Genome sequences of six Phytophthora species threatening forest ecosystems

Abstract

The Phytophthora genus comprises of some of the most destructive plant pathogens and attack a wide range of hosts including economically valuable tree species, both angiosperm and gymnosperm. Many known species of Phytophthora are invasive and have been introduced through nursery and agricultural trade. As part of a larger project aimed at utilizing genomic data for forest disease diagnostics, pathogen detection and monitoring (The TAIGA project: Tree Aggressors Identification using Genomic Approaches; http://taigaforesthealth.com/), we sequenced the genomes of six important Phytophthora species that are important invasive pathogens of trees and a serious threat to the international trade of forest products. This genomic data was used to develop highly sensitive and specific detection assays and for genome comparisons and to make evolutionary inferences and will be useful to the broader plant and tree health community. These WGS data have been deposited in the International Nucleotide Sequence Database Collaboration (DDBJ/ENA/GenBank) under the accession numbers AUPN01000000, AUVH01000000, AUWJ02000000, AUUF02000000, AWVV02000000 and AWVW02000000.

Genome sequencing of oomycete isolates from Chile supports the New Zealand origin of Phytophthora kernoviae and makes available the first Nothophytophthora sp. genome

“…This pattern was also reflected in the predicted proteomes and may indicate that Chile 5 is a hybrid. Similar observations have been made previously with BUSCO analysis of predicted genes by Feau et al () for the genome sequence of P. alni sp. alni , a well‐characterized hybrid Phytophthora species.…”

“…Annotated genome assemblies and raw sequence data are available via GenBank (Table ). The assembly statistics for the genome sequences presented are comparable with those published previously (Feau et al , ; Sambles et al , ; Studholme et al , ), with the exception of Chile 5. This genome assembly had a larger number of scaffolds and appeared to be much larger in total length (Table ).…”

“…Genomes have been sequenced for isolates of P. kernoviae from New Zealand (Studholme et al , ) and the UK (Feau et al , ; Sambles et al , ). Here, we report the first genome sequences for isolates of P. kernoviae from Chile (Table ), the only other geographical location in which this species has been reported so far.…”

“…Completeness for genes from Chile 1, Chile 2, Chile 4, Chile 6 and Chile 7 (95.7%–97.9%) was similar to that of recently published P . kernoviae genomes (97.4%–97.9%) (Feau et al , ; Sambles et al , ; Studholme et al , ) (Table ). The Chile 5 assembly was less complete (87.6%) and had a considerably higher number of duplicated genes (164) compared with the other genomes, which had less than four duplicated genes.…”

In Situ Processing and Efficient Environmental Detection iSPEED of pests and pathogens of trees using point-of-use real-time pcr

“…The standardization of DNA barcoding databases for fungi and insects [2,3] has generated extensive DNA sequence data that can be exploited to design taxon-specific DNA assays [4][5][6]. New approaches make use of whole genomes to identify diagnostic genome regions that are translated into highly accurate detection assays [7,8].…”