Malus prunifolia Fupingqiuzi Genome v1.0 Assembly & Annotation
Li Z, Wang L, He J, Li X, Hou N, Guo J, Niu C, Li C, Liu S, Xu J, Xie Y, Zhang D, Shen X, Lu L, Geng D, Chen P, Jiang L, Wang L, Li H, Malnoy M, Deng C, Zou Y, Li C, Zhan X, Dong Y, Notaguchi M, Ma F, Xu Q, Guan Q. A Chromosome-Scale Reference Genome Provides Insights into the Genetic Origin and Grafting-Mediated Stress Tolerance of Malus prunifolia.. Plant biotechnology journal. 2022 Mar 29 DOI: 10.1111/pbi.13817.
Malus prunifolia is a species of crabapple and M. prunifolia ‘Fupingqiuzi’ is used as a common apple rootstock due to its known tolerances to abiotic and biotic stresses. This paper present a high-quality chromosome-scale genome sequence of M. prunifolia ‘Fupingqiuzi’ (2n = 2x = 34) assembled using a combined strategy of Illumina short reads, PacBio long reads, and Hi-C data. The total length of the assembly was 712 Mb, with a scaffold N50 of 41.6 Mb. Approximately 98.6% of the contigs were anchored into 17 pseudochromosomes. Over 91.36% of non-redundant and single-mapped mate-pair reads were concordant pairs, indicating that Hi-C anchoring has high accuracy. BUSCO revealed a completeness rate of 95.3% . A total of 44 997 protein-coding genes were predicted, with an average gene length of 5516 bp. In addition, 1785 non-coding RNA genes and 484 Mb of repetitive sequences were detected in the ‘Fupingqiuzi’ genome.
Homology of the Malus prunifolia Fupingqiuzi 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-9 was used for the NCBI nr (Release 2021-09) and 1e-6 for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2021-09), and UniProtKB/TrEMBL (Release 2021-09) databases. The best hit reports are available for download in Excel format.
The Malus prunifolia Fupingqiuzi Genome v1.0 assembly file is available in FASTA format.
The Malus prunifolia Fupingqiuzi v1.0 genome gene prediction files are available in FASTA and GFF3 formats.
Functional annotation for the Malus prunifolia Fupingqiuzi Cuiguan Genome v1.0 are available for download below. The Malus prunifolia Fupingqiuzi 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).
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 Malus prunifolia Fupingqiuzi genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3 format.