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

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.

Keywords:

• Black shank
• genomes
• hybrid assembly
• RxLR effector
• buckeye rot agent

Read the peer-reviewed publication(s):

• Liu, H., Ma, X., Yu, H., Fang, D., Li, Y., Wang, X., Wang, W., Dong, Y., & Xiao, B. (2016). Genomes and virulence difference between two physiological races of Phytophthora nicotianae. GigaScience, 5(1). https://doi.org/10.1186/s13742-016-0108-7

Accessions (data included in GigaDB):

BioProject: PRJNA294216