Pythium aphanidermatum (pag1_scaffolds_v1)

Pythium aphanidermatum Assembly and Gene Annotation

About the Pythium aphanidermatum Genome

Pythium aphanidermatum is a plant pathogen causing damping off, root and stem rots, and blights of grasses and fruits. P. aphanidermatum have wide rage of hosts, including the economically important crops like beets, pepper and cotton. It is a major cause of root rot in papaya. It requires warmer temperatures, it is often seen in greenhouses. P. aphanidermatum is responsible for pre and post emergence damping off. Pre-emergence damping off is when the seed is infected prior to germination. This can result in poor or no germination, and is observable as a browning or rotting of the seed. Post emergence damping off takes place after germination and results in a thinning, water-soaked stem near the plant collar, which eventually causes the collapse of the plant.

It belongs to the group oomycetes which was originally classified among the fungi, due to its morphological and functional similarities. They are now classifed as protists based on modern insights on phylogentic relationship with photosynthetic organisms such as brown algae and diatoms.


The genome is ~35.9Mb and 37,384 contigs were assembled into 1,774 scaffolds. The assembly for the genome was provided by Pythium Genome Database and is also available from the EMBL/Genbank/DDBJ databases under the accession GGCA_000387445.2.


12,363 gene models were predicted with 12,370 transcripts. The protein coding genes are imported from the Pythium Genome Database and 58 ncRNAs were predicted using Ensembl pipeline.


  1. Pythium Genome Database.
  2. Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire.
    Lvesque CA, Brouwer H, Cano L, Hamilton JP, Holt C, Huitema E, Raffaele S, Robideau GP, Thines M, Win J et al. 2010. Genome Biol.. 11:R73.
  3. Comparative genomics reveals insight into virulence strategies of plant pathogenic oomycetes.
    Adhikari BN, Hamilton JP, Zerillo MM, Tisserat N, Lvesque CA, Buell CR. 2013. PLoS ONE. 8:e75072.
  4. Carbohydrate-active enzymes in pythium and their role in plant cell wall and storage polysaccharide degradation.
    Zerillo MM, Adhikari BN, Hamilton JP, Buell CR, Lvesque CA, Tisserat N. 2013. PLoS ONE. 8:e72572.

Picture credit: Growing hyphae of Pythium aphanidermatum on creeping bent grass leaf - Photo taken by Dr. Marcelo Zerillo in the laboratory of Ned Tisserat

More information

General information about this species can be found in Wikipedia.



Assemblypag1_scaffolds_v1, INSDC Assembly GCA_000387445.2, Aug 2013
Database version110.2
Golden Path Length35,876,849
Genebuild byPGD
Genebuild methodImport
Data sourcePythium Genome Database

Gene counts

Coding genes12,305
Non coding genes52
Small non coding genes51
Misc non coding genes1
Gene transcripts12,370