Complete mitochondrial genome sequence of lettuce pathogenic fungus, <i>Fusarium oxysporum</i> f. sp. <i>lactucae</i> 09-002

Park, Jongsun; Kwon, Woochan; Kim, Jung-Bun; Park, Mi-Jeong; Kim, Taesung

doi:10.1080/23802359.2019.1667902

Cited by 5 publications

(3 citation statements)

References 15 publications

(25 reference statements)

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“…Instead, this phenomenon was found in genome studies focusing on intraspecific variations of insect, fungal, and marine invertebrate mitochondria. These include Laodelphax striatellus [ 93 , 94 ] and Nilaparvata lugens [ 95 – 97 ] belonging to the Delphacidae family; Fusarium oxysporum which is a fungal plant pathogen [ 98 , 99 ] and Apostichopus japonicus [ 100 ]. Because A. thaliana has a sufficient amount of sequencing data to construct chloroplast genomes, additional studies with more complete chloroplast genomes will provide a clear answer as to whether or not this phenomenon remains.…”

Section: Resultsmentioning

confidence: 99%

The Complete Chloroplast Genome of Arabidopsis thaliana Isolated in Korea (Brassicaceae): An Investigation of Intraspecific Variations of the Chloroplast Genome of Korean A. thaliana

Park¹,

Xi²,

Kim³

2020

International Journal of Genomics

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Arabidopsis thaliana (L.) Heynh. is a model organism of plant molecular biology. More than 1,700 whole genome sequences have been sequenced, but no Korean isolate genomes have been sequenced thus far despite the fact that many A. thaliana isolated in Japan and China have been sequenced. To understand the genetic background of Korean natural A. thaliana (named as 180404IB4), we presented its complete chloroplast genome, which is 154,464 bp long and has four subregions: 85,164 bp of large single copy (LSC) and 17,781 bp of small single copy (SSC) regions are separated by 26,257 bp of inverted repeat (IRs) regions including 130 genes (85 protein-coding genes, eight rRNAs, and 37 tRNAs). Fifty single nucleotide polymorphisms (SNPs) and 14 insertion and deletions (INDELs) are identified between 180404IB4 and Col0. In addition, 101 SSRs and 42 extendedSSRs were identified on the Korean A. thaliana chloroplast genome, indicating a similar number of SSRs on the rest five chloroplast genomes with a preference of sequence variations toward the SSR region. A nucleotide diversity analysis revealed two highly variable regions on A. thaliana chloroplast genomes. Phylogenetic trees with three more chloroplast genomes of East Asian natural isolates show that Korean and Chinese natural isolates are clustered together, whereas two Japanese isolates are not clustered, suggesting the need for additional investigations of the chloroplast genomes of East Asian isolates.

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Section: Resultsmentioning

confidence: 99%

The Complete Chloroplast Genome of Arabidopsis thaliana Isolated in Korea (Brassicaceae): An Investigation of Intraspecific Variations of the Chloroplast Genome of Korean A. thaliana

Park¹,

Xi²,

Kim³

2020

International Journal of Genomics

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“…There were three fewer PCGs for three reasons: the smaller number of LAGLIDADG endonucleases, the absence of one endonuclease and a GIY-YIG endonuclease, and the presence of two additional PCGs—a hypothetical protein and a LAGLIDADG/HNH endonuclease. This particular configuration of PCGs is usually identified in other fungal mitogenomes; for example, two mitogenomes of Fusarium oxysporum (GenBank accessions are MN259514 and MN259515) display two completely different PCGs in each mitogenome [ 54 , 56 ]. There are also five fewer tRNAs because of the different configurations: tRNA-Asp, tRNA-Cys, tRNA-Ile, and two tRNA-Ser (also found in the mitogenome of the fungal symbiont of R. speculum [ 19 ]).…”

Section: Resultsmentioning

confidence: 94%

A Comparative Analyses of the Complete Mitochondrial Genomes of Fungal Endosymbionts in Sogatella furcifera, White-Backed Planthoppers

Choi

Xi²,

Park³

2021

International Journal of Genomics

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Sogatella furcifera Horvath, commonly known as the white-backed planthoppers (WBPH), is an important pest in East Asian rice fields. Fungal endosymbiosis is widespread among planthoppers in the infraorder Fulgoromorpha and suborder Auchenorrhyncha. We successfully obtained complete mitogenome of five WBPH fungal endosymbionts, belonging to the Ophiocordycipitaceae family, from next-generation sequencing (NGS) reads obtained from S. furcifera samples. These five mitogenomes range in length from 55,390 bp to 55,406 bp, which is shorter than the mitogenome of the fungal endosymbiont found in Ricania speculum, black planthoppers. Twenty-eight protein-coding genes (PCGs), 12 tRNAs, and 2 rRNAs were found in the mitogenomes. Two single-nucleotide polymorphisms, two insertions, and three deletions were identified among the five mitogenomes, which were fewer in number than those of four species of Ophiocordycipitaceae, Ophiocordyceps sinensis, Hirsutella thompsonii, Hirsutella rhossiliensis, and Tolypocladium inflatum. Noticeably short lengths (up to 18 bp) of simple sequence repeats were identified in the five WBPH fungal endosymbiont mitogenomes. Phylogenetic analysis based on conserved PCGs across 25 Ophiocordycipitaceae mitogenomes revealed that the five mitogenomes were clustered with that of R. speculum, forming an independent clade. In addition to providing the full mitogenome sequences, obtaining complete mitogenomes of WBPH endosymbionts can provide insights into their phylogenetic positions without needing to isolate the mtDNA from the host. This advantage is of value to future studies involving fungal endosymbiont mitogenomes.

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“…Interestingly, length of Ophiocordyceps sinensis mitochondrial genome is much larger than that of Fusarium mangifere but both were clustered in one clade with high bootstrap values (Figure 2(A)). The mitochondrial genome expansion in Aspergillus genus [16][17][18][19] and variable size of Fusarium mitochondrial genomes [18,20,21] suggested that mitochondrial genome expansion events may be occurred several times during evolution of fungal species. In addition, tree displayed two distinct clades in Colletotrichum genus, which is congruent with previous phylogenetic study [22] ( Figure 2).…”

Section: Koreanmentioning

confidence: 99%

First Record of the Complete Mitochondrial Genome of a Saprotrophic and Opportunistic Human Pathogenic Fungus, Scopulariopsis brevicaulis

Park¹,

Kwon²,

Hong

et al. 2020

Mycobiology

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Scopulariopsis brevicaulis is a widely distributed soil fungus known as a common saprotroph of biodegradation. It is also an opportunistic human pathogen that can produce various secondary metabolites. Here, we report the first complete mitochondrial genome sequence of S. brevicaulis isolated from air in South Korea. Total length of the mitochondrial genome is 28,829 bp and encoded 42 genes (15 protein-coding genes, 2 rRNAs, and 25 tRNAs). Nucleotide sequence of coding region takes over 26.2%, and overall GC content is 27.6%. Phylogenetic trees present that S. brevicaulis is clustered with Lomentospora prolificans with presenting various mitochondrial genome length.

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Complete mitochondrial genome sequence of lettuce pathogenic fungus, Fusarium oxysporum f. sp. lactucae 09-002

Cited by 5 publications

References 15 publications

The Complete Chloroplast Genome of Arabidopsis thaliana Isolated in Korea (Brassicaceae): An Investigation of Intraspecific Variations of the Chloroplast Genome of Korean A. thaliana

The Complete Chloroplast Genome of Arabidopsis thaliana Isolated in Korea (Brassicaceae): An Investigation of Intraspecific Variations of the Chloroplast Genome of Korean A. thaliana

A Comparative Analyses of the Complete Mitochondrial Genomes of Fungal Endosymbionts in Sogatella furcifera, White-Backed Planthoppers

First Record of the Complete Mitochondrial Genome of a Saprotrophic and Opportunistic Human Pathogenic Fungus, Scopulariopsis brevicaulis

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