Fragaria nilgerrensis SCBG Genome v1.0 Assembly & Annotation

Overview
Analysis NameFragaria nilgerrensis SCBG Genome v1.0 Assembly & Annotation
MethodPacbio, FALCON (v0.3.0)
SourceFragaria nilgerrensis SCBG Genome v1.0 Assembly & Annotation
Date performed2020-09-20

Whole genome sequences of  F. nilgerrensis, F. nubicola, and F. viridis were made available in the study of the diploid ancestry of the cultivated octoploid strawberry.

Publication:

Feng C, Wang J, Harris AJ, Folta KM, Zhao M, Kang M. Tracing the diploid ancestry of the cultivated octoploid strawberry. Mol Biol Evol. 2020 Sep 17:msaa238. doi: 10.1093/molbev/msaa238.

Abstract:

The commercial strawberry, Fragaria × ananassa, is a recent allo-octoploid that is cultivated worldwide. However, other than F. vesca, which is universally accepted one of its diploid ancestors, its other early diploid progenitors remain unclear. Here, we performed comparative analyses of the genomes of five diploid strawberries, F. iinumae, F. vesca, F. nilgerrensis, F. nubicola, and F. viridis, of which the latter three are newly sequenced. We found that the genomes of these species share highly conserved gene content and gene order. Using an alignment-based approach, we show that F. iinumae and F. vesca are the diploid progenitors to the octoploid F. × ananassa, whereas the other three diploids that we analyzed in this study are not parental species. We generated a fully resolved, dated phylogeny of Fragaria and determined that the genus arose ca. 6.37 million years ago. Our results effectively resolve conflicting hypotheses regarding the putative diploid progenitors of the cultivated strawberry, establish a reliable backbone phylogeny for the genus, and provide genetic resources for molecular breeding.

Homology Analysis

Homology of the Fragaria nilgerrensis SCBG 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 2018-05) and 1e-6  for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2019-01), and UniProtKB/TrEMBL (Release 2019-01) databases. The best hit reports are available for download in Excel format. 

 

Protein Homologs

Fragaria nilgerrensis SCBG v1.0 proteins with NCBI nr homologs (EXCEL file) Fnil_v1.0_vs_nr.xlsx.gz
Fragaria nilgerrensis SCBG v1.0 proteins with NCBI nr (FASTA file) Fnil_v1.0_vs_nr_hit.fasta.gz
Fragaria nilgerrensis SCBG v1.0 proteins without NCBI nr (FASTA file) Fnil_v1.0_vs_nr_noHit.fasta.gz
Fragaria nilgerrensis SCBG v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Fnil_v1.0_vs_arabidopsis.xlsx.gz
Fragaria nilgerrensis SCBG v1.0 proteins with arabidopsis (Araport11) (FASTA file) Fnil_v1.0_vs_arabidopsis_hit.fasta.gz
Fragaria nilgerrensis SCBG v1.0 proteins without arabidopsis (Araport11) (FASTA file) Fnil_v1.0_vs_arabidopsis_noHit.fasta.gz
Fragaria nilgerrensis SCBG v1.0 proteins with SwissProt homologs (EXCEL file) Fnil_v1.0_vs_swissprot.xlsx.gz
Fragaria nilgerrensis SCBG v1.0 proteins with SwissProt (FASTA file) Fnil_v1.0_vs_swissprot_hit.fasta.gz
Fragaria nilgerrensis SCBG v1.0 proteins without SwissProt (FASTA file) Fnil_v1.0_vs_swissprot_noHit.fasta.gz
Fragaria nilgerrensis SCBG v1.0 proteins with TrEMBL homologs (EXCEL file) Fnil_v1.0_vs_trembl.xlsx.gz
Fragaria nilgerrensis SCBG v1.0 proteins with TrEMBL (FASTA file) Fnil_v1.0_vs_trembl_hit.fasta.gz
Fragaria nilgerrensis SCBG v1.0 proteins without TrEMBL (FASTA file) Fnil_v1.0_vs_trembl_noHit.fasta.gz

 

Download

All assembly and annotation files are available for download by selecting the desired data type in the left-hand "Resources" side bar.  Each data type page will provide a description of the available files and links to download.  Alternatively, you can browse all available files on the FTP repository.

Assembly

Downloads

Chromosomes (FASTA file) Fnil_v1.0.fasta.gz
Repeats (GFF3 file) Fnil_v1.0.repeats.gff3.gz

 

Gene Predictions

The Fragaria nilgerrensis SCBG v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) Fnil_v1.0.proteins.fasta.gz
Tanscript sequences (FASTA file) Fnil_v1.0.transcripts.fasta.gz
Genes (GFF3 file) Fnil_v1.0.genes.gff3.gz

 

Functional Analysis

Functional annotation for the Fragaria nilgerrensis SCBG genome v1.0 are available for download below. The Fragaria nilgerrensis SCBG 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).

Downloads

GO assignments from InterProScan Fnil_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Fnil_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways Fnil_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs Fnil_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 nilgerrensis SCBGgenome 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 Fragaria nilgerrensis SCBG_v1.0_f.x.ananassa_GDR_reftransV1
Malus_x_domestica GDR RefTrans v1 Fragaria nilgerrensis SCBG_v1.0_m.x.domestica_GDR_reftransV1
fragaria avium GDR RefTrans v1 Fragaria nilgerrensis SCBG_v1.0_p.avium_GDR_reftransV1
fragaria persica GDR RefTrans v1 Fragaria nilgerrensis SCBG_v1.0_p.persica_GDR_reftransV1
Pyrus GDR RefTrans v1 Fragaria nilgerrensis SCBG_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Fragaria nilgerrensis SCBG_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Fragaria nilgerrensis SCBG_v1.0_rubus_GDR_reftransV2