Malus fusca Genome v1.1 Assembly & Annotation
|
Overview
*The whole genome data was initially made public with v1.0 but was later changed to v1.1 with the publication. The only difference between the two versions is that the TE annotation column has been added to the gff files. Publication Mansfeld BN, Yocca A, Ou S, Harkess A, Burchard E, Gutierrez B, van Nocker S, Gottschalk C. A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus. The Plant journal : for cell and molecular biology. 2023 Aug 28. https://onlinelibrary.wiley.com/doi/10.1111/tpj.16433 Description The Pacific crabapple (Malus fusca) is a wild relative of commercial apple (Malus x domestica). With a range extending from Alaska to Northern California, M. fusca is extremely hardy and disease resistant, which represents an untapped genetic resource for many biotic and abiotic stresses that may improve apple breeding as well as rootstock development. However, gene discovery and utilization of M. fusca has been hampered by the lack of genomic resources. Here, we present a high-quality, haplotype-resolved, chromosome-scale genome assembly and annotation of M. fusca. The genome was assembled using high-fidelity long-reads and scaffolded using genetic maps and high-throughput chromatin conformation sequencing, resulting in one of the most contiguous apple genomes to date. We annotated the genome using public transcriptomic data of the same species from diverse tissue types and developmental stages. Genome assembly statistics
Homology
Homology of the Malus fusca Genome v1.1 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. Downloads
Assembly
The Malus fusca Genome v1.1 assembly files are available in GFF3 and FASTA format. Downloads
*The whole genome data was initially made public with v1.0 but was later changed to v1.1 with the publication. The only difference between the two versions is that the TE annotation column has been added to the gff files. Gene Predictions
The Malus fusca v1.1 genome gene prediction files are available in GFF3 and FASTA format. Downloads
*The whole genome data was initially made public with v1.0 but was later changed to v1.1 with the publication. The only difference between the two versions is that the TE annotation column has been added to the gff files. Functional Analysis
Functional annotation for the Malus fusca Genome v1.1 are available for download below. The Malus fusca Genome v1.1 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 Malus fusca genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3 format.
|
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||