Fragaria chiloensis KIB CAS Genome v1.0 Assembly & Annotation
Xin Jin, Haiyuan Du, Chumeng Zhu, Hong Wan, Fang Liu, Jiwei Ruan, Jeffrey P. Mower, and Andan Zhu. (2023) Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry. Nature Plants.
Strawberry is an emerging model for studying polyploid genome evolution and rapid domestication of fruit crops. Here we report haplotype-resolved genomes of two wild octoploids (Fragaria chiloensis and Fragaria virginiana), the progenitor species of cultivated strawberry. Substantial variation is identified between species and between haplotypes. We redefine the four subgenomes and track the genetic contributions of diploid species by additional sequencing of the diploid F. nipponica genome. We provide multiple lines of evidence that F. vesca and F. iinumae, rather than other described extant species, are the closest living relatives of these wild and cultivated octoploids. In response to coexistence with quadruplicate gene copies, the octoploid strawberries have experienced subgenome dominance, homoeologous exchanges and coordinated expression of homoeologous genes. However, some homoeologues have substantially altered expression bias after speciation and during domestication. These findings enhance our understanding of the origin, genome evolution and domestication of strawberries.
Table 1 Summary of genome features and quality evaluation of the three sequenced Fragaria species
Homology of the Fragaria chiloensis 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.
The Fragaria chiloensis Genome v1.0 assembly files are available in GFF3 and FASTA format.
The Fragaria chiloensis V1.0 genome gene prediction files are available in GFF3 and FASTA format.
Functional annotation for the Fragaria chiloensis Genome v1.0 are available for download below. The Fragaria chiloensis 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 Fragaria chiloensisKIB CAS genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3 format.