POSTERS: Proteomics / metabolomics / genomics
High-throughput sequencing of Phytophthora ramorum Ex-type using long-read MinION nanopore sequencing
Subodh Srivastava - Department of Entomology and Plant Pathology, NC State University. Leandra Knight- USDA-APHIS-PPQ S&T CPHST, Yazmin Rivera- USDA-APHIS-PPQ S&T CPHST, Vessela Mavrodieva- USDA-APHIS-PPQ S&T CPHST, Z. Gloria Abad- USDA-APHIS-PPQ S&T CPHST, Leandra Knight- Department of Entomology and Plant Pathology, NC State University, K
Sequence information of type specimens is critical in order to make correct molecular identification and develop robust diagnostic systems. Phytophthora ramorum is one of the species of biosecurity concern in the United States, United Kingdom and other areas of the world. Due to the significance of the species there are currently 22 genome sequences for isolates of P. ramorum deposited at the NCBI, however a whole genome sequence for the Ex-type of P. ramorum is not available. Here we report the whole-genome sequence for the Ex-type of Phytophthora ramorum generated using High Throughput Sequencing on the MinION platform from Oxford Nanopore Technology. The quality filtered 625,764 reads were assembled in to 1322 contigs indicated extended genome size of 52.4 Mb. We analyzed our Nanopore assembly of the P. ramorum (CPHST-BL 55G which is a duplicate of specimen P10103) with another isolate CC1011 of EU1 lineage available at the NCBI, and found 251,859 quality Single Nucleotide Polymorphisms (SNPs) genome-wide. When compared to the genome of isolate SOD69/12 of EU2 lineage 441,859 SNPs were found. Completion of Ex-type draft genome of Phytophthora ramorum is highly important since this is the representative specimen for the species of biosecurity concern at different regions of the world.