De Novo Genome Assembly of Toniniopsis dissimilis (Ramalinaceae, Lecanoromycetes) from Long Reads Shows a Comparatively High Composition of Biosynthetic Genes Putatively Involved in Melanin Synthesis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection, DNA Extraction, and Sequencing
2.2. Genome Assembly and Filtering
2.3. Annotation
2.4. Phylogenetic Analysis
2.5. Identification of the Fungal RiPP-like Orthologues Using OrthoFinder
3. Results and Discussion
3.1. Library Prep and Sequencing
3.2. General Characteristics of the De Novo Toniniopsis dissimilis Genome
Toniniopsis dissimilis | Bacidia gigantensis | Bacidia rubella | Niebla homalea | Ramalina farinacea | Ramalina intermedia | Ramalina peruviana | |
---|---|---|---|---|---|---|---|
Assembly Size (Mb) | 29.22 | 33.11 | 33.7 | 50.56 | 32.74 | 26.24 | 27 |
Largest Scaffold (bp) | 1,545,693 | 3,530,911 | 2,353,056 | 3,158,485 | 2,450,536 | 898,913 | 694,821 |
# Scaffolds | 85 | 24 | 246 | 52 | 44 | 196 | 1657 |
N50 (bp) | 741,547 | 1,807,239 | 1,771,855 | 1,266,640 | 1,546,935 | 273,318 | 40,431 |
GC content | 47.33% | 44.67% | 45.25% | 37.96% | 46.69% | 51.89% | 50.66% |
# Genes | 10,058 | 9207 | 9424 | 8586 | 8640 | 8033 | 7133 |
# Proteins | 10,011 | 9158 | 9365 | 8521 | 8575 | 7982 | 7080 |
# tRNA | 47 | 49 | 59 | 65 | 65 | 51 | 53 |
Unique Proteins | 2463 | 1919 | 1781 | 985 | 789 | 387 | 598 |
Prots at least one ortholog | 7422 | 7135 | 7512 | 7501 | 7774 | 7592 | 6467 |
Single-copy orthologs | 2530 | 2462 | 2462 | 2462 | 2462 | 2462 | 2462 |
Number of BGCs | 47 | 39 | 54 | 77 | 72 | 71 | 51 |
3.3. Phylogenetic Analyses of the KS Domain of T1PKS Genes of T. dissimilis
3.4. Putative Melanin Clades That Include B. gigantensis, B. rubella, and T. dissimilis
3.5. Clade with bacrubpred_003614 (bacrub_6), tondispred_004406 (tondis_774), and bacgigpred_005712 (bacgig_10)
3.6. Clade with bacrubpred_007628 (bacrub_15), tondispred_001459 (tondis_191), and bacgigpred_001679 (bacgig_2)
3.7. Other Putative Melanin Genes from Two Bacidia Species
3.8. YWA1: Alternative Precursor for the Melanin Biosynthesis
3.9. An Ecological Perspective of Multiple Copies of Putative Melanin Genes in the Crustose Ramalinaceae
3.10. Putative ‘Menisporopsin A’ Biosynthetic Gene Cluster
3.11. Fungal RiPP-Like Proteins
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene Tag/ antiSMASH Region | MIBiG Accession | % Similarity Score | MIBiG Compound Reference | UniProtKB/ Swiss-Prot Closest Reference | Putative Function (MIBiG) |
---|---|---|---|---|---|
tondispred_002824 (tondis_288) | BGC0002161 | 71 | 1,3,6,8-tetrahydroxynaphthalene | Melanin biosynthesis | |
tondispred_001459 (tondis_191) | BGC0000107 | 100 | Naphthopyrone | Melanin biosynthesis | |
R-PKS:
tondispred_004967 NR-PKS: tondispred_004968 (tondis_787) | BGC0000041 | 65 | Oronofacic acid | A0A6F9DXA0.1 | Menisporopsin A |
tondispred_004406 (tondis_774) | BGC0002175, BGC0000107 | 100 | YWA1 (yellow pigment), Naphthopyrone | Melanin biosynthesis | |
tondispred_004340 (tondis_683) | BGC0001258 | 69 | 1,3,6,8-tetrahydroxynaphthalene | A7UMW1.1 Elsinochromes BGC, PKS1 | Melanin biosynthesis |
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Gerasimova, J.V.; Beck, A.; Scheunert, A.; Kulkarni, O. De Novo Genome Assembly of Toniniopsis dissimilis (Ramalinaceae, Lecanoromycetes) from Long Reads Shows a Comparatively High Composition of Biosynthetic Genes Putatively Involved in Melanin Synthesis. Genes 2024, 15, 1029. https://doi.org/10.3390/genes15081029
Gerasimova JV, Beck A, Scheunert A, Kulkarni O. De Novo Genome Assembly of Toniniopsis dissimilis (Ramalinaceae, Lecanoromycetes) from Long Reads Shows a Comparatively High Composition of Biosynthetic Genes Putatively Involved in Melanin Synthesis. Genes. 2024; 15(8):1029. https://doi.org/10.3390/genes15081029
Chicago/Turabian StyleGerasimova, Julia V., Andreas Beck, Agnes Scheunert, and Om Kulkarni. 2024. "De Novo Genome Assembly of Toniniopsis dissimilis (Ramalinaceae, Lecanoromycetes) from Long Reads Shows a Comparatively High Composition of Biosynthetic Genes Putatively Involved in Melanin Synthesis" Genes 15, no. 8: 1029. https://doi.org/10.3390/genes15081029