[DOI] 10.5524/100712

[Title] Supporting data for "Canfam_GSD: De novo chromosome-length genome
assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination
of long reads, optical mapping and Hi-C"

[Release Date] 2020-02-18

[Citation] Rosen, BD; Enosi Tuipulotu, D; Field, MA; Dudchenko, O; Chan, EK;
Minoche, AE; Barton, K; Lyons, RJ; Edwards, RJ; Hayes, VM; Omer, A; Colaric, Z;
Keilwagen, J; Skvortsova, K; Bogdanovic, O; Aiden, EL; Smith, TP; Zammit, RA;
Smith, MA (2020): Supporting data for "Canfam_GSD: De novo chromosome-length
genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a
combination of long reads, optical mapping and Hi-C" GigaScience Database.
https://dx.doi.org/10.5524/100712

[Data Type] Genomic,Epigenomic

[Data Summary] The German Shepherd Dog (GSD) is one of the most common breeds on
earth and has been bred for its utility and intelligence. It is often first
choice for police and military work, as well as protection, disability
assistance and search-and-rescue. Yet, GSD’s are well known to be afflicted
with a range of genetic diseases that can interfere with their training. Such
diseases are of particular concern when they occur later in life, and fully
trained animals are not able to continue their duties. Here, we provide the
draft genome sequence of a healthy German Shepherd female as a reference for
future disease and evolutionary studies We generated this improved canid
reference genome (CanFam_GSD) utilising a combination of Pacific Bioscience,
Oxford Nanopore,, 10X Genomics, Bionano, and Hi-C technologies. The GSD assembly
is approximately 80 times as contiguous as the current canid reference genome
(20.9 Mb vs 0.267 Mb contig N50), containing far fewer gaps (306 vs 23,876) and
fewer scaffolds (429 vs 3,310) than the current canid reference genome CanFam
v3.1. Two chromosomes (4 and 35) are assembled into single scaffolds with no
gaps. Benchmarking Universal Single-Copy Orthologs analyses of the genome
assembly results show 93.0% of the conserved single-copy genes are complete in
the GSD assembly compared to 92.2% for CanFam v3.1. Homology-based gene
annotation increases this value to about 99%. Detailed examination of the
evolutionary important pancreatic amylase region reveals there are most likely
seven copies of the gene indicative of a duplication of four ancestral copies
and the disruption of one copy. GSD genome assembly and annotation were produced
with major improvement in completeness, continuity and quality over the existing
canid reference. This resource will enable further research related to canine
diseases, the evolutionary relationships of canids, and other aspects of canid
biology.

[File Location] https://s3.ap-northeast-1.wasabisys.com/gigadb-datasets/live/pub/10.5524/100001_101000/100712/

[File name] - [File Description]
mummer_snps_indels.vcf  -  VCF file generated mummer show-snps
EXP_REFINEFINAL1.cmap  -  Assembly consensus genome map set derived from RawMolecules.bnx using Bionano Solve v3.2.2.
Nala_HYBRID_SCAFFOLD_NCBI_Nresized_merged_NOT_SCAFFOLDED_HiC.fasta.gz  -  Hybrid genome assembly fasta
GSD_mitochondria.fna  -  Complete mitochondrial sequence
MoleculeQualityReport.txt  -  A summary report of the RawMolecules.bnx data as produced by Bionano Solve v3.2.2.
proteins.fasta  -  Coding gene translated fasta
GSD_final_combined_assembly.fna  -  Final combined genome assembly fasta
GCA_008641055.1_ASM864105v1_genomic.fna  -  Genome assembly fasta
sample_metadata.txt  -  Tabular data with additional sample details
rRNA_predictions.gff  -  rRNA annotations
readme_100712.txt  -  
busco_Nala.txt  -  BUSCO summary for assembly
busco_CanFam3.1.txt  -  BUSCO summary for current dog reference genome CanFam3.1
mRNA_predictions.gff  -  Coding gene annotations
cds.fasta  -  Coding gene nucleotides fasta
exp_informaticsReport.txt  -  A summary report of EXP_REFINEFINAL1.cmap along with alignment statistics against an in silico digested genome map set of CanFam 3.1, using Bionano Solve v3.2.2.

[License]
All files and data are distributed under the CC0 1.0 Universal (CC0 1.0) Public
Domain Dedication (https://creativecommons.org/publicdomain/zero/1.0/), unless
specifically stated otherwise, see http://gigadb.org/site/term for more details.

[Comments]

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