Genome-Wide Analysis of Four Pathotypes of Wheat Rust Pathogen (Puccinia graminis) Reveals Structural Variations and Diversifying Selection
Abstract
:1. Introduction
2. Materials and Methods
2.1. Materials
2.2. Genomic DNA Isolation
2.3. Genome Sequence and Assembly
2.4. Gene Prediction and Annotations
2.5. Identification of Repeat Elements within the Genomes of P. graminis Pathotypes
2.6. SNP and InDel Analysis
2.7. Secretome Analysis
2.8. Identification of Homologous Genes within and across the P. graminis Pathotypes
2.9. Phylogenetic Analysis
2.10. Diversifying Selection Analysis and Estimation of Substitution Rates
3. Results
3.1. Genome Sequencing and Assembly of the P. graminis Pathotypes
3.2. Gene Prediction and Annotations
3.3. Identification and Analysis of Secretory Proteins
3.4. Genome-Wide Analysis for Cysteine-Rich Genes
3.5. Identification of Pathogenicity-Related Genes
3.6. Genome-Wide Identification of SNPs
3.7. Identification of Repetitive Elements
3.8. Conservation of Orthology and Paralogy Genes in the Pathotypes
3.9. Evolutionary Relationship among the P. graminis Pathotypes
3.10. Genome-Wide Analysis of Diversifying Selection
3.11. Analysis of Substitution Rates of Sequence Divergence
3.12. Identification of Genes under Site-Specific Diversifying Selection and Their Functional Categorization
4. Discussion
5. 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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P.graminis Pathotypes | ||||
---|---|---|---|---|
Parameters | 14 | 40A | 40-3 | 117-6 |
Input reads | 67,098,012 (6.57 Gb) | 61,276,376 (5.98 Gb) | 60,290,992 (5.90 Gb) | 65,648,262 (6.42 Gb) |
Mapped Reads | 62.77% | 67.29% | 67.26% | 52.44% |
Mapped Bases | 62.00% | 66.64% | 66.42% | 51.94% |
Total contigs (assembled genome) | 68,622 (63.31 Mb) | 69,842 (59.15 Mb) | 70,264 (59.25 Mb) | 58,140 (66.25 Mb) |
N50 (contigs) (bp) | 4153 | 3573 | 3584 | 5288 |
Average contig length (bp) | 922 | 846 | 843 | 1139 |
GC content of assembled genome (%) | 43.61 | 43.64 | 43.64 | 43.58 |
Largest contig (bp) | 65,288 | 43,631 | 39,779 | 46,544 |
Contigs ≥ 200 bases | 37,103 (59.08 Mb) | 36,874 (54.69 Mb) | 36,934 (54.76 Mb) | 33,359 (62.88 Mb) |
Contigs ≥ 2Kb | 7352 (42.14 Mb) | 7364 (37.98 Mb) | 7363 (38.07 Mb) | 7499 (47.55 Mb) |
Average contig length (>2 Kb) (bp) | 5732 | 5157 | 5170 | 6341 |
N50 (>2 Kb contigs) (bp) | 7152 | 6013 | 6022 | 8342 |
Depth coverage | 103× | 101× | 99× | 96× |
Repeats (TE) (Mb) | 26.84 | 25.76 | 25.78 | 27.05 |
Repeats (TE) % in assembled genome | 42.40 | 43.56 | 43.51 | 40.83 |
Number of genes predicted | 13,854 | 12,636 | 12,670 | 15,401 |
Mean gene length (bp) | 1132.44 | 1151.94 | 1152.51 | 1092.92 |
Total number of exons | 65,082 | 59,820 | 59,942 | 71,844 |
Mean number of exons per gene | 4.69 | 4.73 | 4.73 | 4.66 |
Largest gene length (bp) | 17,007 | 17,040 | 17,040 | 16,833 |
Genes (>150 bases) | 12,424 | 11,347 | 11,371 | 13,943 |
Genes (>450 bases) | 9419 | 8665 | 8694 | 10,315 |
Average gene length (bp) (>450 bases genes) | 1561.15 | 1578.23 | 1578.19 | 1548.67 |
Mean number of exons per gene (>450 bases genes) | 5.72 | 5.75 | 5.74 | 5.65 |
Pathotypes | 14 | 40A | 40-3 | 117-6 |
---|---|---|---|---|
SNPs | 780,353 | 686,441 | 710,804 | 1,001,341 |
Insertions | 51,662 | 44,403 | 47,055 | 46,206 |
Deletions | 24,105 | 22,336 | 23,630 | 26,882 |
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Kiran, K.; Rawal, H.C.; Dubey, H.; Jaswal, R.; Bhardwaj, S.C.; Deshmukh, R.; Sharma, T.R. Genome-Wide Analysis of Four Pathotypes of Wheat Rust Pathogen (Puccinia graminis) Reveals Structural Variations and Diversifying Selection. J. Fungi 2021, 7, 701. https://doi.org/10.3390/jof7090701
Kiran K, Rawal HC, Dubey H, Jaswal R, Bhardwaj SC, Deshmukh R, Sharma TR. Genome-Wide Analysis of Four Pathotypes of Wheat Rust Pathogen (Puccinia graminis) Reveals Structural Variations and Diversifying Selection. Journal of Fungi. 2021; 7(9):701. https://doi.org/10.3390/jof7090701
Chicago/Turabian StyleKiran, Kanti, Hukam C. Rawal, Himanshu Dubey, Rajdeep Jaswal, Subhash C. Bhardwaj, Rupesh Deshmukh, and Tilak Raj Sharma. 2021. "Genome-Wide Analysis of Four Pathotypes of Wheat Rust Pathogen (Puccinia graminis) Reveals Structural Variations and Diversifying Selection" Journal of Fungi 7, no. 9: 701. https://doi.org/10.3390/jof7090701