Updated assembly of phytophthora ramorum pr102 isolate incorporating long reads from PacBio sequencing

Abstract

The NA1 clonal lineage of Phytophthora ramorum is responsible for sudden oak death, an epidemic that has devastated California coastal forest ecosystems. An NA1 isolate, Pr102, derived from coast live oak in California, was previously sequenced and reported with a 65- Mb assembly containing 12 Mb of gaps in 2,576 scaffolds. Here, we report an improved 70-Mb genome in 1,512 scaffolds with 6,752 bp of gaps after incorporating PacBio P5-C3 long reads. This assembly contains 19,494 gene models (average gene length of 2,515 bp) compared with 16,134 genes (average gene length of 1,673 bp) in the previous version. We predicted 29 new RXLR genes and 76 new paralogs of a total 392 RXLR genes from this assembly. We predicted 35 CRN genes compared with 19 in an earlier version with six paralogs. Our long non-coding RNA prediction identified 255 candidates. This new resource will be invaluable for future evolution studies on the invasive plant pathogen.