Fragaria chiloensis 'GP33' Genome v1.0 Assembly & Annotation

Analysis NameFragaria chiloensis 'GP33' Genome v1.0 Assembly & Annotation
MethodHifiasm (0.13)
SourcePacBio HiFi reads
Date performed2022-06-08


Cauret, C. M. S., Mortimer, S. M. E., Roberti, M. C., Ashman, T.-L., & Liston, A. (2022). Chromosome-scale assembly with a phased sex-determining region resolves features of early Z and W chromosome differentiation in a wild octoploid strawberry. G3 Genes|Genomes|Genetics, 12(8), jkac139


When sex chromosomes stop recombining, they start to accumulate differences. The sex-limited chromosome (Y or W) especially is expected to degenerate via the loss of nucleotide sequence and the accumulation of repetitive sequences. However, how early signs of degeneration can be detected in a new sex chromosome is still unclear. The sex determining region (SDR) of the octoploid strawberries is young, small, and dynamic. Using PacBio HiFi reads, we obtained a chromosome scale assembly of a female (ZW) Fragaria chiloensis plant carrying the youngest and largest of the known SDR on the W in strawberries. We fully characterized the previously incomplete SDR, confirming its gene content, genomic location and evolutionary history. Resolution of gaps in the previous characterization of the SDR added 10 kbp of sequence including a non-canonical LTR-retrotransposon; whereas the Z sequence revealed a Harbinger transposable element adjoining the SDR insertion site. Limited genetic differentiation of the sex chromosomes coupled with structural variation may indicate an early stage of W degeneration. The sex chromosomes have a similar percentage of repeats but differ in their repeat distribution. Differences in the pattern of repeats (transposable element polymorphism) apparently precede sex chromosome differentiation, thus potentially contributing to recombination cessation as opposed to being a consequence of it.

Table S7. Conserved single copy orthologs (BUSCOs) by subgenome and genome for the octoploids F.chiloensis GP33 and F. × ananassa ‘Camarosa’ and diploids F. vesca and F. iinumae. N=2326.

  complete single duplicate fragmented missing
GP33_all    99.0%    3.1%    95.9%    0.2%    0.8%
Camarosa_all    99.1%    3.7%    95.4%    0.1%    0.8%
vesca    98.2%    96.1%    2.1%    0.6%    1.2%
iinumae    97.4%    95.3%    2.1%    0.5%    2.1%

Homology of the Fragaria chiloensis 'GP33' OSU 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), UniProtKB/SwissProt (Release 2021-09), and UniProtKB/TrEMBL (Release 2021-09) databases. The best hit reports are available for download in Excel format. 

Protein Homologs

Fragaria chiloensis v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Fchiloensis_osu_v1.0_vs_arabidopsis.xlsx.gz
Fragaria chiloensis v1.0 proteins with arabidopsis (Araport11) (FASTA file) Fchiloensis_osu_v1.0_vs_arabidopsis_hit.fasta.gz
Fragaria chiloensis v1.0 proteins without arabidopsis (Araport11) (FASTA file) Fchiloensis_osu_v1.0_vs_arabidopsis_noHit.fasta.gz
Fragaria chiloensis v1.0 proteins with SwissProt homologs (EXCEL file) Fchiloensis_osu_v1.0_vs_swissprot.xlsx.gz
Fragaria chiloensis v1.0 proteins with SwissProt (FASTA file) Fchiloensis_osu_v1.0_vs_swissprot_hit.fasta.gz
Fragaria chiloensis v1.0 proteins without SwissProt (FASTA file) Fchiloensis_osu_v1.0_vs_swissprot_noHit.fasta.gz
Fragaria chiloensis v1.0 proteins with TrEMBL homologs (EXCEL file) Fchiloensis_osu_v1.0_vs_trembl.xlsx.gz
Fragaria chiloensis v1.0 proteins with TrEMBL (FASTA file) Fchiloensis_osu_v1.0_vs_trembl_hit.fasta.gz
Fragaria chiloensis v1.0 proteins without TrEMBL (FASTA file) Fchiloensis_osu_v1.0_vs_trembl_noHit.fasta.gz

The Fragaria chiloensis GP33 genome v1.0 assembly file is available in FASTA format.


Chromosomes (FASTA file) Fchiloensis_GP33_v1.0.fasta.gz
Gene Predictions

The Fragaria chiloensis GP33 v1.0 gene prediction files are available in GFF3 and FASTA format. The mRNA and protein sequences were extracted by the GDR team from the genome sequence and the gene GFF3 files provided by the authors using gffread (0.12.4).


Genes (GFF3 file) Fchiloensis_GP33.v1.0.genes.gff3.gz
Protein sequences (FASTA file) GDR-Fchiloensis_GP33.v1.0.protein.fasta.gz
Transcript sequences (FASTA file) GDR-Fchiloensis_GP33.v1.0.transcript.fasta.gz
Functional Analysis

Functional annotation for the Fragaria chiloensis 'GP33' OSU 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).


GO assignments from InterProScan Fchiloensis_osu_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Fchiloensis_osu_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways Fchiloensis_osu_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs Fchiloensis_osu_v1.0_KEGG-pathways.xlsx.gz
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 chiloensis genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3 format.


Fragaria x ananassa GDR RefTrans v1 Fchiloensis_osu_v1.0_f.x.ananassa_GDR_reftransV1
fragaria avium GDR RefTrans v1 Fchiloensis_osu_v1.0_p.avium_GDR_reftransV1
fragaria persica GDR RefTrans v1 Fchiloensis_osu_v1.0_p.persica_GDR_reftransV1
Rubus GDR RefTrans v2 Fchiloensis_osu_v1.0_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 Fchiloensis_osu_v1.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 Fchiloensis_osu_v1.0_pyrus_GDR_reftransV1