Identification of Antimicrobial Peptide Genes in Black Rockfish Sebastes schlegelii and Their Responsive Mechanisms to Edwardsiella tarda Infection
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Samples Collection
2.2. Libraries Construction and Sequencing
2.3. Genome Assembly and Genome Evaluation
2.4. Gene Prediction and Annotation
2.5. Genome Comparison
2.6. Phylogenetic Tree Reconstruction and Divergence Time Estimation
2.7. Identification and Analysis of AMPs
2.8. Healthy Tissues Extraction and Bacterial Challenge
2.9. Gene Expression Analysis of AMP Genes
2.10. Analysis of Hepcidins in Teleost
3. Results
3.1. Genome Sequencing and Assembly
3.2. Genome Prediction and Annotation
3.3. Phylogenetic Tree Construction and Divergence Time Estimation
3.4. Antimicrobial Peptides (AMPs) Identification
3.5. Comparison of AMP Genes in Teleost
3.6. Expression Patterns of AMP Genes in Healthy Tissues
3.7. Phylogenetic Analysis of Hepcidins among Teleost
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Genome Assembly | Length | Number | ||
---|---|---|---|---|
Contig (bp) | Scaffold (bp) | Contig | Scaffold | |
Total | 844,742,280 | 848,872,105 | 2113 | 744 |
Max | 22,693,483 | 81,503,846 | - | - |
Number ≥ 2000 | - | - | 2081 | 714 |
N50 | 5,473,395 | 35,728,622 | 44 | 10 |
N60 | 4,291,763 | 33,987,958 | 62 | 13 |
N70 | 2,952,698 | 33,130,827 | 85 | 15 |
N80 | 1,543,679 | 28,667,948 | 123 | 18 |
N90 | 290,346 | 24,877,842 | 243 | 21 |
AMPs | Ictalurus punctatus | Cyprinus carpio | Danio rerio | Oryzias latipes | Poecilia reticulata | Poecilia latipinna | Monopterus albus | Paralichthys olivaceus | Cynoglossus semilaevis | Sebastes schlegelii | Larimichthys crocea | Latimeria chalumnae |
---|---|---|---|---|---|---|---|---|---|---|---|---|
RegIIIalpha | 57 | 58 | 31 | 121 | 72 | 79 | 23 | 18 | 22 | 17 | 150 | 7 |
RegIIIgamma | 83 | 89 | 95 | 129 | 74 | 87 | 57 | 31 | 34 | 37 | 25 | 42 |
TCP | 134 | 84 | 126 | 113 | 109 | 109 | 93 | 59 | 108 | 67 | 127 | 102 |
Chemokine | 71 | 150 | 72 | 200 | 40 | 39 | 30 | 17 | 22 | 24 | 42 | 33 |
cgUbiquitin | 36 | 71 | 30 | 37 | 31 | 29 | 27 | 13 | 26 | 18 | 46 | 27 |
Hipposin | 30 | 28 | 41 | 23 | 15 | 17 | 19 | 9 | 28 | 5 | 26 | 13 |
Lysozyme | 27 | 9 | 5 | 3 | 7 | 8 | 4 | 3 | 2 | 1 | 5 | 2 |
Histone H2B-1 | 20 | 1 | 17 | 0 | 0 | 0 | 4 | 0 | 3 | 0 | 0 | 0 |
HbbetaP-1 | 11 | 18 | 8 | 5 | 4 | 4 | 2 | 3 | 3 | 1 | 6 | 1 |
Vasoactive intestinal polypeptide | 10 | 15 | 7 | 10 | 7 | 8 | 7 | 2 | 8 | 3 | 7 | 2 |
eNAP-1 | 7 | 12 | 10 | 39 | 5 | 6 | 5 | 3 | 3 | 3 | 4 | 2 |
BHP | 7 | 2 | 1 | 2 | 9 | 7 | 4 | 0 | 1 | 1 | 0 | 1 |
Misgurin | 6 | 0 | 4 | 6 | 0 | 4 | 0 | 0 | 5 | 0 | 5 | 0 |
SK84 | 5 | 1 | 1 | 0 | 2 | 2 | 1 | 1 | 2 | 0 | 1 | 1 |
Porcine NK-Lysin | 4 | 8 | 5 | 2 | 0 | 0 | 2 | 1 | 0 | 0 | 2 | 0 |
Beta-amyloid peptide | 4 | 4 | 2 | 10 | 3 | 4 | 4 | 2 | 11 | 2 | 4 | 1 |
Neuropeptide Y | 3 | 1 | 1 | 5 | 2 | 2 | 2 | 2 | 1 | 1 | 5 | 2 |
Mouse Ang4 | 3 | 4 | 3 | 2 | 5 | 3 | 4 | 1 | 1 | 0 | 1 | 0 |
Adrenomedullin | 3 | 7 | 3 | 10 | 2 | 2 | 2 | 2 | 3 | 2 | 6 | 2 |
YFGAP | 2 | 3 | 2 | 2 | 3 | 4 | 2 | 3 | 2 | 4 | 1 | 1 |
SP-BN | 2 | 9 | 5 | 4 | 5 | 6 | 4 | 3 | 4 | 3 | 6 | 3 |
Omwaprin | 2 | 0 | 1 | 0 | 1 | 2 | 3 | 1 | 1 | 2 | 3 | 0 |
Human TC | 2 | 1 | 1 | 5 | 2 | 3 | 0 | 1 | 0 | 0 | 0 | 4 |
HMGN | 2 | 2 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
Hepcidin | 2 | 4 | 3 | 8 | 2 | 5 | 1 | 2 | 1 | 4 | 2 | 1 |
gcLEAP | 2 | 3 | 2 | 3 | 1 | 1 | 0 | 0 | 1 | 1 | 0 | 1 |
Calcitonin gene-related peptide | 2 | 6 | 1 | 5 | 3 | 3 | 1 | 1 | 2 | 1 | 2 | 2 |
SLPI | 2 | 11 | 2 | 0 | 0 | 0 | 2 | 0 | 1 | 1 | 1 | 1 |
Skin peptide tyrosine-tyrosine | 2 | 4 | 3 | 5 | 2 | 2 | 4 | 0 | 2 | 2 | 0 | 0 |
Ubiquicidin | 1 | 3 | 2 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
Thrombocidin | 1 | 1 | 1 | 5 | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 2 |
pCM19 | 1 | 2 | 1 | 0 | 1 | 1 | 1 | 0 | 2 | 0 | 1 | 1 |
Naegleriapore A | 1 | 2 | 1 | 6 | 1 | 0 | 0 | 0 | 1 | 1 | 1 | 1 |
Human islet amyloid polypeptide | 1 | 2 | 1 | 4 | 2 | 0 | 0 | 0 | 1 | 1 | 4 | 2 |
Ap | 0 | 2 | 0 | 2 | 16 | 2 | 3 | 0 | 2 | 1 | 2 | 2 |
Peptide 3910 | 0 | 2 | 1 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 3 | 1 |
Sushi peptide | 0 | 0 | 2 | 3 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 |
Luxuriosin | 0 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 4 | 4 |
Buforin II | 0 | 0 | 0 | 30 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
hPF4 | 0 | 0 | 0 | 6 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
BD | 0 | 0 | 3 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Ixodidin | 0 | 3 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 2 | 2 | 1 |
gcLEAP | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 |
hGAPDH | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 1 |
Ceratoxin | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 |
Chemerin | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 |
Psoriasin | 0 | 1 | 0 | 0 | 0 | 1 | 2 | 0 | 0 | 0 | 2 | 0 |
Chrombacin | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 5 |
Piscidin 4 | 0 | 0 | 0 | 0 | 2 | 1 | 1 | 0 | 0 | 0 | 0 | 0 |
Misgurin | 0 | 1 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 1 | 0 | 0 |
Kaliocin-1 | 0 | 0 | 1 | 2 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 1 |
LEAP-2 | 0 | 1 | 1 | 3 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 1 |
Chicken LEAP-2 | 1 | 1 | 0 | 3 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
Amoebapore A | 0 | 1 | 2 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
Fa-AMP2 | 0 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Human Rnase | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 2 | 0 | 0 |
Enkelytin | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
Elafin | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
Total | 547 | 633 | 501 | 817 | 435 | 446 | 319 | 182 | 310 | 214 | 504 | 281 |
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Zhang, M.; Cao, M.; Xiu, Y.; Fu, Q.; Yang, N.; Su, B.; Li, C. Identification of Antimicrobial Peptide Genes in Black Rockfish Sebastes schlegelii and Their Responsive Mechanisms to Edwardsiella tarda Infection. Biology 2021, 10, 1015. https://doi.org/10.3390/biology10101015
Zhang M, Cao M, Xiu Y, Fu Q, Yang N, Su B, Li C. Identification of Antimicrobial Peptide Genes in Black Rockfish Sebastes schlegelii and Their Responsive Mechanisms to Edwardsiella tarda Infection. Biology. 2021; 10(10):1015. https://doi.org/10.3390/biology10101015
Chicago/Turabian StyleZhang, Min, Min Cao, Yunji Xiu, Qiang Fu, Ning Yang, Baofeng Su, and Chao Li. 2021. "Identification of Antimicrobial Peptide Genes in Black Rockfish Sebastes schlegelii and Their Responsive Mechanisms to Edwardsiella tarda Infection" Biology 10, no. 10: 1015. https://doi.org/10.3390/biology10101015