Novel Allergen Discovery through Comprehensive De Novo Transcriptomic Analyses of Five Shrimp Species
Abstract
:1. Introduction
2. Results
2.1. Assessment of 15 Assembled Transcriptomes
2.2. Known and Potential Allergens Identified within the Shrimp Transcriptomes
2.3. Identification of Known Crustacean Allergens
2.4. Abundance of Known Crustacean Allergen Transcripts Varies Between Shrimp Species
2.5. Evolutionary Relationship of Shellfish Allergens TM, AK, MLC and SCP
2.6. Discovery of Unreported Allergens in Shrimp
3. Discussion
4. Materials and Methods
4.1. Sample Selection
4.2. Illumina Library Preparation and RNA Sequencing
4.3. De Novo Transcriptome Assembly and Quality Control
4.4. Removal of the Inconclusive Dataset
4.5. Allergen Reference Database Construction
4.6. BLAST Search for Allergens
4.7. Analysing the BLAST Search Results
4.8. Measuring the Abundance of Allergen Sequences
4.9. Molecular Phylogenetic Tree Building of TM, AK, MLC and SCP
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Shrimp Species | Replicates | RNA-Seq | Transcriptome Assembly Metrics | Transrate Quality Assessment | BUSCO Scores | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Normalised Read Count | No. of Contigs | Assembly Size | GC Content (%) | Proportion of Read Pairs Mapped (%) | Assembly Score | Complete (%) | Fragmented (%) | Missing (%) | |||
| L. vannamei (Whiteleg shrimp) | 1 | 1,412,587 | 32,302 | 28.6 Mb | 43.4 | 93.2 | 0.413 | 56 | 21 | 23 |
2 | 1,412,010 | 33,574 | 29.4 Mb | 43.0 | 92.6 | 0.401 | 56 | 23 | 21 | ||
3 | 1,070,376 | 28,101 | 22.7 Mb | 44.8 | 92.8 | 0.419 | 48 | 25 | 27 | ||
| P. monodon (Black Tiger shrimp) | 1 | 1,609,374 | 41,971 | 37.9 Mb | 44.3 | 91.9 | 0.387 | 66 | 20 | 14 |
2 | 1,443,066 | 40,927 | 36.5 Mb | 45.1 | 91.0 | 0.364 | 66 | 19 | 14 | ||
3 | 1,643,259 | 42,510 | 38.1 Mb | 43.7 | 92.3 | 0.390 | 64 | 21 | 14 | ||
| F. merguiensis (Banana shrimp) | 1 | 1,486,264 | 37,572 | 31.4 Mb | 43.0 | 91.8 | 0.385 | 64 | 17 | 19 |
2 | 1,657,940 | 41,336 | 34.8 Mb | 42.6 | 91.7 | 0.385 | 67 | 16 | 17 | ||
3 | 1,602,775 | 38,638 | 33.5 Mb | 42.5 | 92.6 | 0.389 | 65 | 19 | 16 | ||
| M. latisulactus (King shrimp) | 1 | 1,130,898 | 37,128 | 25.6 Mb | 42.9 | 90.7 | 0.410 | 46 | 26 | 27 |
2 | 1,052,237 | 28,125 | 21.7 Mb | 42.8 | 92.2 | 0.411 | 43 | 25 | 32 | ||
| M. endeavouri (Endeavour shrimp) | 1 | 1,142,169 | 35,407 | 25.9 Mb | 42.5 | 90.6 | 0.374 | 48 | 25 | 27 |
2 | 1,035,324 | 30,879 | 23.2 Mb | 42.3 | 91.2 | 0.399 | 48 | 24 | 27 | ||
3 | 1,081,301 | 38,204 | 25.5 Mb | 43.3 | 87.9 | 0.355 | 49 | 26 | 25 |
Allergens | LV Whiteleg Shrimp | PM Black Tiger Shrimp | FM Banana Shrimp | ML King Shrimp | ME Endeavour Shrimp | |||
---|---|---|---|---|---|---|---|---|
Protein Name | Source Name | IUIS Nomenclature | ||||||
Common | Scientific | |||||||
Heat Shock Protein 70 | Storage mite | Tyrophagus putrescentiae | Tyr p 28 | 85.1% (0) | 82.7% (0) | 83.3% (0) | 82.7% (0) | 84.3% (0) |
Alpha-Tubulin | American house dust mite | Dermatophagoides farinae | Der f 33 | 81.8% (0) | 81.7% (0) | 81.6% (0) | 81.6% (0) | 81.6% (0) |
Chymotrypsin | American house dust mite | Dermatophagoides farinae | Der f 6 | 78.7% (4.3 × 10−94) | 78.7% (2.13 × 10−94) | 79.3% (1.45 × 10−94) | 79.9% (3.71 × 10−97) | 80.5% (3.93 × 10−95) |
Enolase 3–2 | Atlantic salmon | Salmo salar | Sal s 2 | 74.8% (0) | 74.6% (0) | 74.1% (0) | 74.6% (0) | 74.5% (0) |
Aldolase A | Yellowfin tuna | Thunnus albacares | Thu a 3 | 66.0% (2.29 × 10−164) | 64.9% (2.25 × 10−164) | 70.1% (4.09 × 10−169) | 69.6% (1.47 × 10−166) | 70.1% (3.65 × 10−167) |
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Karnaneedi, S.; Huerlimann, R.; Johnston, E.B.; Nugraha, R.; Ruethers, T.; Taki, A.C.; Kamath, S.D.; Wade, N.M.; Jerry, D.R.; Lopata, A.L. Novel Allergen Discovery through Comprehensive De Novo Transcriptomic Analyses of Five Shrimp Species. Int. J. Mol. Sci. 2021, 22, 32. https://doi.org/10.3390/ijms22010032
Karnaneedi S, Huerlimann R, Johnston EB, Nugraha R, Ruethers T, Taki AC, Kamath SD, Wade NM, Jerry DR, Lopata AL. Novel Allergen Discovery through Comprehensive De Novo Transcriptomic Analyses of Five Shrimp Species. International Journal of Molecular Sciences. 2021; 22(1):32. https://doi.org/10.3390/ijms22010032
Chicago/Turabian StyleKarnaneedi, Shaymaviswanathan, Roger Huerlimann, Elecia B. Johnston, Roni Nugraha, Thimo Ruethers, Aya C. Taki, Sandip D. Kamath, Nicholas M. Wade, Dean R. Jerry, and Andreas L. Lopata. 2021. "Novel Allergen Discovery through Comprehensive De Novo Transcriptomic Analyses of Five Shrimp Species" International Journal of Molecular Sciences 22, no. 1: 32. https://doi.org/10.3390/ijms22010032