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ARS Home » Pacific West Area » Davis, California » Crops Pathology and Genetics Research » Research » Publications at this Location » Publication #364314
Research Project: Integrated Disease Management Strategies for Woody Perennial Species

Location: Crops Pathology and Genetics Research

Title: Updated assembly of Phytophthora ramorum pr102 isolate incorporating long reads from PacBio sequencing

Author
item MALAR C, MATHU - University Of Ottawa
item YUZON, JENNIFER - University Of California, Davis
item PANDA, ARIJIT - University Of Ottawa
item Kasuga, Takao
item TRIPATHY, SUCHETA - University Of Ottawa

Submitted to: Molecular Plant-Microbe Interactions
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/10/2019
Publication Date: 9/27/2019
Citation: Malar C, M., Yuzon, J.D., Panda, A., Kasuga, T., Tripathy, S. 2019. Updated assembly of Phytophthora ramorum pr102 isolate incorporating long reads from PacBio sequencing. Molecular Plant-Microbe Interactions. 32(11):1472-1474. https://doi.org/10.1094/MPMI-05-19-0147-A.
DOI: https://doi.org/10.1094/MPMI-05-19-0147-A

Interpretive Summary: Phytophthora ramorum is an invasive and devastating plant pathogen that causes sudden oak death in coastal forests in the western United States and ramorum blight in nursery ornamentals and native plants in various landscapes. A genome sequence of isolate Pr102 was released in 2006, which is fragmented and contains 12 million bp assembly gaps in 2,576 scaffolds. Here we report an improved 70 Mb genome in 1512 scaffolds with 6752 bp gaps after incorporating PacBio long reads.

Technical Abstract: The NA1 clonal lineage of Phytophthora ramorum is responsible for Sudden Oak Death, an epidemic that has devastated California’s coastal forest ecosystems. An NA1 isolate Pr102 derived from coast live oak in California was previously sequenced and reported with 65 Mb assembly containing 12 Mb gaps in 2576 scaffolds. Here we report an improved 70 Mb genome in 1512 scaffolds with 6752 bp gaps after incorporating PacBio P5-C3 longreads. This assembly contains 19494 gene models (average gene length 2515 bp) compared to 16134 genes (average gene length of 1673 bp) in the previous version. We predicted 29 new RXLRs of a total 392 RXLRs from this assembly with 76 new paralogs. We predicted 35 CRNs with six paralogs. Our lncRNAs prediction identified 255 candidates. This new resource will be invaluable for future evolution studies on the invasive plant pathogen.