Seventeen Ustilaginaceae High-Quality Genome Sequences Allow Phylogenomic Analysis and Provide Insights into Secondary Metabolite Synthesis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Selection of Fungal Strains
2.2. Genomic DNA Preparation
2.3. Nanopore Library Preparation and GridION® Sequencing
2.4. Illumina Library Preparation and MiSeq Sequencing
2.5. Base Calling, Reads Processing, and Assembly
2.6. Gene Prediction and Genome Annotation
2.7. Comparative Genome Analyses and Phylogenetic Analysis
3. Results and Discussion
3.1. Genomic Data
3.2. Phylogenomic Analysis
3.3. Comparative Genomics
3.3.1. Pairwise Percentage of Conserved Proteins
3.3.2. Average Nucleotide Identity
3.3.3. Average Amino Acid Identity
3.4. Gene-Based Comparison
3.5. Itaconate Cluster Identification
3.6. MEL Cluster Identification
3.7. Ustilagic Acid Cluster Identification
3.8. Macro Synteny Plot of U. maydis Isolates
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Strain No. | Assembly Name | Assembly ACC | Study ID | Sample ID | Contig ACC |
---|---|---|---|---|---|
#2169 | Umay_482_v1 | GCA_928722285 | PRJEB50355 | ERS10392836 | CAKMXG010000001-CAKMXG010000046 |
#2169 | Umay_482_v2 | GCA_928722265 | PRJEB50355 | ERS10392837 | CAKMXF010000001-CAKMXF010000068 |
#2172 | Umay_485 | GCA_928722245 | PRJEB50356 | ERS10381369 | CAKMXD010000001-CAKMXD010000043 |
#2136 | Umay_198 | GCA_928743665 | PRJEB50359 | ERS10419843 | CAKMXO010000001-CAKMXO010000107 |
#2816 | BRIP_26904_a | GCA_928724745 | PRJEB50498 | ERS10395116 | CAKMXJ010000001-CAKMXJ010000042 |
#2701 | NBRC_100157 | GCA_928724775 | PRJEB50365 | ERS10395119 | CAKMXL010000001-CAKMXL010000048 |
#2212 | RK_033 | GCA_928724755 | PRJEB50360 | ERS10395351 | CAKMXK010000001-CAKMXK010000041 |
#2215 | UMa706_1 | GCA_928724875 | PRJEB50363 | ERS10395376 | CAKMXN010000001-CAKMXN010000086 |
#2215 | UMa706_2 | GCA_928724795 | PRJEB50363 | ERS10395377 | CAKMXM010000001-CAKMXM010000036 |
#2814 | BRIP_52549_a | GCA_928852645 | PRJEB50497 | ERS10422304 | CAKMXS010000001-CAKMXS010000079 |
#2821 | BRIP_26929_a | GCA_928722295 | PRJEB50499 | ERS10393563 | CAKMXH010000001-CAKMXH010000039 |
#2214 | RK031 | GCA_928858565 | PRJEB50362 | ERS10422305 | CAKMXV010000001-CAKMXV010000022 |
#1946 | NRRL_Y-7808 | GCA_928872045 | PRJEB50496 | ERS10422313 | CAKMYB010000001-CAKMYB010000027 |
#2706 | NBRC_9727 | GCA_928865425 | PRJEB50366 | ERS10422385 | CAKMXY010000001-CAKMXY010000048 |
#2826 | BRIP_46795_a | GCA_928869825 | PRJEB50500 | ERS10422474 | CAKMYA010000001-CAKMYA010000069 |
#2836 | BRIP_60876_a | GCA_928856705 | RJEB50501 | ERS10422499 | CAKMXT010000001-CAKMXT010000026 |
#2836 * | - | ERZ4998446 | PRJEB50495 | ERS10422500 | ERZ4998446.1-ERZ4998446.260 |
#2213 | UMa698 | GCA_928991175 | PRJEB50361 | ERS10422257 | CAKMYD010000001-CAKMYD010000051 |
#2220 | RK_075 | GCA_928722275 | PRJEB50364 | ERS10392838 | CAKMXE010000001-CAKMXE010000037 |
No. | Organism | Strain | Genome Size (bp) | Contigs | Largest Contig | N50 (bp) | GC (%) | Annotated Genes a |
---|---|---|---|---|---|---|---|---|
#2814 | Macalpinomyces mackinlayi | BRIP 52549a | 20,011,713 | 79 | 2,517,462 | 778,176 | 55.2 | 6780 |
#2816 | Macalpinomyces ordensis | BRIP 26904a | 21,488,978 | 42 | 1,934,029 | 921,621 | 54.4 | 7166 |
#1946 | Pseudozyma antarctica | NRRLY 7808 | 18,256,718 | 27 | 2,397,276 | 72,913 | 60.8 | 6532 |
#2212 | Sporisorium exsertum | RK 033 | 19,675,720 | 41 | 1,762,232 | 1,163,924 | 56.7 | 6772 |
#2213 | Sporisorium scitamineum | UMa698, | 20,280,126 | 51 | 1,999,406 | 881,538 | 54.9 | 6757 |
#2214 | Sporisorium walkeri | RK 031 | 18,415,360 | 22 | 2,584,725 | 1,158,577 | 53.9 | 6584 |
#2215 | Ustanciosporium gigantosporum * | UMa706 | 26,778,318 | 86 | 3,628,339 | 1,232,426 | 55.3 | 8712 |
#2215 | Ustanciosporium gigantosporum | UMa706 | 20,177,783 | 36 | 3,087,333 | 1,238,668 | 52.0 | 6690 |
#2821 | Ustilago curta | BRIP 26929a | 18,446,555 | 39 | 1,762,630 | 682,062 | 55.2 | 6420 |
#2706 | Ustilago cynodontis | NBRC 9727 | 23,130,474 | 48 | 2,786,107 | 1,026,819 | 52.1 | 7322 |
#2826 | Ustilago lituana | BRIP 46795a | 25,770,532 | 69 | 1,993,860 | 819,494 | 54.3 | 7741 |
#2136 | Ustilago maydis | No. 198 | 21,122,121 | 107 | 2,522,778 | 660,941 | 53.8 | 6807 |
#2169 | Ustilago maydis | No. 482 | 20,585,367 | 46 | 3,568,257 | 87,601 | 54.0 | 6827 |
#2169 | Ustilago maydis | No. 482 | 20,591,394 | 68 | 2,499,251 | 674,905 | 53.9 | 6833 |
#2172 | Ustilago maydis | No. 485 | 20,582,581 | 43 | 2,514,809 | 743,668 | 53.9 | 6777 |
#2701 | Ustilago trichophora | NBRC 100157 | 20,713,809 | 48 | 1,974,389 | 794,480 | 53.8 | 6585 |
#2220 | Ustilago vetiveriae | RK 075 | 18,373,116 | 37 | 2,393,662 | 780,848 | 54.8 | 6347 |
#2836 | Ustilago xerochloae * | BRIP 60876a | 36,081,614 | 315 | 4,586,684 | 648,688 | 54.8 | 11,418 |
Organism | Strain | NRPS | Terpene | T1PKS | RIPP | Total |
---|---|---|---|---|---|---|
Ustilago maydis | No. 485 | 11 | 2 | 1 | 0 | 14 |
Ustilago maydis | No. 482 1 | 11 | 2 | 1 | 0 | 14 |
Ustilago maydis | No. 482 2 | 13 | 2 | 1 | 0 | 15 |
Ustilago vetiveriae | RK 075 | 7 | 2 | 1 | 0 | 10 |
Ustilago curta | BRIP 26929a | 7 | 3 | 1 | 0 | 11 |
Macalpinomyces ordensis | BRIP 26904a | 6 | 3 | 1 | 0 | 10 |
Ustilago trichophora | NBRC 100157 | 7 | 2 | 1 | 0 | 10 |
Sporisorium exsertum | RK 033 | 8 | 3 | 1 | 0 | 12 |
Ustanciosporium gigantosporum | UMa706 1 | 7 | 4 | 1 | 1 | 13 |
Sporisorium scitamineum | UMa698 | 9 | 3 | 1 | 0 | 13 |
Ustilago xerochloae | BRIP 60876a * | 8 | 2 | 1 | 0 | 11 |
Ustilago xerochloae | BRIP 60876a * | 5 | 2 | 0 | 0 | 7 |
Macalpinomyces mackinlayi | BRIP 52549a | 7 | 3 | 2 | 0 | 12 |
Ustanciosporium gigantosporum | UMa706 2 | 7 | 2 | 1 | 0 | 10 |
Sporisorium walkeri | RK 031 | 6 | 3 | 1 | 0 | 10 |
Ustilago maydis | No. 198 | 11 | 2 | 1 | 0 | 14 |
Ustilago cynodontis | NBRC 9727 | 9 | 2 | 1 | 0 | 12 |
Ustilago lituana | BRIP 46795a | 6 | 3 | 1 | 0 | 10 |
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Ullmann, L.; Wibberg, D.; Busche, T.; Rückert, C.; Müsgens, A.; Kalinowski, J.; Blank, L.M. Seventeen Ustilaginaceae High-Quality Genome Sequences Allow Phylogenomic Analysis and Provide Insights into Secondary Metabolite Synthesis. J. Fungi 2022, 8, 269. https://doi.org/10.3390/jof8030269
Ullmann L, Wibberg D, Busche T, Rückert C, Müsgens A, Kalinowski J, Blank LM. Seventeen Ustilaginaceae High-Quality Genome Sequences Allow Phylogenomic Analysis and Provide Insights into Secondary Metabolite Synthesis. Journal of Fungi. 2022; 8(3):269. https://doi.org/10.3390/jof8030269
Chicago/Turabian StyleUllmann, Lena, Daniel Wibberg, Tobias Busche, Christian Rückert, Andreas Müsgens, Jörn Kalinowski, and Lars M. Blank. 2022. "Seventeen Ustilaginaceae High-Quality Genome Sequences Allow Phylogenomic Analysis and Provide Insights into Secondary Metabolite Synthesis" Journal of Fungi 8, no. 3: 269. https://doi.org/10.3390/jof8030269