Genome Sequence, Comparative Genome Analysis, and Expression Profiling of the Chitinase GH18 Gene Family in Cordyceps javanica Bd01
Abstract
1. Introduction
- Evolutionary relationships: time-calibrated phylogeny of GH18 orthologs;
- Domain architecture: conserved catalytic (TIM-barrel) and ancillary domains;
- Signature motifs: MEME-identified chitin-binding and processivity motifs;
- 3D structural dynamics: homology modeling of substrate-binding clefts.
2. Results
2.1. Genome Sequencing, Assembly, and Annotation
2.2. Comparative Genomic Analysis
2.3. Genome-Wide Identification and Characterization of GH18 Genes in Cordyceps javanica Bd01
2.4. Conserved Motif and Chromosomal Location of GH18 Genes in Cordyceps javanica Bd01
2.5. Phylogenetic Analysis of GH18 Family Proteins
2.6. Characterization of Physicochemical Properties
2.7. Secondary and Tertiary Structure Analysis
2.8. cis-Regulatory Architecture of GH18 Chitinase Genes in Cordyceps javanica Bd01
3. Discussion
- Actionable biochemical parameters for targeted in vitro purification and functional characterization;
- Structural blueprints facilitating the homology-based functional prediction of uncharacterized GH18 paralogs;
- The evolutionary rationale for biotechnological exploitation, particularly in developing thermostable chitinolytic cocktails for industrial biocatalysis and biocontrol formulations.
4. Materials and Methods
4.1. Culture of Cordyceps javanica Bd01
4.2. DNA Extraction and Sequencing
4.3. Genome Assembly and Annotation
4.4. Orthologous and Phylogenomic Analysis
4.5. Identification and Characterization of GH18 Gene Family in Cordyceps javanica Bd01
4.6. Conserved Domain, Conserved Motif Analyses, and Chromosomal Location
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sample | Cordyceps javanica Bd01 |
---|---|
Coverage (fold) | 229.59X |
No. of all sequences | 698,137 |
Bases in all sequences (bp) | 7,808,156,751 |
Longest length (bp) | 193,316 |
N50 length (bp) | 18,161 |
N90 length (bp) | 4902 |
G+C content | 53.18 |
No. of all contigs | 8 |
Contig Length (bp) | 34,008,118 |
No. of large contigs (>1000 bp) | 8 |
Bases in large contigs (bp) | 34,008,118 |
Contig N50 (bp) | 5,679,179 |
Contig N90 (bp) | 3,285,737 |
Gene number | 9590 |
Gene total length (bp) | 17,091,976 |
Gene average length (bp) | 1782.27 |
ExonLen (bp) | 15,026,841 |
AveExonLen (bp) | 568.12 |
ExonNum | 26,450 |
AveExonNum | 2.76 |
rRNA | 43 |
tRNA | 131 |
Gene Name | Number of Amino Acids | Molecular Weight (kDa) | Total Number of Negatively Charged Residues (Asp + Glu) | Total Number of Positively Charged Residues (Arg + Lys) | Theoretical pI | Instability Index | Aliphatic Index | GRAVY | Subcellular Localization |
---|---|---|---|---|---|---|---|---|---|
Cordyceps0G001980.1 | 787 | 81.41 | 49 | 47 | 7.92 | 39.67 | 63.52 | −0.206 | extr |
Cordyceps0G005200.1 | 1782 | 19.91 | 249 | 206 | 5.33 | 40.35 | 62.25 | −0.604 | nucl |
Cordyceps0G005800.1 | 1310 | 14.35 | 157 | 126 | 5.55 | 44.52 | 76.86 | −0.268 | plas |
Cordyceps0G006260.1 | 333 | 35.07 | 29 | 17 | 4.52 | 33.17 | 68.68 | −0.186 | extr |
Cordyceps0G015440.1 | 353 | 38.95 | 50 | 31 | 4.73 | 43.44 | 89.41 | −0.194 | mito |
Cordyceps0G019620.1 | 392 | 43.82 | 57 | 43 | 5.03 | 48.63 | 78.65 | −0.329 | mito |
Cordyceps0G022620.1 | 958 | 10.54 | 107 | 92 | 5.58 | 45.09 | 64.73 | −0.421 | extr |
Cordyceps0G026500.1 | 1473 | 15.9 | 180 | 148 | 5.39 | 28.36 | 63.65 | −0.443 | extr |
Cordyceps0G027540.1 | 367 | 39.06 | 33 | 28 | 6.11 | 46.74 | 83.32 | −0.126 | extr |
Cordyceps0G029850.1 | 1486 | 16.06 | 182 | 143 | 5.2 | 30.46 | 67.27 | −0.412 | extr |
Cordyceps0G033590.1 | 389 | 42.6 | 36 | 32 | 6.2 | 33.37 | 64.73 | −0.456 | extr |
Cordyceps0G038130.1 | 395 | 44.06 | 54 | 33 | 4.72 | 37.83 | 67.72 | −0.508 | extr |
Cordyceps0G049700.1 | 1409 | 15.1 | 138 | 125 | 5.83 | 43.01 | 65.44 | −0.376 | extr |
Cordyceps0G051520.1 | 430 | 45.22 | 45 | 36 | 5.44 | 30.03 | 73.35 | −0.231 | extr |
Cordyceps0G053220.1 | 423 | 46.19 | 39 | 38 | 6.53 | 26.44 | 73.22 | −0.319 | extr |
Cordyceps0G053360.1 | 365 | 39.84 | 31 | 25 | 5.74 | 38.65 | 80.47 | −0.147 | extr |
Cordyceps0G054290.1 | 1842 | 20.43 | 251 | 204 | 5.63 | 36.42 | 72.49 | −0.461 | extr |
Cordyceps0G055830.1 | 320 | 34.08 | 29 | 30 | 7.53 | 24.01 | 76.34 | −0.218 | extr |
Cordyceps0G061300.1 | 1286 | 14.03 | 150 | 127 | 5.68 | 43.02 | 73.79 | −0.265 | extr |
Cordyceps0G061550.1 | 348 | 36.71 | 24 | 23 | 6.12 | 31.95 | 84.45 | 0.009 | extr |
Cordyceps0G061740.1 | 401 | 42.25 | 28 | 24 | 4.94 | 36.66 | 59.48 | −0.183 | extr |
Cordyceps0G062810.1 | 1404 | 15.14 | 140 | 104 | 5.3 | 41.7 | 70.89 | −0.236 | mito |
Cordyceps0G070700.1 | 315 | 34.54 | 35 | 32 | 5.69 | 28.53 | 78.44 | −0.320 | extr |
Cordyceps0G077050.1 | 372 | 41.41 | 52 | 47 | 5.63 | 33.53 | 64.87 | −0.483 | extr |
Cordyceps0G079200.1 | 445 | 46.94 | 24 | 23 | 6.29 | 41.27 | 61.21 | −0.290 | extr |
Cordyceps0G081320.1 | 324 | 33.98 | 31 | 19 | 4.4 | 37.51 | 80.46 | −0.108 | extr |
Cordyceps0G081330.1 | 392 | 43.13 | 34 | 31 | 5.5 | 35.96 | 73.67 | −0.246 | extr |
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Zhu, T.; Hussain, M.; Ning, J.; Chen, X.; Shi, C.; Yang, D.; Gao, X.; Wu, G. Genome Sequence, Comparative Genome Analysis, and Expression Profiling of the Chitinase GH18 Gene Family in Cordyceps javanica Bd01. Int. J. Mol. Sci. 2025, 26, 2031. https://doi.org/10.3390/ijms26052031
Zhu T, Hussain M, Ning J, Chen X, Shi C, Yang D, Gao X, Wu G. Genome Sequence, Comparative Genome Analysis, and Expression Profiling of the Chitinase GH18 Gene Family in Cordyceps javanica Bd01. International Journal of Molecular Sciences. 2025; 26(5):2031. https://doi.org/10.3390/ijms26052031
Chicago/Turabian StyleZhu, Tao, Mehboob Hussain, Jingyi Ning, Xiao Chen, Chunlan Shi, Dewei Yang, Xi Gao, and Guoxing Wu. 2025. "Genome Sequence, Comparative Genome Analysis, and Expression Profiling of the Chitinase GH18 Gene Family in Cordyceps javanica Bd01" International Journal of Molecular Sciences 26, no. 5: 2031. https://doi.org/10.3390/ijms26052031
APA StyleZhu, T., Hussain, M., Ning, J., Chen, X., Shi, C., Yang, D., Gao, X., & Wu, G. (2025). Genome Sequence, Comparative Genome Analysis, and Expression Profiling of the Chitinase GH18 Gene Family in Cordyceps javanica Bd01. International Journal of Molecular Sciences, 26(5), 2031. https://doi.org/10.3390/ijms26052031