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Background  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.  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.    Results  Our 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.    Conclusions  This 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.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-08079-y.

A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans