Tags

Type your tag names separated by a space and hit enter

Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans.
BMC Genomics. 2010 Nov 16; 11:637.BG

Abstract

BACKGROUND

Phytophthora infestans is the most devastating pathogen of potato and a model organism for the oomycetes. It exhibits high evolutionary potential and rapidly adapts to host plants. The P. infestans genome experienced a repeat-driven expansion relative to the genomes of Phytophthora sojae and Phytophthora ramorum and shows a discontinuous distribution of gene density. Effector genes, such as members of the RXLR and Crinkler (CRN) families, localize to expanded, repeat-rich and gene-sparse regions of the genome. This distinct genomic environment is thought to contribute to genome plasticity and host adaptation.

RESULTS

We used in silico approaches to predict and describe the repertoire of P. infestans secreted proteins (the secretome). We defined the "plastic secretome" as a subset of the genome that (i) encodes predicted secreted proteins, (ii) is excluded from genome segments orthologous to the P. sojae and P. ramorum genomes and (iii) is encoded by genes residing in gene sparse regions of P. infestans genome. Although including only ~3% of P. infestans genes, the plastic secretome contains ~62% of known effector genes and shows >2 fold enrichment in genes induced in planta. We highlight 19 plastic secretome genes induced in planta but distinct from previously described effectors. This list includes a trypsin-like serine protease, secreted oxidoreductases, small cysteine-rich proteins and repeat containing proteins that we propose to be novel candidate virulence factors.

CONCLUSIONS

This work revealed a remarkably diverse plastic secretome. It illustrates the value of combining genome architecture with comparative genomics to identify novel candidate virulence factors from pathogen genomes.

Authors+Show Affiliations

The Sainsbury Laboratory, John Innes Centre, Norwich NR4 7UH, UK.No affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

21080964

Citation

Raffaele, Sylvain, et al. "Analyses of Genome Architecture and Gene Expression Reveal Novel Candidate Virulence Factors in the Secretome of Phytophthora Infestans." BMC Genomics, vol. 11, 2010, p. 637.
Raffaele S, Win J, Cano LM, et al. Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans. BMC Genomics. 2010;11:637.
Raffaele, S., Win, J., Cano, L. M., & Kamoun, S. (2010). Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans. BMC Genomics, 11, 637. https://doi.org/10.1186/1471-2164-11-637
Raffaele S, et al. Analyses of Genome Architecture and Gene Expression Reveal Novel Candidate Virulence Factors in the Secretome of Phytophthora Infestans. BMC Genomics. 2010 Nov 16;11:637. PubMed PMID: 21080964.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans. AU - Raffaele,Sylvain, AU - Win,Joe, AU - Cano,Liliana M, AU - Kamoun,Sophien, Y1 - 2010/11/16/ PY - 2010/04/28/received PY - 2010/11/16/accepted PY - 2010/11/18/entrez PY - 2010/11/18/pubmed PY - 2011/3/8/medline SP - 637 EP - 637 JF - BMC genomics JO - BMC Genomics VL - 11 N2 - BACKGROUND: Phytophthora infestans is the most devastating pathogen of potato and a model organism for the oomycetes. It exhibits high evolutionary potential and rapidly adapts to host plants. The P. infestans genome experienced a repeat-driven expansion relative to the genomes of Phytophthora sojae and Phytophthora ramorum and shows a discontinuous distribution of gene density. Effector genes, such as members of the RXLR and Crinkler (CRN) families, localize to expanded, repeat-rich and gene-sparse regions of the genome. This distinct genomic environment is thought to contribute to genome plasticity and host adaptation. RESULTS: We used in silico approaches to predict and describe the repertoire of P. infestans secreted proteins (the secretome). We defined the "plastic secretome" as a subset of the genome that (i) encodes predicted secreted proteins, (ii) is excluded from genome segments orthologous to the P. sojae and P. ramorum genomes and (iii) is encoded by genes residing in gene sparse regions of P. infestans genome. Although including only ~3% of P. infestans genes, the plastic secretome contains ~62% of known effector genes and shows >2 fold enrichment in genes induced in planta. We highlight 19 plastic secretome genes induced in planta but distinct from previously described effectors. This list includes a trypsin-like serine protease, secreted oxidoreductases, small cysteine-rich proteins and repeat containing proteins that we propose to be novel candidate virulence factors. CONCLUSIONS: This work revealed a remarkably diverse plastic secretome. It illustrates the value of combining genome architecture with comparative genomics to identify novel candidate virulence factors from pathogen genomes. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/21080964/Analyses_of_genome_architecture_and_gene_expression_reveal_novel_candidate_virulence_factors_in_the_secretome_of_Phytophthora_infestans_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-11-637 DB - PRIME DP - Unbound Medicine ER -