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Misas E, Chow NA, Gómez OM, Muñoz JF, McEwen JG, Litvintseva AP, Clay OK. Mitochondrial Genome Sequences of the Emerging Fungal Pathogen Candida auris. Front Microbiol 2020; 11:560332. [PMID: 33193142 PMCID: PMC7652928 DOI: 10.3389/fmicb.2020.560332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/30/2020] [Indexed: 11/25/2022] Open
Abstract
Candida auris is an emerging fungal pathogen capable of causing invasive infections in humans. Since its first appearance around 1996, it has been isolated in countries spanning five continents. C. auris is a yeast that has the potential to cause outbreaks in hospitals, can survive in adverse conditions, including dry surfaces and high temperatures, and has been frequently misidentified by traditional methods. Furthermore, strains have been identified that are resistant to two and even all three of the main classes of antifungals currently in use. Several nuclear genome assemblies of C. auris have been published representing different clades and continents, yet until recently, the mitochondrial genomes (mtDNA chromosomes) of this species and the closely related species of C. haemulonii, C. duobushaemulonii, and C. pseudohaemulonii had not been analyzed in depth. We used reads from PacBio and Illumina sequencing to obtain a de novo reference assembly of the mitochondrial genome of the C. auris clade I isolate B8441 from Pakistan. This assembly has a total size of 28.2 kb and contains 13 core protein-coding genes, 25 tRNAs and the 12S and 16S ribosomal subunits. We then performed a comparative analysis by aligning Illumina reads of 129 other isolates from South Asia, Japan, South Africa, and South America with the B8441 reference. The clades of the phylogenetic tree we obtained from the aligned mtDNA sequences were consistent with those derived from the nuclear genome. The mitochondrial genome revealed a generally low genetic variation within clades, although the South Asian clade displayed two sub-branches including strains from both Pakistan and India. In particular, the 86 isolates from Colombia and Venezuela had mtDNA sequences that were all identical at the base level, i.e., a single conserved haplotype or mitochondrial background that exhibited characteristic differences from the Pakistan reference isolate B8441, such as a unique 25-nt insert that may affect function.
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Affiliation(s)
- Elizabeth Misas
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Wisconsin One Health Consortium, Universidad Nacional de Colombia, Medellín, Colombia
| | - Nancy A. Chow
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Oscar M. Gómez
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- School of Microbiology, Universidad de Antioquia, Medellín, Colombia
- Genoma CES, Universidad CES, Medellín, Colombia
| | - José F. Muñoz
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Juan G. McEwen
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | | | - Oliver K. Clay
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Translational Microbiology and Emerging Diseases, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
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Misas E, Gómez OM, Botero V, Muñoz JF, Teixeira MM, Gallo JE, Clay OK, McEwen JG. Updates and Comparative Analysis of the Mitochondrial Genomes of Paracoccidioides spp. Using Oxford Nanopore MinION Sequencing. Front Microbiol 2020; 11:1751. [PMID: 32849380 PMCID: PMC7417371 DOI: 10.3389/fmicb.2020.01751] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 07/06/2020] [Indexed: 02/03/2023] Open
Abstract
The mitochondrial genome of the Paracoccidioides brasiliensis reference isolate Pb18 was first sequenced and described by Cardoso et al. (2007), as a circular genome with a size of 71.3 kb and containing 14 protein coding genes, 25 tRNAs, and the large and small subunits of ribosomal RNA. Later in 2011, Desjardins et al. (2011) obtained partial assemblies of mitochondrial genomes of P. lutzii (Pb01), P. americana (Pb03), and P. brasiliensis sensu stricto (Pb18), although with a size of only 43.1 kb for Pb18. Sequencing errors or other limitations resulting from earlier technologies, and the advantages of NGS (short and long reads), prompted us to improve and update the mtDNA sequences and annotations of two Paracoccidioides species. Using Oxford Nanopore and Illumina read sequencing, we generated high-quality complete de novo mitochondrial genome assemblies and annotations for P. brasiliensis (Pb18) and P. americana (Pb03). Both assemblies were characterized by an unusually long spacer or intron region (>50 kb) between exons 2 and 3 of the nad5 gene, which was moderately conserved between Pb03 and Pb18 but not similar to other reported sequences, except for an unassigned contig in the 2011 assembly of Pb03. The reliability of the insert missing from previous mtDNA genome assemblies was confirmed by inspection of the individual Nanopore read sequences containing nad5 coding DNA, and experimentally by PCR for Pb18. We propose that the insert may aid replication initiation and may be excised to produce a smaller structural variant. The updated mtDNA genomes should enable more accurate SNP and other comparative or evolutionary analyses and primer/probe designs. A comparative analysis of the mtDNA from 32 isolates of Paracoccidioides spp., using the SNPs of the aligned mitochondrial genomes, showed groupings within the brasiliensis species complex that were largely consistent with previous findings from only five mitochondrial loci.
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Affiliation(s)
- Elizabeth Misas
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Colombia Wisconsin One Health Consortium, Universidad Nacional de Colombia, Medellín, Colombia
| | - Oscar M. Gómez
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Genoma CES, Universidad CES, Medellín, Colombia
| | - Vanessa Botero
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
| | - José F. Muñoz
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | | | - Juan E. Gallo
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- Genoma CES, Universidad CES, Medellín, Colombia
| | - Oliver K. Clay
- Translational Microbiology and Emerging Diseases (MICROS), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Juan G. McEwen
- Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia
- School of Medicine, Universidad de Antioquia, Medellín, Colombia
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Deng Y, Zhang X, Xie B, Lin L, Hsiang T, Lin X, Lin Y, Zhang X, Ma Y, Miao W, Ming R. Intra-specific comparison of mitochondrial genomes reveals host gene fragment exchange via intron mobility in Tremella fuciformis. BMC Genomics 2020; 21:426. [PMID: 32580700 PMCID: PMC7315562 DOI: 10.1186/s12864-020-06846-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 06/17/2020] [Indexed: 01/21/2023] Open
Abstract
Background Mitochondrial genomic sequences are known to be variable. Comparative analyses of mitochondrial genomes can reveal the nature and extent of their variation. Results Draft mitochondrial genomes of 16 Tremella fuciformis isolates (TF01-TF16) were assembled from Illumina and PacBio sequencing data. Mitochondrial DNA contigs were extracted and assembled into complete circular molecules, ranging from 35,104 bp to 49,044 bp in size. All mtDNAs contained the same set of 41 conserved genes with identical gene order. Comparative analyses revealed that introns and intergenic regions were variable, whereas genic regions (including coding sequences, tRNA, and rRNA genes) were conserved. Among 24 introns detected, 11 were in protein-coding genes, 3 in tRNA genes, and the other 10 in rRNA genes. In addition, two mobile fragments were found in intergenic regions. Interestingly, six introns containing N-terminal duplication of the host genes were found in five conserved protein-coding gene sequences. Comparison of genes with and without these introns gave rise to the following proposed model: gene fragment exchange with other species can occur via gain or loss of introns with N-terminal duplication of the host genes. Conclusions Our findings suggest a novel mechanism of fungal mitochondrial gene evolution: partial foreign gene replacement though intron mobility.
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Affiliation(s)
- Youjin Deng
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Department of Plant Biology, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, Urbana, IL, 61801, USA
| | - Xunxiao Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Baogui Xie
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Longji Lin
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Tom Hsiang
- Environmental Sciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Xiangzhi Lin
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yiying Lin
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xingtan Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yanhong Ma
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenjing Miao
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ray Ming
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Department of Plant Biology, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, Urbana, IL, 61801, USA.
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Li W, Freudenberg J, Freudenberg J. Alignment-free approaches for predicting novel Nuclear Mitochondrial Segments (NUMTs) in the human genome. Gene 2019; 691:141-152. [PMID: 30630097 DOI: 10.1016/j.gene.2018.12.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/07/2018] [Accepted: 12/14/2018] [Indexed: 10/27/2022]
Abstract
The nuclear human genome harbors sequences of mitochondrial origin, indicating an ancestral transfer of DNA from the mitogenome. Several Nuclear Mitochondrial Segments (NUMTs) have been detected by alignment-based sequence similarity search, as implemented in the Basic Local Alignment Search Tool (BLAST). Identifying NUMTs is important for the comprehensive annotation and understanding of the human genome. Here we explore the possibility of detecting NUMTs in the human genome by alignment-free sequence similarity search, such as k-mers (k-tuples, k-grams, oligos of length k) distributions. We find that when k=6 or larger, the k-mer approach and BLAST search produce almost identical results, e.g., detect the same set of NUMTs longer than 3 kb. However, when k=5 or k=4, certain signals are only detected by the alignment-free approach, and these may indicate yet unrecognized, and potentially more ancestral NUMTs. We introduce a "Manhattan plot" style representation of NUMT predictions across the genome, which are calculated based on the reciprocal of the Jensen-Shannon divergence between the nuclear and mitochondrial k-mer frequencies. The further inspection of the k-mer-based NUMT predictions however shows that most of them contain long-terminal-repeat (LTR) annotations, whereas BLAST-based NUMT predictions do not. Thus, similarity of the mitogenome to LTR sequences is recognized, which we validate by finding the mitochondrial k-mer distribution closer to those for transposable sequences and specifically, close to some types of LTR.
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Affiliation(s)
- Wentian Li
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA.
| | - Jerome Freudenberg
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Jan Freudenberg
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
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