Fragaria nilgerrensis YNU Genome v1.0 Assembly & Annotation

Overview
Analysis NameFragaria nilgerrensis YNU Genome v1.0 Assembly & Annotation
MethodPacbio, FALCON (v0.3.0)
SourceFragaria nilgerrensis YNU 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. Proceedings of the National Academy of Sciences Nov 2021, 118 (45) e2105431118DOI: 10.1073/pnas.2105431118

 

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.

Homology Analysis

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

 

Protein Homologs

Fragaria nilgerrensis v1.0 proteins with NCBI nr homologs (EXCEL file) fnilgerrensis_v1.0_vs_nr.xlsx.gz
Fragaria nilgerrensis v1.0 proteins with NCBI nr (FASTA file) fnilgerrensis_v1.0_vs_nr_hit.fasta.gz
Fragaria nilgerrensis v1.0 proteins without NCBI nr (FASTA file) fnilgerrensis_v1.0_vs_nr_noHit.fasta.gz
Fragaria nilgerrensis v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) fnilgerrensis_v1.0_vs_arabidopsis.xlsx.gz
Fragaria nilgerrensis v1.0 proteins with arabidopsis (Araport11) (FASTA file) fnilgerrensis_v1.0_vs_arabidopsis_hit.fasta.gz
Fragaria nilgerrensis v1.0 proteins without arabidopsis (Araport11) (FASTA file) fnilgerrensis_v1.0_vs_arabidopsis_noHit.fasta.gz
Fragaria nilgerrensis v1.0 proteins with SwissProt homologs (EXCEL file) fnilgerrensis_v1.0_vs_swissprot.xlsx.gz
Fragaria nilgerrensis v1.0 proteins with SwissProt (FASTA file) fnilgerrensis_v1.0_vs_swissprot_hit.fasta.gz
Fragaria nilgerrensis v1.0 proteins without SwissProt (FASTA file) fnilgerrensis_v1.0_vs_swissprot_noHit.fasta.gz
Fragaria nilgerrensis v1.0 proteins with TrEMBL homologs (EXCEL file) fnilgerrensis_v1.0_vs_trembl.xlsx.gz
Fragaria nilgerrensis v1.0 proteins with TrEMBL (FASTA file) fnilgerrensis_v1.0_vs_trembl_hit.fasta.gz
Fragaria nilgerrensis v1.0 proteins without TrEMBL (FASTA file) fnilgerrensis_v1.0_vs_trembl_noHit.fasta.gz

 

Assembly

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

Downloads

Chromosomes (FASTA file) fnilgerrensis_v1.0.fasta.gz
Repeats (GFF3 file) fnilgerrensis_v1.0.repeats.gff3.gz

 

Gene Predictions

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

Downloads

Protein sequences  (FASTA file) fnilgerrensis_v1.0.proteins.fasta.gz
CDS  (FASTA file) fnilgerrensis_v1.0.cds.fasta.gz
Genes (GFF3 file) fnilgerrensis_v1.0.genes.gff3.gz

 

Functional Analysis

Functional annotation for the Fragaria nilgerrensis Genome v1.0 are available for download below. The Fragaria nilgerrensis 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 fnilgerrensis_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan fnilgerrensis_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways fnilgerrensis_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs fnilgerrensis_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 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 fnilgerrensis_v1.0_f.x.ananassa_GDR_reftransV1
fragaria avium GDR RefTrans v1 fnilgerrensis_v1.0_p.avium_GDR_reftransV1
fragaria persica GDR RefTrans v1 fnilgerrensis_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 fnilgerrensis_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 fnilgerrensis_v1.0_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 fnilgerrensis_v1.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 fnilgerrensis_v1.0_pyrus_GDR_reftransV1