Fragaria pentaphylla YNU Genome v1.0 Assembly & Annotation

Overview
Analysis NameFragaria pentaphylla YNU Genome v1.0 Assembly & Annotation
MethodPacbio, FALCON (v 0.3.0)
SourceFragaria pentaphylla YNG Genome v1.0
Date performed2021-09-27

Publication:

Qiao Q, Edger PP, Xue L, La Q, Lu J, Zhang YC, Alan EY, Adrian EP, Steven JK, Montagu MV, Van de Peer Y, Lei JJ, Zhang TC. Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.). 2021. Accepted to PNAS

 

Abstract:

Strawberry (Fragaria spp.) has emerged as a model system for various fundamental and applied research in recent years. In total, the genomes of five different species have been sequenced over the past ten years. Here, we report chromosome-scale reference genomes for five strawberry species, including three newly sequenced species’ genomes, and genome re-sequencing data for 128 additional accessions to estimate the genetic diversity and structure of key Fragaria species. Our analyses obtained fully resolved and strongly supported phylogenies and divergence times for most diploid strawberry species. These analyses also uncovered a new diploid species (F. emeiensis Lei). Lastly, we constructed a pan-genome for Fragaria and examined the evolutionary dynamics of gene families associated with important agronomic traits. Notably, we identified multiple independent single base mutations of the MYB10 gene associated with white pigmented fruit shared by different strawberry species. These new reference genomes and datasets, combined with our new phylogenetic estimates, should serve as a powerful comparative genomic platform and resource for future studies in strawberry.

Assembly

The Fragaria pentaphylla Genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) fpentaphylla_v1.0.fasta.gz
Repeats (GFF3 file) fpentaphylla_v1.0.repeats.gff3.gz

 

Gene Predictions

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

Downloads

Protein sequences  (FASTA file) fpentaphylla_v1.0.proteins.fasta.gz
CDS  (FASTA file) fpentaphylla_v1.0.cds.fasta.gz
Genes (GFF3 file) fpentaphylla_v1.0.genes.gff3.gz

 

Functional Analysis

Functional annotation for the Fragaria pentaphylla Genome v1.0 are available for download below. The Fragaria pentaphylla 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 fpentaphylla_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan fpentaphylla_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways fpentaphylla_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs fpentaphylla_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 pentaphylla 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 fpentaphylla_v1.0_f.x.ananassa_GDR_reftransV1
fragaria avium GDR RefTrans v1 fpentaphylla_v1.0_p.avium_GDR_reftransV1
Rosa GDR RefTrans v1 fpentaphylla_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 fpentaphylla_v1.0_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 fpentaphylla_v1.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 fpentaphylla_v1.0_pyrus_GDR_reftransV1