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Data released on January 25, 2016

Genomic assembled sequences and annotation for Phytophthora nicotianae race 0 and race 1

Bingguang, X; Dunhuang, F; Haiqin, Y; Hui, L; Wen, W; Xiao, M; Xiao, W; Yang, D (2016): Genomic assembled sequences and annotation for Phytophthora nicotianae race 0 and race 1 GigaScience Database. RIS BibTeX Text

Black shank is a severe plant disease caused by soil-born pathogen Phytophthora nicotianae. Two physiological races of P. nicotianae, race 0 and race 1, were predominantly observed in the cultivated tobacco field around the world. Race 0 was reported to be more aggressive, having shorter incubation period and causing worse root rot symptoms, while race 1 causing greater necrosis. So far, the molecular mechanisms underlying the virulence difference between race 0 and 1 remain elusive.
We assembled and annotated genomes of P. nicotianae race 0 and 1, which were obtained by a combination of PacBio single molecular real time sequencing and second-generation sequencing (both HiSeq and MiSeq platforms). Gene family analysis found an ATP-binding cassette transporter gene family under expansion in P. nicotianae Particularly, more RxLR effector genes were found in the genome of race 0 than that of race 1. Besides, RxLR effector genes are mainly distributed in gene-sparse, repeat-rich regions of the P. nicotianae genome.
The final assembled genome sizes for race 0 and race 1 were 80 Mb and 69 Mb, which is slightly different from the previous estimation of P. nicotianae (90 Mb). The corresponding contig N50 sizes were 23 Kb and 30 Kb, respectively A total of 17,797 and 14,542 protein-coding genes were annotated in P. nicotianae race 0 and race 1, respectively.

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Accessions (data included in GigaDB):

BioProject: PRJNA294216


Black shank genomes hybrid assembly RxLR effector buckeye rot agent 


Samples: Table Settings


Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN040179594790buckeye rot agent Phytophthora nicotianae Infra_specific_name:race 0
Sample material processing:Tobacco plants infected...
Specific host:Tobacco
SAMN040179604790buckeye rot agent Phytophthora nicotianae Infra_specific_name:race 1
Sample material processing:Tobacco plants infected...
Specific host:Tobacco
Displaying 1-2 of 2 Sample(s).

Files: (FTP site) Table Settings


File Description
Sample ID
File Type
File Format
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
SAMPLE:SAMN04017959Coding sequenceFASTA27.51 MB2016-01-05
SAMPLE:SAMN04017959AnnotationGFF3.59 MB2016-01-05
SAMPLE:SAMN04017959Protein sequenceFASTA10.3 MB2016-01-05
SAMPLE:SAMN04017959Transcriptome sequenceFASTA79.16 MB2016-01-05
SAMPLE:SAMN04017960Coding sequenceFASTA15.24 MB2016-01-05
SAMPLE:SAMN04017960AnnotationGFF2.25 MB2016-01-05
SAMPLE:SAMN04017960Protein sequenceFASTA5.84 MB2016-01-05
SAMPLE:SAMN04017960Transcriptome sequenceFASTA68.91 MB2016-01-05
ReadmeTEXT1.2 KB2016-01-05
Displaying 1-9 of 9 File(s).



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