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Comparison of different developmental stages of jujube (Ziziphus jujuba) fruit and identification of Hub genes Cover

Comparison of different developmental stages of jujube (Ziziphus jujuba) fruit and identification of Hub genes

Folia Horticulturae
Volume 36 (2024): Issue 3 (December 2024)
By: Yalan Li,  Tian Ren,  Siyu Qu,  Qing Hao,  Dingyu Fan and  Alimu Alimire  
Open Access
|Dec 2024

Figures & Tables

Figure 1.

Photographs of Z. jujuba cv. 'Dongzao' at four different stages of development (63 days, 78 days, 98 days, 108 days after flower blooming corresponding to the expansion stage, the FE stage, WM stage, ER stage, and FR stage, respectively). ER, early red; FE, fruit expanding; FR, full red; WM, white-mature.
Photographs of Z. jujuba cv. 'Dongzao' at four different stages of development (63 days, 78 days, 98 days, 108 days after flower blooming corresponding to the expansion stage, the FE stage, WM stage, ER stage, and FR stage, respectively). ER, early red; FE, fruit expanding; FR, full red; WM, white-mature.

Figure 2.

Global assessment of transcriptome data. (A) Sequencing of single-base conversion types. (B) Distribution density of SNP counts, which shows the quality of transcriptome libraries. (C) SNP annotation categorisation. (D) INDEL-annotated classification. INDEL, insertion-deletion; SNP, single nucleotide polymorphism.
Global assessment of transcriptome data. (A) Sequencing of single-base conversion types. (B) Distribution density of SNP counts, which shows the quality of transcriptome libraries. (C) SNP annotation categorisation. (D) INDEL-annotated classification. INDEL, insertion-deletion; SNP, single nucleotide polymorphism.

Figure 3.

Transcriptome analysis of fruit at the WM and FE stages. (A) Volcano plot showing the DEGs; the blue dots represent downregulated genes and the red dots represent upregulated genes. (B) Clustering heat maps of the top 10 DEGs, each row represents a gene and each column represents a sample, with the colour bands on the right indicating different gene expressions; the closer to yellow the higher the gene expression, the closer to green the lower the expression. (C) GO functional enrichment analysis of the genes in the FE and WM jujube groups. (D) KEGG functional enrichment analysis of the genes in the FE and WM jujube groups. DEGs, differentially expressed genes; FE, fruit expanding; GO, gene ontology; KEGG, Kyoto encyclopedia of genes and genomes; WM, white-mature.
Transcriptome analysis of fruit at the WM and FE stages. (A) Volcano plot showing the DEGs; the blue dots represent downregulated genes and the red dots represent upregulated genes. (B) Clustering heat maps of the top 10 DEGs, each row represents a gene and each column represents a sample, with the colour bands on the right indicating different gene expressions; the closer to yellow the higher the gene expression, the closer to green the lower the expression. (C) GO functional enrichment analysis of the genes in the FE and WM jujube groups. (D) KEGG functional enrichment analysis of the genes in the FE and WM jujube groups. DEGs, differentially expressed genes; FE, fruit expanding; GO, gene ontology; KEGG, Kyoto encyclopedia of genes and genomes; WM, white-mature.

Figure 4.

Transcriptome analysis of fruit at the ER and WM stages. (A) Volcano plot demonstrating the DEGs; blue dots represent downregulated genes and the red dots represent upregulated genes. (B) Clustering heat maps of the top 10 DEGs, each row represents a gene and each column represents a sample, with the colour bands on the right indicating different gene expressions; the closer to the yellow the higher the gene expression, while the closer to the green the lower the expression. (C) GO functional enrichment analysis of genes in the WM and ER jujube groups. (D) KEGG functional enrichment analysis of genes in the WM and ER jujube groups. DEGs, differentially expressed genes; ER, early red; GO, gene ontology; KEGG, Kyoto encyclopedia of genes and genomes; WM, white-mature.
Transcriptome analysis of fruit at the ER and WM stages. (A) Volcano plot demonstrating the DEGs; blue dots represent downregulated genes and the red dots represent upregulated genes. (B) Clustering heat maps of the top 10 DEGs, each row represents a gene and each column represents a sample, with the colour bands on the right indicating different gene expressions; the closer to the yellow the higher the gene expression, while the closer to the green the lower the expression. (C) GO functional enrichment analysis of genes in the WM and ER jujube groups. (D) KEGG functional enrichment analysis of genes in the WM and ER jujube groups. DEGs, differentially expressed genes; ER, early red; GO, gene ontology; KEGG, Kyoto encyclopedia of genes and genomes; WM, white-mature.

Figure 5.

Transcriptome analysis of fruit at the ER and FR stage. (A) Volcano plot showing the DEGs, the blue dots represent downregulated genes and the red dots represent upregulated genes. (B) Clustering heat maps of the top 10 DEGs, each row represents a gene and each column represents a sample, with the colour bands on the right indicating different gene expressions; the closer to the yellow the higher the gene expression, and the closer to the green the lower the expression. (C) GO functional enrichment analysis of genes in the ER and FR groups of jujuba. (D) KEGG functional enrichment analysis of genes in the ER and FR groups. DEGs, differentially expressed genes; ER, early red; FR, full red; GO, gene ontology; KEGG, Kyoto encyclopedia of genes and genomes.
Transcriptome analysis of fruit at the ER and FR stage. (A) Volcano plot showing the DEGs, the blue dots represent downregulated genes and the red dots represent upregulated genes. (B) Clustering heat maps of the top 10 DEGs, each row represents a gene and each column represents a sample, with the colour bands on the right indicating different gene expressions; the closer to the yellow the higher the gene expression, and the closer to the green the lower the expression. (C) GO functional enrichment analysis of genes in the ER and FR groups of jujuba. (D) KEGG functional enrichment analysis of genes in the ER and FR groups. DEGs, differentially expressed genes; ER, early red; FR, full red; GO, gene ontology; KEGG, Kyoto encyclopedia of genes and genomes.

Figure 6.

Transcriptome analysis of fruit at the FE and WM stages. (A) Volcano plot indicating the DEGs; blue dots represent downregulated genes and the red dots represent upregulated genes. (B) Clustering heat maps of the top 10 DEGs, each row represents a gene and each column represents a sample, with the colour bands on the right indicating different gene expressions; the closer to the yellow the higher the gene expression, and the closer to the green the lower the expression. (C) GO functional enrichment analysis of the genes in the FE and WM jujube groups. DEGs, differentially expressed genes; FE, fruit expanding; GO, gene ontology; WM, white-mature.
Transcriptome analysis of fruit at the FE and WM stages. (A) Volcano plot indicating the DEGs; blue dots represent downregulated genes and the red dots represent upregulated genes. (B) Clustering heat maps of the top 10 DEGs, each row represents a gene and each column represents a sample, with the colour bands on the right indicating different gene expressions; the closer to the yellow the higher the gene expression, and the closer to the green the lower the expression. (C) GO functional enrichment analysis of the genes in the FE and WM jujube groups. DEGs, differentially expressed genes; FE, fruit expanding; GO, gene ontology; WM, white-mature.

Figure 7.

Gene interaction network diagram. The pink nodes represent non-hub genes obtained, the yellow nodes represent hub genes after correlation coefficient screening and black lines indicate the presence of correlation between genes. The black line indicates the correlation between genes: (A) WM vs FE; (B) ER vs WM; (C) FR vs ER; (D) FR vs FE. ER, early red; FE, fruit expanding; FR, full red; WM, white-mature.
Gene interaction network diagram. The pink nodes represent non-hub genes obtained, the yellow nodes represent hub genes after correlation coefficient screening and black lines indicate the presence of correlation between genes. The black line indicates the correlation between genes: (A) WM vs FE; (B) ER vs WM; (C) FR vs ER; (D) FR vs FE. ER, early red; FE, fruit expanding; FR, full red; WM, white-mature.

Figure 8.

Differential expression boxplot of the four hub genes. (A), LOC107409707; (B), LOC107416546; (C), LOC107415777; (D), LOC107414679.
Differential expression boxplot of the four hub genes. (A), LOC107409707; (B), LOC107416546; (C), LOC107415777; (D), LOC107414679.

Figure S1.

GSEA functional enrichment analysis of genes. (A) the WM and FE jujube groups. (B) the ER and WM jujube groups. (C) the FR and FE jujube groups. ER, early red stage; FE, fruit expanding stage; FR, full red; WM, white-mature; GSEA, gene set enrichment analysis.
GSEA functional enrichment analysis of genes. (A) the WM and FE jujube groups. (B) the ER and WM jujube groups. (C) the FR and FE jujube groups. ER, early red stage; FE, fruit expanding stage; FR, full red; WM, white-mature; GSEA, gene set enrichment analysis.

The efficiency of the reads of each sample against the reference genome_

SampleTotal ReadsMapped ReadsUniq Mapped ReadsMultiple Map ReadsReads Map to ‘+’Reads Map to ‘-’
ER134,967,79028,610,083 (81.82%)27,551,138 (78.79%)1,058,945 (3.03%)14,885,522 (42.57%)15,022,253 (42.96%)
ER235,866,75229,195,000 (81.40%)28,071,485 (78.27%)1,123,515 (3.13%)15,216,825 (42.43%)15,347,299 (42.79%)
ER333,722,95227,256,909 (80.83%)26,159,026 (77.57%)1,097,883 (3.26%)14,276,092 (42.33%)14,408,408 (42.73%)
FE133,362,78626,937,644 (80.74%)26,038,012 (78.05%)899,632 (2.70%)13,973,789 (41.88%)14,067,875 (42.17%)
FE231,701,81425,501,408 (80.44%)24,663,212 (77.80%)838,196 (2.64%)13,186,007 (41.59%)13,325,312 (42.03%)
FE332,862,05626,304,992 (80.05%)25,421,257 (77.36%)883,735 (2.69%)13,658,562 (41.56%)13,717,436 (41.74%)
FR136,467,94429,673,467 (81.37%)28,546,895 (78.28%)1,126,572 (3.09%)15,467,804 (42.41%)15,596,106 (42.77%)
FR239,654,15031,656,269 (79.83%)30,480,071 (76.86%)1,176,198 (2.97%)16,471,579 (41.54%)16,614,054 (41.90%)
FR333,872,16427,548,123 (81.33%)26,547,492 (78.38%)1,000,631 (2.95%)14,325,410 (42.29%)14,444,203 (42.64%)
WM132,694,05026,445,979 (80.89%)25,496,018 (77.98%)949,961 (2.91%)13,810,980 (42.24%)13,824,743 (42.29%)
WM232,516,75826,331,369 (80.98%)25,402,482 (78.12%)928,887 (2.86%)13,708,981 (42.16%)13,780,517 (42.38%)
WM333,679,48427,547,095 (81.79%)26,549,486 (78.83%)997,609 (2.96%)14,362,487 (42.64%)14,401,510 (42.76%)
DOI: https://doi.org/10.2478/fhort-2024-0028 | Journal eISSN: 2083-5965 | Journal ISSN: 0867-1761
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Language: English
Page range: 435 - 448
Submitted on: Apr 10, 2024
Accepted on: Oct 17, 2024
Published on: Dec 20, 2024
Published by: Polish Society for Horticultural Sciences (PSHS)
In partnership with: Paradigm Publishing Services
Publication frequency: 2 issues per year
Keywords:
differentially expressed genes,
enrichment analysis,
hub genes,
jujube,
transcriptomics
Related subjects:
Life sciences,
Plant science,
Zoology,
Ecology,
Life sciences, other

© 2024 Yalan Li, Tian Ren, Siyu Qu, Qing Hao, Dingyu Fan, Alimu Alimire, published by Polish Society for Horticultural Sciences (PSHS)
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

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