Complete Mitochondrial Genome Sequence of
            <i>Colletotrichum siamense</i>
            Isolated in South Korea

Cho, Sung-Eun; Oh, Ji Yeon; Lee, Dong‐Hyeon

doi:10.1128/mra.01055-21

Cited by 3 publications

(3 citation statements)

References 8 publications

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“…The lack of a telomere in Chr10 could be attributed to the rDNA content (Wu et al, 2009 ), although we cannot rule out the possibility that the missing telomeres are due to incomplete sequencing. The mitochondrial genome has a GC content of 29.6%, similar to that of the previous assembly (29.9%) (O'Connell et al, 2012 ), C. acutatum (30.10%) (Baroncelli et al, 2014 ), C. lupini 29.90% (Baroncelli et al, 2021 ), and C. siamense (35.45%) (Cho et al, 2022 ).…”

Section: Discussionsupporting

confidence: 68%

Chromosome-level analysis of the Colletotrichum graminicola genome reveals the unique characteristics of core and minichromosomes

et al. 2023

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The fungal pathogen Colletotrichum graminicola causes the anthracnose of maize (Zea mays) and is responsible for significant yield losses worldwide. The genome of C. graminicola was sequenced in 2012 using Sanger sequencing, 454 pyrosequencing, and an optical map to obtain an assembly of 13 pseudochromosomes. We re-sequenced the genome using a combination of short-read (Illumina) and long-read (PacBio) technologies to obtain a chromosome-level assembly. The new version of the genome sequence has 13 chromosomes with a total length of 57.43 Mb. We detected 66 (23.62 Mb) structural rearrangements in the new assembly with respect to the previous version, consisting of 61 (21.98 Mb) translocations, 1 (1.41 Mb) inversion, and 4 (221 Kb) duplications. We annotated the genome and obtained 15,118 predicted genes and 3,614 new gene models compared to the previous version of the assembly. We show that 25.88% of the new assembly is composed of repetitive DNA elements (13.68% more than the previous assembly version), which are mostly found in gene-sparse regions. We describe genomic compartmentalization consisting of repeat-rich and gene-poor regions vs. repeat-poor and gene-rich regions. A total of 1,140 secreted proteins were found mainly in repeat-rich regions. We also found that ~75% of the three smallest chromosomes (minichromosomes, between 730 and 551 Kb) are strongly affected by repeat-induced point mutation (RIP) compared with 28% of the larger chromosomes. The gene content of the minichromosomes (MCs) comprises 121 genes, of which 83.6% are hypothetical proteins with no predicted function, while the mean percentage of Chr1–Chr10 is 36.5%. No predicted secreted proteins are present in the MCs. Interestingly, only 2% of the genes in Chr11 have homologs in other strains of C. graminicola, while Chr12 and 13 have 58 and 57%, respectively, raising the question as to whether Chrs12 and 13 are dispensable. The core chromosomes (Chr1–Chr10) are very different with respect to the MCs (Chr11–Chr13) in terms of the content and sequence features. We hypothesize that the higher density of repetitive elements and RIPs in the MCs may be linked to the adaptation and/or host co-evolution of this pathogenic fungus.

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Section: Discussionsupporting

confidence: 68%

Chromosome-level analysis of the Colletotrichum graminicola genome reveals the unique characteristics of core and minichromosomes

et al. 2023

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“… 2018 ; Cho et al. 2022 , 2023 ). In brief, trimmed high-quality read sequences of 3.0 Gb were de novo assembled using the clc_novo_assemble program with default parameters in the CLC Assembly Cell.…”

Section: Methodsmentioning

confidence: 98%

The complete mitochondrial genome of a wood-decaying fungus Vanderbylia fraxinea (Polyporaceae, Polyporales)

Cho,

Kang,

Lee

et al. 2023

Mitochondrial DNA Part B

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Vanderbylia fraxinea (Bull.) D.A. Reid, 1973 is an important wood-inhabiting fungus that plays a significant role in nutrient recycling in most forest ecosystems. In this study, the complete mitochondrial genome of V. fraxinea was characterized through de novo assembly using Illumina sequencing data and genome annotation. The mitochondrial genome is a circular molecule of 115,473 bp with a GC content of 28.66%. It comprises a total of 62 genes. Among these, 36 are protein-coding genes including 21 free-standing open reading frames (ORFs), 24 transfer RNA genes, and two ribosomal RNA genes. Core gene set commonly found in fungal mitochondrial genomes is also present in this genome, such as the apocytochrome b ( cob ), three subunits of the cytochrome c oxidase ( cox1 , cox2 , and cox3 ), seven subunits of the NADH dehydrogenase ( nad1 , nad2 , nad3 , nad4 , nad4L , nad5 , and nad6 ), and three subunits of the ATP synthase ( atp6 , atp8 , and atp9 ), as well as ribosomal RNA subunits ( rns and rnl ) and a set of transfer RNA genes. Phylogenetic analysis of the protein-coding sequences from the mitochondrial genome revealed a close relationship between V. fraxinea and the Ganoderma species within the Polyporaceae family.

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“… 2018 , Cho et al. 2022 ). Trimmed high-quality read sequences of 1.8 Gb were de novo assembled using the clc_novo_assemble program with default parameters in the CLC Assembly Cell and then mitochondrial contigs were selected and ordered by similarity searches using BLAST against mitochondrial sequences from NCBI organelle genome resources ( https://www.ncbi.nlm.nih.gov/genome/organelle/ ).…”

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confidence: 97%

The complete mitochondrial genome of Cladosporium anthropophilum (cladosporiaceae, dothideomycetes)

Cho

Lee

2023

Mitochondrial DNA Part B

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The genus Cladosporium (Cladosporiaceae, Capnodiales) is a large genus of Ascomycota. Although the genus is mostly reported as saprobes from a wide range of substrates with a worldwide distribution, members of this genus comprise infectious agents in animals and plants. Of those, Cladosporium anthropophilum is a common saprophytic fungus and has been found to be a human opportunistic pathogen and plant pathogen. The complete mitochondrial genome of C. anthropophilum is characterized through the de novo assembly of Illumina sequencing data. The mitochondrial genome is a circular molecule of 35,937 bp with 30.23% GC content and has a total of 47 genes including 16 protein-coding genes, 29 transfer RNA genes, and two ribosomal RNA genes. Based on protein-coding sequences of the mitochondrial genome sequence, a phylogenetic tree was constructed to demonstrate the phylogenetic relationship of C. anthropophilum and its related genera.

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Complete Mitochondrial Genome Sequence of Colletotrichum siamense Isolated in South Korea

Abstract: The complete mitochondrial genome of Colletotrichum siamense is characterized. The circular genome has a size of 52,710 bp, with a GC content of 34.45%, and contains 15 protein-coding genes, 23 tRNA genes, and 2 rRNA genes.

Cited by 3 publications

References 8 publications

Chromosome-level analysis of the Colletotrichum graminicola genome reveals the unique characteristics of core and minichromosomes

Chromosome-level analysis of the Colletotrichum graminicola genome reveals the unique characteristics of core and minichromosomes

The complete mitochondrial genome of a wood-decaying fungus Vanderbylia fraxinea (Polyporaceae, Polyporales)

The complete mitochondrial genome of Cladosporium anthropophilum (cladosporiaceae, dothideomycetes)

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