Download
| File type | Description | File link |
|---|---|---|
| Sequence | Genome sequence of NDH108 | NDH108.fa.gz |
| Annotation | Repeat annotation of NDH108 | NDH108.repeat.bed.gz |
| Annotation | Gene structure annotation of NDH108 | NDH108.gff3.gz |
| Annotation | Novel gene structure annotation of NDH108 | novelTr.gtf |
| Table | Gene functional annotation of NDH108 | NDH108_gene_annotation.txt.gz |
| Table | Novel gene supported by proteomics | CodingEventClassCode.xlsx |
| Table | WGCNA module gene information | WGCNA_Node_all.txt.gz |
| Table | protein-protein interactions with experimentally verified and predicted interactions | reason_result_NDH108_conbined_PPI.tsv.gz |
| Table | Correlation of transcript/protein/metabolite (|Pearson| > 0.8) | pcm_long.08.tsv.gz |
| Table | Correlation of transcript/protein/metabolite (|Pearson| > 0.7) | pcm_long.07.tsv.gz |
| Table | Correlation of transcript/protein/metabolite (|Spearman| > 0.8) | scm_long.08.tsv.gz |
| Table | Correlation of transcript/protein/metabolite (|Spearman| > 0.7) | scm_long.07.tsv.gz |
- Genome sequence: The long (ONT Ultra-long / PacBio HIFI) reads were corrected and assembled using NextDenovo. First, contigs were polished using Racon and NextPolish with long reads. Next, the contigs were further clustered, ordered, and oriented scaffolds onto chromosomes by LACHESIS. The details were in the previous published article.
- Repeat annotation: The gene prediction was performed using EDTA and Repeatmasker. The details were in the previous published article.
- Gene annotation: The gene prediction was performed using GeMoMa, PASA, Augustus and EVidenceModeler, combing de novo, transcript and homolog protein based strategy. The details were in the previous published article.
- Novel transcript detection: The novel transcript detection was performed using Stringtie2, with support of RNAseq data.
Manual
Genome browser page
Transcriptome and proteome page
PPI page
Metabolome page
Citation
[1] Xue H, Zhao K, Dong X, et al. PeanutOmics: A comprehensive platform with integrative multi-omics atlas throughout the life cycle. Plant Communications, 2025 (online). doi: 10.1016/j.xplc.2025.101622 (when using PeanutOmics platform)
[2] Zhao K, Xue H, Li G, et al. Pangenome analysis reveals structural variation associated with seed size and weight traits in peanut. Nature Genetics, 2025;57(5):1250-1261. doi: 10.1038/s41588-025-02170-w (when using peanut NDH108 genome sequence)
[3] Gong F, Cao D, Sun X, et al. Homologous mapping yielded a comprehensive predicted protein–protein interaction network for peanut (Arachis hypogaea L.). Bmc Plant Biol, 2024 24:873. doi: 10.1186/s12870-024-05580-w (when using PPI network)
Contact Information
Hongzhang Xue: xuehzh95@sjtu.edu.cn
Chaochun Wei: ccwei@sjtu.edu.cn
Dongmei Yin: yindm@henau.edu.cn
