Vaccinium darrowii clone NJ8810/NJ8807 v1.2 genome sequence

Genome Overview
Analysis NameVaccinium darrowii clone NJ8810/NJ8807 v1.2 genome sequence
MethodPacBio, Illumina, Hi-C (MECAT2, Arrow, Pilon, Purge_dups, Juicer, 3D-DNA)
SourceV. darrowii clone NJ8810/NJ8807
Date performed2021-06-18

 

This is the primary haplotype genome assembly. 

GDV Accession: GDV21003

NCBI Accession: JAFMTH000000000

Reference:  Yu J, Hulse-Kemp A, Babiker E and Staton M. High-quality reference genome and annotation aids understanding of berry development for evergreen blueberry (Vaccinium darrowii). Revision for Horticulture Research.  

Materials and Methods:  Vaccinium darrowii genome assembly was generated from DNA extracted from clone NJ8810/NJ8807 leaves. De novo assembly was performed using MECAT2. The draft genome assembly was polished by consensus calling with Arrow from PacBio SMRT Tools using the PacBio long reads. The genome assembly was further polished by two rounds of error correction with Pilon using Illumina short reads. At this stage the assembly represented a partially fused set of heterozygous sequences representing both haplotypes. This mostly diploid representation of the genome was separated into a primary haplotype assembly and secondary haplotype assembly by purge_dups. To anchor contigs into chromosomes, the primary assemblies were scaffolded using Hi-C sequencing reads through the Dovetail HiRiseTM pipeline (Dovetail Genomics, LLC). The secondary haplotype assembly was scaffolded using the same Hi-C data with the software packages juicer and 3D-DNA.

The primary assembly and secondary haplotype assembly (i.e. the haplotigs removed by purging) were annotated separately using RNAseq, Iso-Seq and V. corymbosum proteins by the BRAKER2 pipeline. First, repetitive elements were identified and masked by RepeatModeler and RepeatMasker using previously characterized plant repetitive elements from RepBase. Next, trimmed Illumina RNASeq reads were aligned to both masked assemblies by STAR v2.7.3a. Iso-Seq reads were aligned to genome assemblies by minimap2. Both aligned RNASeq and Iso-Seq reads were merged by samtools and used as transcript evidence in the BRAKER2 pipeline. Additionally, 128,559 proteins from the  V. corymbosum ‘Draper’ genome were mapped to masked assemblies by Prothint as protein evidence. Repeat masked assemblies were annotated by BRAKER2 under ‘etpmode’ with both transcript and protein evidence. The predicted gene models were then filtered with structural and functional annotation by EnTAP and gFACS. 

Genome Assembly Summary:

Total size 582,669,857
Number of scaffolds 107
N50 47,393,601
Assembly BUSCO score (embryophyta_odb10) 94.0%
Annotation BUSCO score (embryophyta_odb10) 92.3%

 

Properties
Additional information about this analysis:
Property NameValue
JBrowse URLhttps://www.vaccinium.org/jbrowse/index.html?data=data%2FBlueberry%2FV_darrowii_v1.2_H1&loc=
Analysis Typewhole_genome
Downloads

All the files below are also available on the GDV Data Repository.

V. darrowii genome, v1.2 assembly files:

These files will become available after publication

 

Homology Analysis:

The protein homolog searches were performed using BLAST (e-value cutoff of 1e-6) and the Swissprot and TrEMBL protein databases by the Main Bioinformatics Lab.  Results were parsed into an Excel format.