Prunus salicina Lindl cv. Wushancuili Genome v1.0 Assembly & Annotation
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Overview
Publication Zhou, K., Wang, J., Pan, L., Xiang, F., Zhou, Y., Xiong, W., Zeng, M., Grierson, D., Kong, W., Hu, L., & Xi, W. (2023). A chromosome-level genome assembly for Chinese plum 'Wushancuili' reveals the molecular basis of its fruit color and susceptibility to rain-cracking. Horticultural Plant Journal, https://doi.org/10.1016/j.hpj.2023.04.011 Description Here we present a chromosome-level genome assembly of Prunus salicina Lindl cv. Wushancuili with the combination of PacBio sequencing, Illumina Sequencing and Hi-C technology. The assembly has a total size of 302.17 Mb, with contig N50 of 23,590,757bp and scaffold N50 of 33,711,648bp. 96.56% of the Prunus salicina Lindl cv. Wushancuili assembled sequences were anchored onto 8 pseudo-chromosomes. De novo, homology-based, and RNA-seq methods were used together to predict were used together to predict 25,304 protein-coding genes, 99.23% of which were functionally annotated. BUSCO analysis showed 98.95% complete genes. CEGMA assessment showed that our assembly captured 233 (93.95%) complete core genes. Table 1. Summary of ‘Wushancuili’ genome assembly and annotation.
Homology
Homology of the Prunus salicina Lindl cv. Wushancuili genome v1.0 proteins was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e-6 for the Arabidoposis proteins (Araport11, 2022-09), UniProtKB/SwissProt (Release 2023-07), and UniProtKB/TrEMBL (Release 2023-07) databases. The best hit reports are available for download in Excel format. Protein Homologs
Assembly
The Prunus salicina Genome v1.0 assembly files are available in FASTA and GFF3 formats. Downloads
Gene Predictions
The Prunus salicina v1.0 genome gene prediction files are available in FASTA and GFF3 formats. Downloads
Functional Analysis
Functional annotation for the Prunus salicina Lindl cv. Wushancuili genome v1.0 are available for download below. The Prunus salicina genome v1.0 proteins were analyzed using InterProScan in order to assign InterPro domains and Gene Ontology (GO) terms. Pathways analysis was performed using the KEGG Automatic Annotation Server (KAAS). Downloads
Transcript Alignments
Transcript alignments were performed by the GDR Team of Main Bioinformatics Lab at WSU. The alignment tool 'BLAT' was used to map transcripts to the Prunus salicina Lindl cv. Wushancuili genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3 format.
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