Potentilla micrantha Draft Genome v1.0 Assembly & Annotation

Overview
Analysis NamePotentilla micrantha Draft Genome v1.0 Assembly & Annotation
MethodALLPATHS and PBJelly
SourcePotentilla_micrantha_Draft_Genome_v1_Assembly_Annotation
Date performed2018-05-04

Publication:

Buti M, Moretto M, Barghini E, Mascagni F, Natali L, Brilli M, Lomsadze A, Sonego P, Giongo L, Alonge M, Velasco R, Varotto C, Šurbanovski N, Borodovsky M, Ward JA, Engelen K, Cavallini A, Cestaro A, Sargent DJ. The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry). GigaScience. 2018 Apr 01; 7(4):1-14. | PubMed | GDR |

About the Assembly:

In this study, the P. micrantha genome was sequenced and annotated, and RNA-Seq data from the different developmental stages of flowering and fruiting were used to develop a set of gene predictions. A 327 Mbp sequence and annotation of the genome of P. micrantha, spanning 2674 sequence contigs, with an N50 size of 335,712, estimated to cover 80% of the total genome size of the species was developed. The genus Potentilla has a characteristically larger genome size than Fragaria, but the recovered sequence scaffolds were remarkably collinear at the micro-syntenic level with the genome of F. vesca, its closest sequenced relative. A total of 33,602 genes were predicted, and 95.1% of bench-marking universal single-copy orthologous genes were complete within the presented sequence. Thus, we argue that the majority of the gene-rich regions of the genome have been sequenced.

 

Assembly

The Potentilla micrantha v1.0 genome assembly file is available in FASTA format.

Downloads

Scaffolds (FASTA file)  Potentilla_micrantha_v1.0_draft_genome.fasta.gz

 

Gene Predictions

The Potentilla micrantha v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Transcript CDS sequences (FASTA file) Potentilla_micrantha_v1.0.transcripts.fasta.gz
Protein sequences  (FASTA file) Potentilla_micrantha_v1.0.proteins.fasta.gz
Genes (GFF3 file) Potentilla_micrantha_v1.0.genes.gff3.gz
Repetitive elements(FASTA file) Potentilla_micrantha_v1.0.Repetitive elements.fasta.gz
Repetitive elements(GFF3 file) Potentilla_micrantha_v1.0.Repetitive elements.gff3.gz

 

Downloads

All assembly and annotation files are available for download by selecting the desired data type in the right-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.

Homology

Homology of the Potentilla micrantha v1.0 protein 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 2017-07) and 1e-6  for the Arabidoposis proteins (TAIR10), UniProtKB/SwissProt (Release 2018-04), and UniProtKB/TrEMBL (Release 2018-04) databases. The best hit reports are available for download in Excel format. 

 

Protein Homologs

Potentilla micrantha v1.0 proteins with NCBI nr homologs (EXCEL file) potentilla_micrantha_v1.0_vs_nr.xlsx.gz
Potentilla micrantha v1.0 proteins with NCBI nr (FASTA file) potentilla_micrantha_v1.0_vs_nr_hit.fasta.gz
Potentilla micrantha v1.0 proteins without NCBI nr (FASTA file) potentilla_micrantha_v1.0_vs_nr_noHit.fasta.gz
Potentilla micrantha v1.0 proteins with arabidopsis (TAIR10) homologs (EXCEL file) potentilla_micrantha_v1.0_vs_tair.xlsx.gz
Potentilla micrantha v1.0 proteins with arabidopsis (TAIR10) (FASTA file) potentilla_micrantha_v1.0_vs_tair_hit.fasta.gz
Potentilla micrantha v1.0 proteins without arabidopsis (TAIR10) (FASTA file) potentilla_micrantha_v1.0_vs_tair_noHit.fasta.gz
Potentilla micrantha v1.0 proteins with SwissProt homologs (EXCEL file) potentilla_micrantha_v1.0_vs_swissprot.xlsx.gz
Potentilla micrantha v1.0 proteins with SwissProt (FASTA file) potentilla_micrantha_v1.0_vs_swissprot_hit.fasta.gz
Potentilla micrantha v1.0 proteins without SwissProt (FASTA file) potentilla_micrantha_v1.0_vs_swissprot_noHit.fasta.gz
Potentilla micrantha v1.0 proteins with TrEMBL homologs (EXCEL file) potentilla_micrantha_v1.0_vs_trembl.xlsx.gz
Potentilla micrantha v1.0 proteins with TrEMBL (FASTA file) potentilla_micrantha_v1.0_vs_trembl_hit.fasta.gz
Potentilla micrantha v1.0 proteins without TrEMBL (FASTA file) potentilla_micrantha_v1.0_vs_trembl_noHit.fasta.gz

 

Functional Analysis

Functional annotation for the Potentilla micrantha v1.0 genome are available for download below. The Potentilla micrantha 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 Potentilla_micrantha_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Potentilla_micrantha_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways Potentilla_micrantha_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs Potentilla_micrantha_v1.0_KEGG-pathways.xlsx.gz