Exploring the Genetic Basis of Calonectria spp. Resistance in Eucalypts
Abstract
:1. Introduction
1.1. Background and Significance of Research on Eucalypt Leaf Blight
1.2. Eucalyptus pellita
1.3. Variety Improvement Is the Solution to the Impacts of Disease
2. Materials and Methods
2.1. Genetic Material
2.2. Transcriptome Sequencing and Analysis
3. Results
3.1. Quality Control of Sequence Data (QC)
3.1.1. Sequencing Data Quality
3.1.2. Mapping Sequencing Information to E. grandis Reference Genome and Its Regional Distribution
3.2. Quantitative Analysis of the Genes Sequenced
3.2.1. Detection of Expression Distribution of Genes Sequenced in Different Eucalypt Genotypes
3.2.2. The Correlation of Gene Expression of Eucalypt Genotypes Sequenced
3.2.3. Principal Component Analysis of Gene Expression
3.3. Gene Co-Expression Venn Diagram and Differential Gene Venn Diagram
3.4. Gene Expression Analysis (Differential Gene Screening and Clustering)
3.5. Enrichment Analysis of Differential Genes in Comparison Groups
3.6. Alternative Splicing Event Analysis
3.7. SNP Variation Loci Analysis
3.8. Weighted Gene Co-Expression Network Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Hybrids | Susceptibility | Female | Species | Male | Species |
---|---|---|---|---|---|
EC338 | Resistant | W1767 | E. wetarensis | P9060 | E. pellita |
EC333 | Susceptible | H1522 | E. urophylla × E. pellita | Unknown | E. urophylla |
Comparisons | GO | KEGG |
---|---|---|
EC338 vs. EC333 | Carbohydrate binding, pattern binding, polysaccharide binding (−log10(padj) > 6) | Phenylpropanoid biosynthesis, flavonoid biosynthesis, plant–pathogen interaction, sesquiterpenoid and triterpenoid biosynthesis (−log10(padj) > 2.5) |
EC338 vs. P9060 | Terpene synthase activity, carbon–oxygen lyase acting on phosphates, carbon−oxygen lyase activity (−log10(padj) > 10) | Phenylpropanoid biosynthesis, sesquiterpenoid and triterpenoid biosynthesis (−log10(padj) > 5) |
EC338 vs. W1767 | DNA binding transcription factor activity, terpene synthase activity, carbon–oxygen lyase acting on phosphates, iron ion binding, transcription regulator activity (−log10(padj) > 6) | Phenylpropanoid biosynthesis, plant hormone signal transduction, sesquiterpenoid and triterpenoid biosynthesis, plant–pathogen interaction, biosynthesis of various plant secondary, flavonoid biosynthesis (−log10(padj) > 4) |
EC333 vs. H1522 | Carbohydrate binding, terpene synthase activity, carbon–oxygen lyase acting on phosphates, carbon–oxygen lyase activity (−log10(padj) > 4) | Phenylpropanoid biosynthesis (−log10(padj) > 7.5) |
Differential Genotypes | Genotypes | Name | Size | ES | NES | NOM p-Value | FDR q-Value | FWER p-Value | Rank at Max | Leading Edge |
---|---|---|---|---|---|---|---|---|---|---|
EC338 vs. EC333 | EC333 | Carbohydrate binding (GO:0030246) | 286 | −0.519 | −1.580 | 0 | 0.171 | 0.75 | 5450 | tags = 40%, list = 17%, signal = 48% |
EC338 vs. P9060 | EC338 | Terpene synthase activity (GO:0010333) | 86 | 0.469 | 1.952 | 0 | 0.201 | 0.188 | 2191 | tags = 36%, list = 7%, signal = 39% |
EC338 | Carbon–oxygen lyase acting on phosphates (GO:0016838) | 89 | 0.462 | 1.939 | 0 | 0.149 | 0.188 | 2191 | tags = 35%, list = 7%, signal = 37% | |
EC338 | Carbon–oxygen lyase activity (GO:0016835) | 112 | 0.429 | 2.024 | 0 | 0.098 | 0.047 | 3561 | tags = 35%, list = 11%, signal = 39% |
Differential Genotypes | Genotypes | Name | Size | ES | NES | NOM p-Value | FDR q-Value | FWER p-Value | Rank at Max | Leading Edge |
---|---|---|---|---|---|---|---|---|---|---|
EC338 vs. EC333 | EC338 | Sesquiterpenoid and triterpenoid biosynthesis (EGR00909) | 65 | 0.610 | 1.714 | 0 | 0.066 | 0.093 | 3071 | tags = 35%, list = 10%, signal = 39% |
EC338 vs. W1767 | EC338 | Phenylpropanoid biosynthesis (EGR00940) | 224 | 0.369 | 1.900 | 0 | 0.048 | 0.048 | 3594 | tags = 27%, list = 11%, signal = 30% |
W1767 | Plant–pathogen interaction (EGR04626) | 281 | −0.455 | −1.501 | 0 | 0.178 | 0.599 | 4752 | tags = 37%, list = 15%, signal = 43% | |
EC338 | Flavonoid biosynthesis (EGR00941) | 89 | 0.521 | 1.455 | 0 | 0.103 | 0.760 | 4985 | tags = 42%, list = 15%, signal = 49% |
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Su, Z.; Lu, W.; Lin, Y.; Luo, J.; Liu, G.; Huang, A. Exploring the Genetic Basis of Calonectria spp. Resistance in Eucalypts. Curr. Issues Mol. Biol. 2024, 46, 10854-10879. https://doi.org/10.3390/cimb46100645
Su Z, Lu W, Lin Y, Luo J, Liu G, Huang A. Exploring the Genetic Basis of Calonectria spp. Resistance in Eucalypts. Current Issues in Molecular Biology. 2024; 46(10):10854-10879. https://doi.org/10.3390/cimb46100645
Chicago/Turabian StyleSu, Zhiyi, Wanhong Lu, Yan Lin, Jianzhong Luo, Guo Liu, and Anying Huang. 2024. "Exploring the Genetic Basis of Calonectria spp. Resistance in Eucalypts" Current Issues in Molecular Biology 46, no. 10: 10854-10879. https://doi.org/10.3390/cimb46100645