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

Jason E Stajich,Christine D Smart,Jennifer Jacobi,Joann Mudge,Kurt H Lamour,Maryn O Carlson,Howard S Judelson,Nicholas Devitt,Michael A Gore,Gregory M Vogel,Andrea L Vu

doi:10.1128/mra.00295-21

Abstract

ABSTRACTThe 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.

Highlights

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)
Correction, and genome assembly were performed with MaSuRCA v3.3.1 [16, 17] with Illumina and LoRDEC-corrected PacBio reads
The assembly was screened for adaptors and contamination using AAFTF v0.2.3 [18]

Summary

Introduction

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). Correction, and genome assembly were performed with MaSuRCA v3.3.1 [16, 17] with Illumina and LoRDEC-corrected PacBio reads Polishing with masurca-polish.sh corrected 1,025 substitutions and 2,643 indels, resulting in 99.9961% computed consensus quality.

Results

Conclusion