Abstract
BackgroundPathogens of the genus Phytophthora are the etiological agents of many devastating diseases in several high-value crops and forestry species such as potato, tomato, cocoa, and oak, among many others. Phytophthora betacei is a recently described species that causes late blight almost exclusively in tree tomatoes, and it is closely related to Phytophthora infestans that causes the disease in potato crops and other Solanaceae. This study reports the assembly and annotation of the genomes of P. betacei P8084, the first of its species, and P. infestans RC1-10, a Colombian strain from the EC-1 lineage, using long-read SMRT sequencing technology.ResultsOur results show that P. betacei has the largest sequenced genome size of the Phytophthora genus so far with 270 Mb. A moderate transposable element invasion and a whole genome duplication likely explain its genome size expansion when compared to P. infestans, whereas P. infestans RC1-10 has expanded its genome under the activity of transposable elements. The high diversity and abundance (in terms of copy number) of classified and unclassified transposable elements in P. infestans RC1-10 relative to P. betacei bears testimony of the power of long-read technologies to discover novel repetitive elements in the genomes of organisms. Our data also provides support for the phylogenetic placement of P. betacei as a standalone species and as a sister group of P. infestans. Finally, we found no evidence to support the idea that the genome of P. betacei P8084 follows the same gene-dense/gense-sparse architecture proposed for P. infestans and other filamentous plant pathogens.ConclusionsThis study provides the first genome-wide picture of P. betacei and expands the genomic resources available for P. infestans. This is a contribution towards the understanding of the genome biology and evolutionary history of Phytophthora species belonging to the subclade 1c.
Highlights
Pathogens of the genus Phytophthora are the etiological agents of many devastating diseases in several high-value crops and forestry species such as potato, tomato, cocoa, and oak, among many others
A k-mer coverage frequency analysis of the Illumina data obtained for P. betacei P8084 showed a very likely scenario for a highly-heterozygous diploid organism (Supplementary Fig. 1), after which we performed the assembly using only longreads and assuming both organisms to be diploid
Phytophthora betacei P8084 has the largest genome of the genus due to a lineage-specific process of whole genome duplication
Summary
Pathogens of the genus Phytophthora are the etiological agents of many devastating diseases in several high-value crops and forestry species such as potato, tomato, cocoa, and oak, among many others. Pathogens of the genus Phytophthora are the etiological agents of many devastating diseases in a wide range of plant hosts, that include several high-value crops and forestry species such as potato, tomato, cocoa, and oak among many others [1, 2]. The data from 22 788 SNPs revealed a clear genetic structure among the three evaluated species, except for two individuals (likely misclassified) of P. andina clustering within the EC-3 lineage along with P. betacei individuals This suggested that P. infestans, P. andina, and P. betacei are genetic differentiated groups with negligible gene flow between them [5]
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