Genome-Wide Identification and Analysis of Chitinase GH18 Gene Family in Trichoderma longibrachiatum T6 Strain: Insights into Biocontrol of Heterodera avenae
Abstract
1. Introduction
2. Materials and Methods
2.1. Fungal and H. avenae Preparation
2.2. Identification and Physicochemical Characterization of the GH18 Family Genes in T6
2.3. Genes Chromosomal Location and Ka (Nonsynonymous)/Ks (Synonymous) Analysis
2.4. Proteins Domain, Genes Structure, and Conserved Motif Analysis
2.5. Phylogenetic Analysis
2.6. Cis-Acting Element Analysis
2.7. GO and KEGG Enrichment Analysis
2.8. GH18 Proteins Structural Prediction and Interaction Network Analysis
2.9. Gene Expression Characteristics Analysis
3. Results
3.1. Genome-Wide Identification and Physicochemical Properties Analysis of GH18 Family Genes in T6
3.2. Chromosomal Localization, Ka (Nonsynonymous)/Ks (Synonymous) Analysis of GH18 Family Genes in T6
3.3. Phylogenetic Analysis of GH18 Family Members in T6
3.4. Conserved Motif, Domain, and Gene Structure Analysis of GH18 Family Members in T6
3.5. Cis-Acting Element Analysis of GH18 Family Genes in T6
3.6. Prediction of GH18 Interacting Proteins and Analysis of Protein Secondary and Tertiary Structures in T6
3.7. GO and KEGG Enrichment Analysis of GH18 Family Genes in T6
3.8. Relative Expression Level of GH18 Family Genes in T6 After Inoculation with Cysts
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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Genes | Genes ID | Genes Locus | Amino Acid (aa) | ORF (bp) | Molecular Weight (kDa) | Theoretical pI | Instability Index | Aliphatic Index | GRAVY Score | Transmembrane Domain | Signal Peptides | Subcellular Localization |
---|---|---|---|---|---|---|---|---|---|---|---|---|
GH18-1 | M440DRAFT_1367966 | KZ679126 | 401 | 1206 | 44.25 | 5.96 | 46.59 | 72.02 | −0.458 | No | No | Mitochondrion |
GH18-2 | M440DRAFT_1459816 | KZ679126 | 990 | 2973 | 106.44 | 5.44 | 37.22 | 69.76 | −0.304 | No | No | extracellular |
GH18-3 | M440DRAFT_1436691 | KZ679128 | 321 | 966 | 34.53 | 4.20 | 40.03 | 67.04 | −0.213 | No | Yes | extracellular |
GH18-4 | M440DRAFT_1326396 | KZ679128 | 1386 | 4161 | 147.06 | 4.69 | 35.20 | 69.07 | −0.260 | No | Yes | extracellular |
GH18-5 | M440DRAFT_1390232 | KZ679129 | 342 | 1029 | 38.24 | 5.33 | 39.97 | 90.38 | −0.234 | No | No | extracellular |
GH18-6 | M440DRAFT_1400047 | KZ679129 | 343 | 1032 | 36.22 | 4.64 | 27.72 | 85.13 | 0.093 | No | Yes | extracellular |
GH18-7 | M440DRAFT_1400627 | KZ679130 | 397 | 1194 | 44.26 | 5.11 | 30.76 | 64.18 | −0.592 | No | No | extracellular |
GH18-8 | M440DRAFT_1239474 | KZ679131 | 390 | 1173 | 40.68 | 4.55 | 45.97 | 71.38 | −0.142 | No | Yes | extracellular |
GH18-9 | M440DRAFT_66100 | KZ679132 | 975 | 2928 | 107.32 | 5.64 | 42.07 | 75.34 | −0.296 | No | No | extracellular |
GH18-10 | M440DRAFT_1470525 | KZ679133 | 1503 | 4512 | 159.28 | 6.01 | 33.86 | 67.86 | −0.338 | No | Yes | extracellular |
GH18-11 | M440DRAFT_1392779 | KZ679134 | 403 | 1212 | 41.22 | 4.60 | 28.17 | 71.59 | −0.031 | No | Yes | extracellular |
GH18-12 | M440DRAFT_1338469 | KZ679137 | 393 | 1182 | 43.99 | 4.78 | 33.72 | 89.11 | −0.204 | No | Yes | extracellular |
GH18-13 | M440DRAFT_1058965 | KZ679137 | 357 | 1074 | 38.57 | 6.20 | 40.29 | 83.39 | −0.087 | No | No | Mitochondrion |
GH18-14 | M440DRAFT_59808 | KZ679140 | 392 | 1179 | 41.45 | 4.21 | 42.60 | 65.99 | −0.174 | No | Yes | extracellular |
GH18-15 | M440DRAFT_1434173 | KZ679145 | 410 | 1233 | 42.47 | 4.48 | 42.28 | 69.78 | −0.134 | No | Yes | extracellular |
GH18-16 | M440DRAFT_1406318 | KZ67914 | 424 | 1275 | 45.89 | 5.29 | 25.35 | 80.42 | −0.204 | No | Yes | extracellular |
GH18-17 | M440DRAFT_1344625 | KZ679151 | 492 | 1479 | 54.31 | 5.37 | 44.63 | 77.74 | −0.383 | No | Yes | extracellular |
GH18-18 | M440DRAFT_1395841 | KZ679151 | 366 | 1101 | 40.49 | 4.89 | 32.96 | 72.57 | −0.269 | No | No | extracellular |
Motifs | Width (aa) | Motifs Sequence |
---|---|---|
Motif 1 | 36 | SHVNLTETDBAVSMYTKAGVPANKIVLGIPSYGRSF |
Motif 2 | 21 | SVVRFLGNYGLDGIDIDWEYP |
Motif 3 | 48 | FNKKTWGWNGCPNLLVGYKICLSKGSPMPAPVPNAVCGPQKPGTKRP |
Motif 4 | 29 | AFKYJDLAAIDQYLDYINLMAYDYAGSWD |
Motif 5 | 15 | AGVKVJLSJGGWTYS |
Motif 6 | 14 | ITHVIYAFANITED |
Motif 7 | 18 | LNPCPLNACCNIWGQCGT |
Motif 8 | 29 | EEEAEBYLLLLREVRKALPADAALSIAVP |
Motif 9 | 37 | YNDTQWVAYMSDKTKASRIDKYPALNFLGIVDWAIDL |
Motif 10 | 32 | FCTPAKSSTGAPGTAPPGENGCISNCGTSIVT |
Proteins | Alpha Helix (%) | Extended Strand (%) | Beta Turn (%) | Random Coil (%) | Distribution of Secondary Structure Elements |
---|---|---|---|---|---|
GH18-1 | 27.43 | 15.71 | 0.00 | 56.86 | |
GH18-2 | 20.30 | 10.40 | 0.00 | 69.29 | |
GH18-3 | 31.46 | 17.13 | 0.00 | 51.40 | |
GH18-4 | 15.80 | 14.86 | 0.00 | 69.34 | |
GH18-5 | 26.61 | 14.33 | 0.00 | 59.06 | |
GH18-6 | 27.70 | 16.03 | 0.00 | 56.27 | |
GH18-7 | 28.97 | 15.37 | 0.00 | 55.67 | |
GH18-8 | 27.18 | 14.87 | 0.00 | 57.95 | |
GH18-9 | 32.72 | 11.69 | 0.00 | 55.59 | |
GH18-10 | 14.50 | 13.91 | 0.00 | 71.59 | |
GH18-11 | 25.56 | 13.65 | 0.00 | 60.79 | |
GH18-12 | 36.64 | 16.28 | 0.00 | 47.07 | |
GH18-13 | 29.69 | 17.93 | 0.00 | 52.38 | |
GH18-14 | 26.79 | 15.05 | 0.00 | 58.16 | |
GH18-15 | 23.66 | 16.10 | 0.00 | 60.24 | |
GH18-16 | 32.55 | 14.86 | 0.00 | 52.59 | |
GH18-17 | 23.58 | 13.62 | 0.00 | 62.80 | |
GH18-18 | 28.42 | 17.49 | 0.00 | 54.10 |
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Duan, C.; Liu, J.; Zhang, S.; Xu, B. Genome-Wide Identification and Analysis of Chitinase GH18 Gene Family in Trichoderma longibrachiatum T6 Strain: Insights into Biocontrol of Heterodera avenae. J. Fungi 2025, 11, 714. https://doi.org/10.3390/jof11100714
Duan C, Liu J, Zhang S, Xu B. Genome-Wide Identification and Analysis of Chitinase GH18 Gene Family in Trichoderma longibrachiatum T6 Strain: Insights into Biocontrol of Heterodera avenae. Journal of Fungi. 2025; 11(10):714. https://doi.org/10.3390/jof11100714
Chicago/Turabian StyleDuan, Cizhong, Jia Liu, Shuwu Zhang, and Bingliang Xu. 2025. "Genome-Wide Identification and Analysis of Chitinase GH18 Gene Family in Trichoderma longibrachiatum T6 Strain: Insights into Biocontrol of Heterodera avenae" Journal of Fungi 11, no. 10: 714. https://doi.org/10.3390/jof11100714
APA StyleDuan, C., Liu, J., Zhang, S., & Xu, B. (2025). Genome-Wide Identification and Analysis of Chitinase GH18 Gene Family in Trichoderma longibrachiatum T6 Strain: Insights into Biocontrol of Heterodera avenae. Journal of Fungi, 11(10), 714. https://doi.org/10.3390/jof11100714