Cantu Lab at UC Davis

Department of Viticulture & Enology

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Data

cabernet

Vitis vinifera
cv. Cabernet Sauvignon

Diploid contig assembly

Primary contigs:
718 contigs; total size: 591,420,921 bp; N50: 4,372,253 bp
Download (Fasta is divided in 8 files, need to concatenated):
CS8_74SMRTcells_FALCON-unzip_primary.fasta - 1 2 3 4 5 6 7 8

Haplotigs:
2,037 contigs; total size: 367,781,855 bp; N50: 779,223 bp
Download (Fasta is divided in 2 files, need to be concatenated):
CS8_74SMRTcells_FALCON-unzip_haplotigs.fasta - 1 2


NCBI Bioproject (SRA data): PRJNA316730
Citation: Chin et al., 2016. Nature Methods 13, 1050–1054 (2016) doi:10.1038/nmeth.4035


phomopsis

Diaporthe ampelina

Draft Genome (isolate DA912)
collaboration with Philippe Rolshausen and Kendra Baumgartner

Assembly size: 47.3 Mb (gaps: 72 kb; n.scaffolds: 2,383)
N50: 132 Kb
L50: 103
Predicted protein coding genes: 10,704


Scaffolds: DA912_scaffolds.v0.1.fasta.gz
Peptides (ab initio): DA912_peptides.v0.2.fasta.gz
Transcripts (ab initio): DA912_transcripts.v0.2.fasta.gz
WGS Accession: LCUC00000000
Citation: Morales-Cruz A. et al., 2015. BMC Genomics 16: 469


diplodia_seriata

Diplodia seriata

Draft Genome (isolate DS831)
collaboration with Philippe Rolshausen and Kendra Baumgartner

Assembly size: 37 Mb (gaps: 72 kb; n.scaffolds: 694)
N50: 304 Kb
L50: 39
Predicted protein coding genes: 9,343


Scaffolds: DS831_scaffolds-v1.0.fasta.gz
Peptides (ab initio): DS831_peptides-v2.0.fasta.gz
Transcripts (ab initio): DS831_transcripts-v2.0.fasta.gz
WGS Accession: LAQI00000000
Citation: Morales-Cruz A. et al., 2015. BMC Genomics 16: 469


Erysiphe necator

Erysiphe necator


Reference: Jones et al., 2014 BMC Genomics 15:1081

Mean assembly size: 50.5 ± 1.2 Mb (Est. genome size: 126.5 ± 18.4 Mb)
Mean N50: 17.1 ± 3.1 Kb
Mean L50: 897.2 ± 73.7 scaffolds
Predicted protein coding genes: 6,533


Gene models (C-strain): e-necator.c-strain.gff.gz
Transcripts (C-strain): e.necator.transcripts.NCBI.6533.fasta.gz
Peptides (C-strain): e.necator.proteins.NCBI.6533.fasta.gz


Scaffolds (C-strain): e-necator.scaffolds.c.NCBI.fasta.gz
Scaffolds (Lodi): e-necator.scaffolds.lodi.NCBI.fasta.gz
Scaffolds (branching): e-necator.scaffolds.branching.NCBI.fasta.gz
Scaffolds (e1-101): e-necator.scaffolds.e1-101.NCBI.fasta.gz
Scaffolds (Ranch9): e-necator.scaffolds.ranch-9.NCBI.fasta.gz



esca

Togninia minima

Draft Genome (isolate UCR-PA7) - collaboration with Philippe Rolshausen

Assembly size: 47.5 Mb (gaps: 83 kb; n.scaffolds: 624)
Median coverage: 103X
N50: 336 Kb
L50: 45
G+C: 49.66%
Predicted protein coding genes: 8,926


Scaffolds: PA7_scaffolds.v0.4.fasta.gz
Contigs: PA7_contigs.v0.4.fasta.gz
Peptides (ab initio): PA7_proteins.v0.4.fasta.gz
Transcripts (ab initio): PA7_transcripts.v0.4.fasta.gz
WGS Accession: AORD00000000
Raw reads: Short Read Archive
Citation: Blanco-Ulate et al., 2013 Genome Announcements 1(3):e00390-13


phaeomoniella_chlamydospora"/

Phaeomoniella chlamydospora

Draft Genome (isolate UCR-PC4)
collaboration with Philippe Rolshausen and Kendra Baumgartner

Assembly size: 27.5 Mb (gaps: 18 kb; n.scaffolds: 702)
N50: 179 Kb
L50: 50
Predicted protein coding genes: 10,704


Scaffolds: UCRPC4_scaffolds.v0.1.fasta.gz
Peptides (ab initio): UCRPC4_peptides.v0.2.fasta.gz
Transcripts (ab initio): UCRPC4_transcripts.v0.2.fasta.gz
WGS Accession: LCWF00000000
Citation: Morales-Cruz A. et al., 2015. BMC Genomics 16: 469


Neofusicoccum

Neofusicoccum parvum

Draft Genome (isolate UCR-NP2) - collaboration with Philippe Rolshausen

Assembly size: 42.5 Mb (gaps: 69 kb; n.scaffolds: 1,287)
Median coverage: 113X
N50: 83 Kb
L50: 149
G+C: 56.7%
Predicted protein coding genes: 10,470


Scaffolds: NP2_scaffolds.v0.4.fasta.gz
Contigs: NP2_contigs.v0.4.fasta.gz
Peptides (ab initio): NP2_proteins.v0.4.fasta.gz
Transcripts (ab initio): NP2_transcripts.v0.4.fasta.gz
WGS Accession: AORE00000000
Raw reads: Short Read Archive
Citation: Blanco-Ulate et al., 2013 Genome Announcements 1(3):e00339-13


eutypa

Eutypa lata

Draft Genome (isolate UCR-EL1) - collaboration with Philippe Rolshausen

Assembly size: 54.0 Mb (gaps: 103 kb; n.scaffolds: 2,334)
Median coverage: 97X
N50: 68.3 kb
L50: 238
G+C: 46.6%
Predicted protein coding genes: 11,818


Scaffolds: EL1_scaffolds.v0.4.fasta.gz
Contigs: EL1_contigs.v0.4.fasta.gz
Peptides (ab initio): EL1_proteins.v0.4.fasta.gz
Transcripts (ab initio): EL1_transcripts.v0.4.fasta.gz
WGS Accession: AORF00000000
Raw reads: Short Read Archive
Citation: Blanco-Ulate et al., 2013 Genome Announcements 1(3) e00228-13


bcdw1

Botrytis cinerea

Draft Genome (isolate BcDW1)

Assembly size: 42.1 Mb (gaps: 58 kb; n.scaffolds: 453; median coverage: 125.3X)
N50: 194 kb
L50: 69
G+C: 42%
Predicted protein coding genes: 11,073


Scaffolds: BcDW1_scaffolds.v0.42.fasta.gz
Contigs: BcDW1_contigs.v0.42.fasta.gz
Peptides (ab initio): BcDW1_proteins-v0.1.fasta.gz
Transcripts (ab initio): BcDW1_transcripts-v0.1.fasta.gz
WGS Accession: AORW00000000
Raw reads: Short Read Archive
Citation: Blanco-Ulate et al., 2013 Genome Announcements 1(3) e00252-13


pst

Puccinia striiformis f.sp. tritici

Draft genomes - collaboration with Jorge Dubcovsky and Cristobal Uauy

Pst-21: AORR00000000
Pst-43: AORQ00000000
Pst-130: AEEW00000000
Pst-87/7: AORT00000000
Pst-08/21: AORS00000000
Ab initio gene models are available from yellowrust.com


Citations:
Cantu et al., 2011 PLoS ONE
Cantu et al., 2013 BMC Genomics