Comparative Whole-Genome Sequence Analyses of Fusarium Wilt Pathogen (Foc R1, STR4 and TR4) Infecting Cavendish (AAA) Bananas in India, with a Special Emphasis on Pathogenicity Mechanisms
Abstract
:1. Introduction
2. Materials and Methods
2.1. Collection of Foc Races
2.2. DNA Extraction and Quantification
2.3. Genome Sequencing and Assembly
2.4. Mapping of Foc Genome
2.5. Identification and Analysis of Variants in the Foc Genome
2.6. Genome and Functional Annotation
2.7. Molecular Characterization of Indian VCGs for SIX genes
3. Results and Discussion
3.1. Genome Sequencing and General Features
3.2. Transposable Elements in the Foc Genomes
3.3. Gene Content in the Foc Genomes
3.4. GO and KEGG in the Foc Genome
3.5. SNPs, InDels and Phylogenetic Relationship
3.6. Virulent Genes and Their Functions in the Genome of Foc
3.7. The Organisation of Secreted in Xylem Protein-Encoding Genes in Foc Genome
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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Characteristics | Fol 4287 | Foc R1 (VCG0124) | Foc STR4 (VCG0120) | Foc TR4 (VCG01213/16) |
---|---|---|---|---|
Genome size (bp) | 61,386,934 | 61,471,473 | 61,380,681 | 63,220,715 |
No. of scaffolds (Count) | 114 | 88 | 85 | 88 |
No. of contig (Count) | 1362 | 1371 | 1362 | 6560 |
Scaffold N50 (Mb) | 1,976,106 | 4,781,098 | 4,589,962 | 4,589,937 |
Maximum contig length | 6,854,980 | 8,732,082 | 6,853,100 | 7,450,211 |
Minimum contig length | 900 | 898 | 888 | 886 |
Average contig length | 698,542 | 884,718 | 722,130 | 718,421 |
Median contig length | 15,960 | 17,299 | 14,354 | 15,960 |
GC content | 48.4 | 48.5 | 48.4 | 48.5 |
Protein count | 27,347 | 22,151 | 18,946 | 19,651 |
Total genes (Augustus) | 20,925 | 21,842 | 17,118 | 17,745 |
BUSCO (%) | 96.4 | 98.4 | 96.9 | 98.9 |
Secretome Genes | 1847 | 1949 | 1870 | 2330 |
tRNA | 320 | 524 | 304 | 358 |
rRNA | 125 | 223 | 121 | 134 |
ORF | 892,698 | 1,149,990 | 891,736 | 926,420 |
Repeats (bp) | 10,770,810 ‡ | 10,755,517 | 10,901,072 | 8,844,756 |
Total transposable elements (bp) | 2,446,574 ‡ | 346,254 | 342,987 | 273,767 |
Retroelements | 433,505 ‡ | 87,052 | 85,124 | 56,365 |
DNA transposons | 506,130 ‡ | 2527 | 2591 | 2391 |
Total interspersed repeats | 342,368 ‡ | 89,579 | 87,787 | 58,756 |
Simple repeats | 115,058 | 110,011 | 99,987 | |
Low complexity region | 141,331 | 144,912 | 114,926 |
Accession | SIX1 | SIX2 | SIX3 | SIX4 | SIX5 | SIX6 | SIX7 | SIX8 | SIX9 | SIX10 | SIX11 | SIX12 | SIX13 | SIX14 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Fol 4287 | + | + | + | − | + | + | − | + | + | + | − | − | + | − |
Foc VCG0124 (TC1 ‡) | + | − | − | + | − | + | − | − | − | − | − | − | + | − |
Foc VCG0124 (TC1 *) | + | ++ | + | ++ | ++ | ++ | + | − | − | + | − | + | + | − |
Foc VCG0120 STR4 ‡ | + | + | − | − | − | − | + | + | + | − | − | − | + | − |
Foc VCG0120 STR4 * | + | ++ | + | ++ | ++ | ++ | + | + | ++ | + | − | − | + | − |
Foc VCG01213/16 (BC2-4 ‡) | + | + | − | − | − | − | − | + | + | − | − | − | + | − |
Foc VCG01213/16 (BC2-4 *) | + | ++ | + | ++ | ++ | + | + | + | ++ | + | − | ++ | + | − |
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Raman, T.; Edwin Raj, E.; Muthukathan, G.; Loganathan, M.; Periyasamy, P.; Natesh, M.; Manivasakan, P.; Kotteeswaran, S.; Rajendran, S.; Subbaraya, U. Comparative Whole-Genome Sequence Analyses of Fusarium Wilt Pathogen (Foc R1, STR4 and TR4) Infecting Cavendish (AAA) Bananas in India, with a Special Emphasis on Pathogenicity Mechanisms. J. Fungi 2021, 7, 717. https://doi.org/10.3390/jof7090717
Raman T, Edwin Raj E, Muthukathan G, Loganathan M, Periyasamy P, Natesh M, Manivasakan P, Kotteeswaran S, Rajendran S, Subbaraya U. Comparative Whole-Genome Sequence Analyses of Fusarium Wilt Pathogen (Foc R1, STR4 and TR4) Infecting Cavendish (AAA) Bananas in India, with a Special Emphasis on Pathogenicity Mechanisms. Journal of Fungi. 2021; 7(9):717. https://doi.org/10.3390/jof7090717
Chicago/Turabian StyleRaman, Thangavelu, Esack Edwin Raj, Gopi Muthukathan, Murugan Loganathan, Pushpakanth Periyasamy, Marimuthu Natesh, Prabaharan Manivasakan, Sharmila Kotteeswaran, Sasikala Rajendran, and Uma Subbaraya. 2021. "Comparative Whole-Genome Sequence Analyses of Fusarium Wilt Pathogen (Foc R1, STR4 and TR4) Infecting Cavendish (AAA) Bananas in India, with a Special Emphasis on Pathogenicity Mechanisms" Journal of Fungi 7, no. 9: 717. https://doi.org/10.3390/jof7090717