High-Quality Reference Genome Sequence for the Oomycete Vegetable Pathogen Phytophthora capsici Strain LT1534

The oomycete Phytophthora capsici is a destructive pathogen of a wide range of vegetable hosts, especially peppers and cucurbits. A 94.17-Mb genome assembly was constructed using PacBio and Illumina data and annotated with support from transcriptome sequencing (RNA-Seq) reads. P hytophthora capsici is a highly destructive pathogen of vegetables worldwide, especially those in the Solanaceae and Cucurbitaceae families (Fig. 1). Efforts to understand the role of genes in pathogenesis and host range (1–8), population structure (9, 10), genomic variation (11), and development (12) benefit from an accurate genome assembly. P. capsici belongs to the eukaryotic phylum Oomycota, many members of which have repeat-rich genomes that are difficult to assemble with short reads. Strain LT1534, A2 mating type, is an inbred strain derived from crossing isolates from infected cucurbits in Michigan (cucumber) and Tennessee (pumpkin) (11). An earlier assembly for LT1534, generated with Roche 454 and Sanger sequencing (11), was 64Mb in 917 scaffolds (N50, 706 kb). A single oospore-derived isolate (LT1534) was maintained axenically on PARP (25 ppm pimaricin, 100 ppm ampicillin, 25 ppm rifampicin, and 100 ppm pentachloronitrobenzene) agar plates, and a small weft of mycelium was transferred to clarified V8 juice broth amended with PARP and grown at 22 to 23°C for 7 days prior to harvesting, freeze-drying, disruption, and extraction of genomic DNA (13) using a GeneJet genomic DNA purification kit (Thermo Fisher). Libraries were constructed with a TruSeq DNA kit and sequenced on an Illumina HiSeq X Ten system by Novogene (Shenzen, China), yielding 34.9 million, 2 150-bp read pairs (10.48 Gbp). PacBio libraries were constructed by the National Center for Genome Resources (Santa Fe, NM) following the 20-kb protocol (14). One single-molecule real-time (SMRT) cell was sequenced on a PacBio RS II system using P6 polymerase and C4 chemistry, yielding 964,374 subreads (n= 964,374; N50, 12.5 kb; maximum, 47.5 kb; total, 8.15 Gbp) as processed by the SMRT pipeline v2.3.0.1. PacBio reads were corrected with Illumina by LoRDEC v0.9 (15) using the default parameters. To provide gene model support, mRNA was extracted from 2.5-, 3-, and 4.5-day V8 agar cultures grown at 23°C under 12-h light/dark conditions using a Spectrum plant total RNA kit (Sigma). Strand-specific transcriptome sequencing (RNA-Seq) libraries were constructed and sequenced by Cofactor Genomics (St. Louis, MO) using oligo(dT) priming on an Illumina NextSeq 500 instrument to obtain;25 million single-end reads per library. Read trimming, correction, and genome assembly were performed with MaSuRCA v3.3.1 (16, 17) with Illumina and LoRDEC-corrected PacBio reads (LHE_COVERAGE=25 Citation Stajich JE, Vu AL, Judelson HS, Vogel GM, Gore MA, Carlson MO, Devitt N, Jacobi J, Mudge J, Lamour KH, Smart CD. 2021. Highquality reference genome sequence for the oomycete vegetable pathogen Phytophthora capsici strain LT1534. Microbiol Resour Announc 10:e00295-21. https://doi.org/10 .1128/MRA.00295-21. Editor Antonis Rokas, Vanderbilt University Copyright © 2021 Stajich et al. This is an openaccess article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Jason E. Stajich, jason.stajich@ucr.edu. * Present address: Andrea L. Vu, Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA; Maryn O. Carlson, Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, Illinois, USA. Received 22 March 2021 Accepted 7 May 2021 Published 27 May 2021 Volume 10 Issue 21 e00295-21 mra.asm.org 1 GENOME SEQUENCES