Fragaria chiloensis KIB CAS Genome v1.0 Assembly & Annotation

Overview
Analysis NameFragaria chiloensis KIB CAS Genome v1.0 Assembly & Annotation
MethodHifiasm (v.0.15.1. )
SourcePacbio HiFi reads for the F. chiloensis
Date performed2023-06-20

Publication:

Xin Jin, Haiyuan Du, Chumeng Zhu, Hong Wan, Fang Liu, Jiwei Ruan, Jeffrey P. Mower, and Andan Zhu. (2023) Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry. Nature Plants.

https://www.nature.com/articles/s41477-023-01473-2

Abstract:

Strawberry is an emerging model for studying polyploid genome evolution and rapid domestication of fruit crops. Here we report haplotype-resolved genomes of two wild octoploids (Fragaria chiloensis and Fragaria virginiana), the progenitor species of cultivated strawberry. Substantial variation is identified between species and between haplotypes. We redefine the four subgenomes and track the genetic contributions of diploid species by additional sequencing of the diploid F. nipponica genome. We provide multiple lines of evidence that F. vesca and F. iinumae, rather than other described extant species, are the closest living relatives of these wild and cultivated octoploids. In response to coexistence with quadruplicate gene copies, the octoploid strawberries have experienced subgenome dominance, homoeologous exchanges and coordinated expression of homoeologous genes. However, some homoeologues have substantially altered expression bias after speciation and during domestication. These findings enhance our understanding of the origin, genome evolution and domestication of strawberries.

Table 1 Summary of genome features and quality evaluation of the three sequenced Fragaria species

Category

F. chiloensis 

hap1

F. chiloensis 

hap2

F. virginiana 

hap1

F. virginiana 

hap2

F. nipponica

Genome estimate

         

Ploidy level (x = 7)

2n = 8x = 56

2n = 8x = 56

2n = 2x = 14

Genome size by flow cytometry (Mb)

841.6

758.8

259.6

Genome size by k-mer analysis (Mb)

834.1

740.7

253.4

Assembly feature

         

Assembled genome size (Mb)

839.9

824.2

787.8

769.2

290.9

Number of contigs

1,305

632

995

531

334

N50 (Mb)

11.3

8.9

14.3

14.2

1.9

Base completeness

         

Assigned rate (%)

95.3

96.4

95.5

97.2

99.4

Number of haploid chromosomes

28

28

28

28

7

Illumina reads mappability (%)

99.3

99.4

94.9

Continuity

         

Number of gaps

129

136

110

83

361

LAI value

13.2

13.7

17.9

17.3

14.5

Base accuracy

         

k-mer QV (HiFi reads)

68.1

68.3

24.9

k-mer completeness (HiFi reads) (%)

98.5

98.8

87.9

Haplotype phasing

         

Proportion of error phasing (%)

0.37

1.05

Annotation feature and completeness

         

Repeat density (%)

44.2

44.4

41.9

41.6

43.0

Number of genes

96,759

95,830

94,294

94,143

36,059

Transcript mappability (%)

99.3

99.2

99.2

BUSCO completeness (%)

96.3

96.1

96.3

96.4

91.7

Homology

Homology of the Fragaria chiloensis 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, 2022-09), UniProtKB/SwissProt (Release 2023-07), and UniProtKB/TrEMBL (Release 2023-07) 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_KIB-CAS_v1.0_vs_arabidopsis.xlsx.gz
Fragaria chiloensis v1.0 proteins with arabidopsis (Araport11) (FASTA file) Fchiloensis_KIB-CAS_v1.0_vs_arabidopsis_hit.fasta.gz
Fragaria chiloensis v1.0 proteins without arabidopsis (Araport11) (FASTA file) Fchiloensis_KIB-CAS_v1.0_vs_arabidopsis_noHit.fasta.gz
Fragaria chiloensis v1.0 proteins with SwissProt homologs (EXCEL file) Fchiloensis_KIB-CAS_v1.0_vs_swissprot.xlsx.gz
Fragaria chiloensis v1.0 proteins with SwissProt (FASTA file) Fchiloensis_KIB-CAS_v1.0_vs_swissprot_hit.fasta.gz
Fragaria chiloensis v1.0 proteins without SwissProt (FASTA file) Fchiloensis_KIB-CAS_v1.0_vs_swissprot_noHit.fasta.gz
Fragaria chiloensis v1.0 proteins with TrEMBL homologs (EXCEL file) Fchiloensis_KIB-CAS_v1.0_vs_trembl.xlsx.gz
Fragaria chiloensis v1.0 proteins with TrEMBL (FASTA file) Fchiloensis_KIB-CAS_v1.0_vs_trembl_hit.fasta.gz
Fragaria chiloensis v1.0 proteins without TrEMBL (FASTA file) Fchiloensis_KIB-CAS_v1.0_vs_trembl_noHit.fasta.gz
Assembly

The Fragaria chiloensis Genome v1.0 assembly files are available in GFF3 and FASTA format.

Downloads

Chromosomes (masked HAP 1) (FASTA file) Fchiloensis_Hap1.masked_V1.0.a1.fasta.gz
Chromosomes (masked HAP 2) (FASTA file) Fchiloensis_Hap2.masked_V1.0.a1.fasta.gz
Chromosomes (HAP 1) (FASTA file) Fchiloensis_Hap1_V1.0.a1.fasta.gz
Chromosomes (HAP 2) (FASTA file) Fchiloensis_Hap2_V1.0.a1.fasta.gz
Repeats (HAP 1) (GFF3 file) Fchiloensis_Hap1.repeats.gff.gz
Repeats (HAP 2) (GFF3 file) Fchiloensis_Hap2.repeats.gff.gz

 

Gene Predictions

The Fragaria chiloensis V1.0 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (HAP 1) (GFF3 file) Fchiloensis_Hap1_V1.0.a1.genes.gff3.gz
Genes (HAP 2) (GFF3 file) Fchiloensis_Hap2_V1.0.a1.genes.gff3.gz
Protein sequences (HAP 1) (FASTA file) Fchiloensis_Hap1_V1.0.a1.pep.fasta.gz
Protein sequences (HAP 2) (FASTA file) Fchiloensis_Hap2_V1.0.a1.pep.fasta.gz
CDS sequences (HAP 1) (FASTA file) Fchiloensis_Hap1_V1.0.a1.cds.fasta.gz
CDS sequences (HAP 2) (FASTA file) Fchiloensis_Hap2_V1.0.a1.cds.fasta.gz

 

Functional Analysis

Functional annotation for the Fragaria chiloensis 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).

Downloads

GO assignments from InterProScan Fchiloensis_KIB-CAS_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Fchiloensis_KIB-CAS_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Fchiloensis_KIB-CAS_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways Fchiloensis_KIB-CAS_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 chiloensisKIB CAS 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_KIB-CAS_v1.0_f.x.ananassa_GDR_reftransV1
Prunus avium GDR RefTrans v1 Fchiloensis_KIB-CAS_v1.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Fchiloensis_KIB-CAS_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Fchiloensis_KIB-CAS_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Fchiloensis_KIB-CAS_v1.0_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 Fchiloensis_KIB-CAS_v1.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 Fchiloensis_KIB-CAS_v1.0_pyrus_GDR_reftransV1