Rubus occidentalis Whole Genome Assembly v1.1

Genome Overview
Analysis NameRubus occidentalis Whole Genome Assembly v1.1
MethodModification of the assembly of the v1.0.a1
SourceRubus occidentalis Whole Genome Assembly v1.1
Date performed2017-12-19

Publication:

Jibran R, Dzierzon H, Bassil N, Bushakra JM, Edger PP, Sullivan S, Finn CE, Dossett M, Vining KJ, VanBuren R, Mockler TC, Liachko I, Davies KM, Foster TM, Chagné D. Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data. Horticulture research. 2018; 5:8. | Journal | GDR |

About the Assembly:

The recently released draft genome for black raspberry (ORUS 4115-3) lacks assembly of scaffolds to chromosome scale. High-throughput chromatin conformation capture (Hi-C) and Proximity-Guided Assembly (PGA) was used to cluster and order 9,650 out of 11,936 contigs of this draft genome assembly into seven pseudo-chromosomes. The seven pseudo-chromosomes cover ~97.2% of the total contig length (~223.8 Mb). Locating existing genetic markers on the physical map resolved multiple discrepancies in marker order on the genetic map. Centromeric regions were inferred from recombination frequencies of genetic markers, alignment of 303 bp centromeric sequence with the PGA, and heat map showing the physical contact matrix over the entire genome. 98.3% of the v1.0.a1 genes have been aligned to the v1.1 assembly.

 

Properties
Additional information about this analysis:
Property NameValue
Analysis Typewhole_genome
JBrowse URLhttps://www.rosaceae.org/jbrowse/index.html?data=data/rubus/roccidentalis_v1.1&loc=
Assembly

The Rubus occidentalis v1.1 genome assembly files are available in FASTA and GFF3 formats.

Downloads

Chromosomes (FASTA file)  Rubus_occidentalis_v1.1_chromosomes.fasta.gz
Chromosomes (FASTA file)  Rubus_occidentalis_masked_v1.1_chromosomes.fasta.gz
Chromosomes (GFF3 file)  Rubus_occidentalis_v1.1.gff3
Chromosomes (GFF3 file)  Rubus_occidentalis_masked_v1.1.gff3.gz

 

Gene Predictions

The Rubus occidentalis v1.1 genome gene prediction files are available in GFF3 format.

Downloads

Alignment of  R. occidentalis v1.0.a1 to R. occidentalis v1.1(GFF3 file) Rubus_occidentalis_v1.0.a1_on_v1.1_genome.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 do download.  Alternatively, you can use the FTP repository for bulk download.