
1. Introduction
2. Materials and Methods
2.1. Culture, Medium, Growth Conditions and DNA Isolation
2.2. Genome Sequencing
2.3. Variant Calling
2.4. Assembly and Annotation
2.5. Variant-Based Analysis
2.6. Phylogenetic Analysis
2.7. Core Genome, GO Enrichment
2.8. Mating-Type Loci
3. Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Culture Collection Strain Number * | Number in This Study | Isolation Habitat | Sampling Site Location |
---|---|---|---|
EXF-277 | 1 | hypersaline saltern water | Spain |
EXF-757 | 2 | hypersaline saltern water | Dominican Republic |
EXF-1274 (CBS 110588) | 3 | peanuts | Indonesia |
EXF-1277 (CBS 110589) | 4 | Channa striata dried salted fish | Indonesia |
EXF-1279 (CBS 110593) | 5 | straw hat | Philippines |
EXF-5677 | 6 | air | Slovenia |
EXF-5829 | 7 | chocolate | Slovenia |
EXF-6156 (UAMH 2651) | 8 | moldy white bread | United Kingdom |
EXF-6157 (UAMH 2757) | 9 | soil | Canada |
EXF-6158 (UAMH 6689) | 10 | maple syrup | Canada |
EXF-8738 | 11 | house dust | Uruguay |
EXF-8740 | 12 | house dust | Micronesia |
EXF-8747 | 13 | house dust | Indonesia |
EXF-8749 | 14 | house dust | Thailand |
EXF-8757 | 15 | house dust | Mexico |
EXF-10633 | 16 | dry common fig | Slovenia |
EXF-483 | 17 | hypersaline saltern water | Spain |
EXF-1262 (CBS 213.34) | 18 | Unknown | Italy |
EXF-1443 (IBT 19078) | 19 | Unknown | Denmark |
EXF-5828 | 20 | chocolate | Slovenia |
EXF-5830 | 21 | chocolate | Slovenia |
EXF-5922 | 22 | chocolate | Slovenia |
EXF-6152 (MUCL 45613) | 23 | forest plant (Clusia rosea) | Cuba |
EXF-6151 (MUCL 45615) | 24 | forest plant (Verbena officinalis) | Cuba |
EXF-8741 | 25 | house dust | Micronesia |
Statistic * | Minimum ** | Mean ** | Maximum ** | Standard Deviation** |
---|---|---|---|---|
Coverage | 194 | 318 | 558 | 92 |
Genome assembly size (Mbp) | 9.68 | 9.75 | 9.95 | 0.05 |
Number of contigs | 202 | 239 | 422 | 43 |
Contig N50 | 115375 | 144560 | 170540 | 13888 |
GC content (%) | 39.91% | 39.95% | 39.97% | 0.01% |
CDS total length (Mbp) | 6.44 | 6.50 | 6.53 | 0.02 |
CDS total length (% of genome) | 66.45% | 66.64% | 67.08% | 0.32% |
Gene models (n) | 4317 | 4475 | 4509 | 37 |
CDS average length (bp) | 1438 | 1453 | 1512 | 13 |
Exons per gene (average) | 3.98 | 4.02 | 4.17 | 0.04 |
Intron average length (bp) | 63 | 64 | 66 | 0.57 |
Complete BUSCOs | 87.40% | 88.18% | 89.80% | 0.50% |
Complete and single-copy BUSCOs | 85.90% | 87.91% | 88.60% | 0.56% |
Complete and duplicated BUSCOs | 0.10% | 0.27% | 3.90% | 0.76% |
Fragmented BUSCOs | 5.50% | 5.94% | 6.50% | 0.31% |
Missing BUSCOs | 4.60% | 5.89% | 6.50% | 0.38% |
SNP density | 0.41% | 0.52% | 0.60% | 0.04% |
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Sun, X.; Gostinčar, C.; Fang, C.; Zajc, J.; Hou, Y.; Song, Z.; Gunde-Cimerman, N. Genomic Evidence of Recombination in the Basidiomycete Wallemia mellicola. Genes 2019, 10, 427. https://doi.org/10.3390/genes10060427
Sun X, Gostinčar C, Fang C, Zajc J, Hou Y, Song Z, Gunde-Cimerman N. Genomic Evidence of Recombination in the Basidiomycete Wallemia mellicola. Genes. 2019; 10(6):427. https://doi.org/10.3390/genes10060427
Chicago/Turabian StyleSun, Xiaohuan, Cene Gostinčar, Chao Fang, Janja Zajc, Yong Hou, Zewei Song, and Nina Gunde-Cimerman. 2019. "Genomic Evidence of Recombination in the Basidiomycete Wallemia mellicola" Genes 10, no. 6: 427. https://doi.org/10.3390/genes10060427
APA StyleSun, X., Gostinčar, C., Fang, C., Zajc, J., Hou, Y., Song, Z., & Gunde-Cimerman, N. (2019). Genomic Evidence of Recombination in the Basidiomycete Wallemia mellicola. Genes, 10(6), 427. https://doi.org/10.3390/genes10060427