Fragaria iinumae KIB CAS Genome v2.0
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Overview
Publication: Abstract: Fragaria iinumae is one of the diploid progenitor species of octoploid strawberries and represents the basal taxon of the genus Fragaria. It plays a significant role in the evolution of octoploid strawberries, being equally or even more important than the Fragaria vesca as a diploid ancestor. While extensive studies have been conducted on the genome of F. vesca, the genome quality of F. iinumae needs further improvement, the phylogenetic position of F. iinumae within the Fragaria genus require further confirmation. In this study, we generated a near-complete genome of F. iinumae v2.0, spanning 241.14 Mb, the assembly contig N50 value was 33.31 Mb, 12 telomeres and 7 centromeres were identified across the 7 chromosomes. A total of 27,809 protein-coding genes were predicted and annotated and a complete BUSCO score of 96.4%. Compared to the previously published version (v1.0), F. iinumae v2.0 showed major improvement in both genome continuity and annotation completeness. Interestingly, we identified several large segments of structural variants between F. iinumae v1.0 and v2.0 genomes, and most gaps of F. iinumae v1.0 genome overlapped with the positions of structural variant breakpoints. In addition, we provide multiple lines of genomic evidence, including phylogenetic relationships, genetic distance matrix, specific LTR insertion times and NLR resistance gene distributions, confirming that F. iinumae represents an early branch within the strawberry genus. This work provides a valuable F. iinumae genomic resource as well as enhancer our understanding of the origin and evolution of Fragaria genus. Homology
Homology of the Fragaria iinumae KIB CAS v2.0 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 2024-03), and UniProtKB/TrEMBL (Release 2024-03) databases. The best hit reports are available for download in Excel format. Protein Homologs
Assembly
The Fragaria iinumae KIB CAS Genome v2.0 assembly files are available in FASTA format. Downloads
Gene Predictions
The Fragaria iinumae KIB CAS v2.0.a1 genome gene prediction file are available in GFF3 and FASTA format. Downloads
Functional Analysis
Functional annotation for the Fragaria iinumae KIB CAS v2.0 are available for download below. The F. iinumae KIB CAS v2.0 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 Fragaria iinumae KIB CAS genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3.
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