Fragaria nilgerrensis Genome v1.0 Assembly & Annotation

Overview
Analysis NameFragaria nilgerrensis Genome v1.0 Assembly & Annotation
MethodFalcon and Canu (2017)
Source
Date performed2020-07-01

Publication:

Zhang J, Lei Y, Wang B, Li S, Yu S, Wang Y, Li H, Liu Y, Ma Y, Dai H, Wang J, Zhang Z. The high-quality genome of diploid strawberry (Fragaria nilgerrensis) provides new insights into anthocyanin accumulation.. Plant biotechnology journal. 2020 Jan 31. 

Overview:

Fragaria nilgerrensis is a wild diploid strawberry species endemic to east and southeast region in Asia and provides a rich source of genetic variations for strawberry improvement. Here, we present a chromosome-scale assembly of F. nilgerrensis using single-molecule real-time (SMRT) Pacific Biosciences sequencing and chromosome conformation capture (Hi-C) genome scaffolding. The genome assembly size was 270.3 Mb, with a contig N50 of ∼8.5 Mb. A total of 28,780 genes and 117.2 Mb of transposable elements were annotated for this genome. Next, detailed comparative genomics with the high-quality F. vesca reference genome was conducted to obtain the difference among transposable elements, SNPs, Indels, and so on. The genome size of F. nilgerrensis was enhanced by around 50 Mb relatively to F. vesca, which is mainly due to expansion of transposable elements. In comparison to the F. vesca genome, we identified 4,561,825 SNPs, 846,301 Indels, 4,243 inversions, 35,498 translocation, and 10,099 relocation. We also found a marked expansion of genes involved in phenylpropanoid biosynthesis, starch and sucrose metabolism, cyanoamino acid metabolism, plant-pathogen interaction, brassinosteroid biosynthesis, and plant hormone signal transduction in F. nilgerrensis, which may account for its specific phenotypes and considerable environmental adaptability. Interestingly, we found sequence variations in the upstream regulatory region of FnMYB10, a core transcriptional activator of anthocyanin biosynthesis, resulted in the low expression level of the FnMYB10 gene, which is likely responsible for white fruit phenotype of F. nilgerrensis. The high-quality F. nilgerrensis genome will be a valuable resource for biological research and comparative genomics research.

 

 

 

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 2019-01), and UniProtKB/TrEMBL (Release 2019-01) 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

 

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

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

Downloads

Chromosomes (FASTA file) fnilgerrensis_v1.0.fasta.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 Fragaria nilgerrensis_v1.0_f.x.ananassa_GDR_reftransV1
Malus_x_domestica GDR RefTrans v1 Fragaria nilgerrensis_v1.0_m.x.domestica_GDR_reftransV1
Prunus avium GDR RefTrans v1 Fragaria nilgerrensis_v1.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Fragaria nilgerrensis_v1.0_p.persica_GDR_reftransV1
Pyrus GDR RefTrans v1 Fragaria nilgerrensis_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Fragaria nilgerrensis_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Fragaria nilgerrensis_v1.0_rubus_GDR_reftransV2