Complete Mitochondrial Genome Sequences of Korean Phytophthora infestans Isolates and Comparative Analysis of Mitochondrial Haplotypes

Abstract

Potato late blight caused by Phytophthora infestans is a destructive disease in Korea. To elucidate the genomic variation of the mitochondrial (mt) genome, we assembled its complete mt genome and compared its sequence among different haplotypes. The mt genome sequences of four Korean P. infestans isolates were revealed by Illumina HiSeq. The size of the circular mt genome of the four major genotypes, KR_1_A1, KR_2_A2, SIB-1, and US-11, was 39,872, 39,836, 39,872, and 39,840 bp, respectively. All genotypes contained the same 61 genes in the same order, comprising two RNA-encoding genes, 16 ribosomal genes, 25 transfer RNA, 17 genes encoding electron transport and ATP synthesis, 11 open reading frames of unknown function, and one protein import-related gene, tatC. The coding region comprised 91% of the genome, and GC content was 22.3%. The haplotypes were further analyzed based on sequence polymorphism at two hypervariable regions (HVRi), carrying a 2 kb insertion/deletion sequence, and HVRii, carrying 36 bp variable number tandem repeats (VNTRs). All four genotypes carried the 2 kb insertion/deletion sequence in HVRi, whereas HVRii had two VNTRs in KR_1_A1 and SIB-1 but three VNTRs in US-11 and KR_2_A2. Minimal spanning network and phylogenetic analysis based on 5,814 bp of mtDNA sequences from five loci, KR_1_A1 and SIB-1 were classified as IIa-6 haplotype, and isolates KR_1_A2 and US-11 as haplotypes IIa-5 and IIb-2, respectively. mtDNA sequences of KR_1_A1 and SIB-1 shared 100% sequence identity, and both were 99.9% similar to those of KR_2_A2 and US-11.

Selective Isolation and Characterization of Phytophthora infestans from Potatoes Using Rye Agar Media in India

“…The total volume of each reaction mixture was 40 µL. It consisted of 20 µL of TaqPCR MasterMix, 1 µL of each primer (PINF:5' -TCGCTACAAT AGGAGGGTC3' and ITS5:5'GGA AGTAAA AGTCGTAACAAGG3'), 1 µL of template DNA, and sterilized double-distilled water [18]. All reactions were performed in a thermocycler, which was set for an initial denaturation step at 96°C for 2 minutes, followed by 35 cycles of denaturation at 96°C for 1 minute, annealing for 1 minute at 55°C, extension for 1 minute at 72°C, and a final extension temperature of 72°C for 10 minutes.…”

“…While all Phytophthora species grow well on oatmeal agar, the medium is dense and opaque [16]. Most Phytophthora strains are unable to produce sporangia or develop oospores on potato dextrose agar (PDA) [17,18]. In a preliminary screen [6], the components of locally accessible rye agar media for P. infestans culture were investigated.…”