Signatures of TRI5, TRI8 and TRI11 Protein Sequences of Fusarium incarnatum-equiseti Species Complex (FIESC) Indicate Differential Trichothecene Analogue Production
Abstract
:1. Introduction
2. Results
2.1. Comparative DNA Polymorphism
2.1.1. TRI5
2.1.2. TRI8
2.1.3. TRI11
2.2. Phylogeny
2.2.1. TRI5 Gene Tree
2.2.2. TRI5 Protein Tree
2.2.3. TRI8 Gene Tree
2.2.4. TRI8 Protein Tree
2.2.5. TRI11 Gene Tree
2.2.6. TRI11 Protein Tree
2.3. Mutation Effect Prediction
2.4. TRI5p and PDB Mapping
2.5. TRI8p and PDB Mapping
3. Discussion
3.1. Singletons
3.2. Protein Order and Disorder
3.3. Use of Protein Trees over Nucleotide Trees
3.4. TRI5—Trichodiene Synthase
3.5. TRI8 Trichothecene C-3 Esterase
3.6. TRI11—Trichothecene C-15 Hydroxylase
3.7. Use of TRI Protein Sequence Data
4. Materials and Methods
4.1. Collection and Identification of FIESC Isolates
4.2. DNA Extraction, PCR Amplification and Sequencing
4.3. TRI Gene Sequence Analysis
4.4. TRI Protein Sequence Analysis
4.5. Trichodiene Synthase and Trichothecene C-3 Esterase Protein Structure Conservation Analysis
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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DNA Alignment Statistic | TRI5nt | TRI8nt | TRI11nt | ||||||
---|---|---|---|---|---|---|---|---|---|
Trinidad | Reference Sequences | Total | Trinidad | Reference Sequences | Total | Trinidad | Reference Sequences | Total | |
N | 32 | 8 | 40 | 32 | 10 | 42 | 32 | 12 | 44 |
No. of sites analyzed | 394 | 394 | 394 | 470 | 470 | 470 | 705 | 705 | 705 |
No. of singleton variable sites | 0 | 16 | 13 | 0 | 62 | 33 | 0 | 93 | 60 |
Total number of singleton mutations, Eta(s) | 0 | 18 | 14 | 0 | 65 | 36 | 0 | 118 | 86 |
Total number of mutations, Eta | 55 | 56 | 86 | 108 | 102 | 176 | 78 | 237 | 264 |
Number of polymorphic sites, S | 52 | 53 | 81 | 100 | 97 | 158 | 77 | 203 | 217 |
Average no. nucleotide differences, k | 17.091 | 24.214 | 20.023 | 29.734 | 28.089 | 40.11 | 26.938 | 64.061 | 49.969 |
Nucleotide diversity, Pi | 0.04498 | 0.06372 | 0.05269 | 0.06326 | 0.05976 | 0.08534 | 0.03881 | 0.09244 | 0.07211 |
Number of haplotypes, h | 7 | 6 | 13 | 7 | 8 | 15 | 4 | 12 | 16 |
Haplotype (gene) diversity, Hd | 0.792 | 0.893 | 0.864 | 0.738 | 0.956 | 0.847 | 0.651 | 1 | 0.817 |
Fu and Li’s D test statistic, FLD; p < 0.02 | 1.72888 | 0.4508 | 0.57684 | 1.87228 | −1.1548 | 0.29559 | 1.90862 | −0.63889 | −0.82709 |
Fu and Li’s F test statistic, FLF; p < 0.02 | 1.72973 | 0.5375 | 0.41238 | 1.63219 | −1.28824 | 0.19375 | 2.08398 | −0.79709 | −0.91004 |
Recombination | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
TRI5p | Mutation Data |
---|---|
N, total no. of mutations | 32 |
No. of neutral mutations | 28 |
No. of non-neutral mutations | 4 |
Non-neutral mutations | Isolates (strains) |
A54L | LN995579 (15511); LN995580 (11348) |
Y56E | ACZ56393 (13381),ACZ56398 (31160),ACZ56401 (FRC R-06979), AXP09554 (64414) |
I57T | TRI5_5,TRI5_6,TRI5_7,TRI5_8,TRI5_9,TRI5_11,TRI5_13 (Trinidad strains) |
I57Q | ACZ56393 (13381),ACZ56398 (31160),ACZ56401 (FRC R-06979), AXP09554 (64414) |
TRI8p | Mutation Data |
---|---|
N, total no. of mutations | 73 |
No. of neutral mutations | 62 |
No. of non-neutral mutations | 11 |
Non-neutral mutations | Isolates (strains) |
Y20H | TRI8_5, TRI8_9 (Trinidad strains) |
H41Y | TRI8_5,TRI8_6,TRI8_7,TRI8_8,TRI8_9,TRI8_11,TRI8_13 (Trinidad strains) |
R62P | TRI8_26, TRI8_29, TRI8_30, TRI8_31, TRI8_32, TRI8_33, TRI8_34 (Trinidad strains) |
S112W | TRI8_ 5, TRI8_9 (Trinidad strains) |
R115H | LN995594 (11363) |
A125T | LN995587 (15511) |
Y133C | TRI8_15, TRI8_19 (Trinidad strains) |
P134S | TRI8_6, TRI8_7, TRI8_8, TRI8_13 (Trinidad strains) |
E135D | LN995588 (11348) |
L140F | TRI8_ 1, TRI8_12, TRI8_16, TRI8_17, TRI8_18, TRI8_23, TRI8_28 (Trinidad strains) |
N187D | LN995587 (15511), LN995588 (11348), LN995591 (10395) |
TRI11p | Mutation Data |
---|---|
N, total no. of mutations | 28 |
No. of neutral mutations | 22 |
No. of non-neutral mutations | 6 |
Non-neutral mutations | Isolates (strains) |
E4V | GQ915566 (FRC R-06979) |
G47D | LN995598 (11401), LN995599 (11407) |
P50N | LN995603 (11363) |
P50V | TRI11_5,TRI11_6,TRI11_7,TRI11_8,TRI11_9,TRI11_11,TRI11_13 (Trinidad strains) |
G75S | LN995596 (15511), LN995597 (11348), LN995598 (11401), LN995599 (11407), LN995600 (10395), LN995601 (11294), LN995602 (11345), LN995603 (11363) |
P117S | LN995596 (15511) |
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Villafana, R.T.; Rampersad, S.N. Signatures of TRI5, TRI8 and TRI11 Protein Sequences of Fusarium incarnatum-equiseti Species Complex (FIESC) Indicate Differential Trichothecene Analogue Production. Toxins 2020, 12, 386. https://doi.org/10.3390/toxins12060386
Villafana RT, Rampersad SN. Signatures of TRI5, TRI8 and TRI11 Protein Sequences of Fusarium incarnatum-equiseti Species Complex (FIESC) Indicate Differential Trichothecene Analogue Production. Toxins. 2020; 12(6):386. https://doi.org/10.3390/toxins12060386
Chicago/Turabian StyleVillafana, Ria T., and Sephra N. Rampersad. 2020. "Signatures of TRI5, TRI8 and TRI11 Protein Sequences of Fusarium incarnatum-equiseti Species Complex (FIESC) Indicate Differential Trichothecene Analogue Production" Toxins 12, no. 6: 386. https://doi.org/10.3390/toxins12060386
APA StyleVillafana, R. T., & Rampersad, S. N. (2020). Signatures of TRI5, TRI8 and TRI11 Protein Sequences of Fusarium incarnatum-equiseti Species Complex (FIESC) Indicate Differential Trichothecene Analogue Production. Toxins, 12(6), 386. https://doi.org/10.3390/toxins12060386