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Fonseca PLC, De-Paula RB, Araújo DS, Tomé LMR, Mendes-Pereira T, Rodrigues WFC, Del-Bem LE, Aguiar ERGR, Góes-Neto A. Global Characterization of Fungal Mitogenomes: New Insights on Genomic Diversity and Dynamism of Coding Genes and Accessory Elements. Front Microbiol 2021; 12:787283. [PMID: 34925295 PMCID: PMC8672057 DOI: 10.3389/fmicb.2021.787283] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/11/2021] [Indexed: 01/13/2023] Open
Abstract
Fungi comprise a great diversity of species with distinct ecological functions and lifestyles. Similar to other eukaryotes, fungi rely on interactions with prokaryotes and one of the most important symbiotic events was the acquisition of mitochondria. Mitochondria are organelles found in eukaryotic cells whose main function is to generate energy through aerobic respiration. Mitogenomes (mtDNAs) are double-stranded circular or linear DNA from mitochondria that may contain core genes and accessory elements that can be replicated, transcribed, and independently translated from the nuclear genome. Despite their importance, investigative studies on the diversity of fungal mitogenomes are scarce. Herein, we have evaluated 788 curated fungal mitogenomes available at NCBI database to assess discrepancies and similarities among them and to better understand the mechanisms involved in fungal mtDNAs variability. From a total of 12 fungal phyla, four do not have any representative with available mitogenomes, which highlights the underrepresentation of some groups in the current available data. We selected representative and non-redundant mitogenomes based on the threshold of 90% similarity, eliminating 81 mtDNAs. Comparative analyses revealed considerable size variability of mtDNAs with a difference of up to 260 kb in length. Furthermore, variation in mitogenome length and genomic composition are generally related to the number and length of accessory elements (introns, HEGs, and uORFs). We identified an overall average of 8.0 (0–39) introns, 8.0 (0–100) HEGs, and 8.2 (0–102) uORFs per genome, with high variation among phyla. Even though the length of the core protein-coding genes is considerably conserved, approximately 36.3% of the mitogenomes evaluated have at least one of the 14 core coding genes absent. Also, our results revealed that there is not even a single gene shared among all mitogenomes. Other unusual genes in mitogenomes were also detected in many mitogenomes, such as dpo and rpo, and displayed diverse evolutionary histories. Altogether, the results presented in this study suggest that fungal mitogenomes are diverse, contain accessory elements and are absent of a conserved gene that can be used for the taxonomic classification of the Kingdom Fungi.
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Affiliation(s)
- Paula L C Fonseca
- Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Department of Biological Science (DCB), Center of Biotechnology and Genetics (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
| | - Ruth B De-Paula
- Graduate School of Biomedical Sciences, Baylor College of Medicine, Houston, TX, United States
| | - Daniel S Araújo
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, United States
| | - Luiz Marcelo Ribeiro Tomé
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Thairine Mendes-Pereira
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Luiz-Eduardo Del-Bem
- Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Department of Botany, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Eric R G R Aguiar
- Department of Biological Science (DCB), Center of Biotechnology and Genetics (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, Brazil
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Program of Bioinformatics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Nugent CM, Elliott TA, Ratnasingham S, Adamowicz SJ. coil: an R package for cytochrome c oxidase I (COI) DNA barcode data cleaning, translation, and error evaluation. Genome 2020; 63:291-305. [DOI: 10.1139/gen-2019-0206] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Biological conclusions based on DNA barcoding and metabarcoding analyses can be strongly influenced by the methods utilized for data generation and curation, leading to varying levels of success in the separation of biological variation from experimental error. The 5′ region of cytochrome c oxidase subunit I (COI-5P) is the most common barcode gene for animals, with conserved structure and function that allows for biologically informed error identification. Here, we present coil ( https://CRAN.R-project.org/package=coil ), an R package for the pre-processing and frameshift error assessment of COI-5P animal barcode and metabarcode sequence data. The package contains functions for placement of barcodes into a common reading frame, accurate translation of sequences to amino acids, and highlighting insertion and deletion errors. The analysis of 10 000 barcode sequences of varying quality demonstrated how coil can place barcode sequences in reading frame and distinguish sequences containing indel errors from error-free sequences with greater than 97.5% accuracy. Package limitations were tested through the analysis of COI-5P sequences from the plant and fungal kingdoms as well as the analysis of potential contaminants: nuclear mitochondrial pseudogenes and Wolbachia COI-5P sequences. Results demonstrated that coil is a strong technical error identification method but is not reliable for detecting all biological contaminants.
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Affiliation(s)
- Cameron M. Nugent
- Department of Integrative Biology, University of Guelph. Guelph, Ontario, Canada
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph. Guelph, Ontario, Canada
| | - Tyler A. Elliott
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph. Guelph, Ontario, Canada
| | - Sujeevan Ratnasingham
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph. Guelph, Ontario, Canada
| | - Sarah J. Adamowicz
- Department of Integrative Biology, University of Guelph. Guelph, Ontario, Canada
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Zervakis GI, Venturella G, Fryssouli V, Inglese P, Polemis E, Gargano ML. Pleurotus opuntiae revisited - An insight to the phylogeny of dimitic Pleurotus species with emphasis on the P. djamor complex. Fungal Biol 2018; 123:188-199. [PMID: 30798874 DOI: 10.1016/j.funbio.2018.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 12/04/2018] [Accepted: 12/20/2018] [Indexed: 10/27/2022]
Abstract
The name Pleurotus opuntiae is indiscriminately used for describing mushrooms with white to off-white to white-grey pilei with short or absent stipe and dimitic hyphal system, which grow on plants of the genera Opuntia, Yucca, Agave, Phytolacca etc. However, the outcome of the present study evidences that this name should be reserved for specimens deriving from the Mediterranean area only; an epitype originating from Italy on Opuntia ficus-indica is designated. Pertinent material was sequenced by using the internal transcribed spacer region (ITS) and found to be phylogenetically related to P. djamor from Kenya and Nigeria, while members of the P. djamor complex from other continents were clearly more distant. Results were further corroborated by examining the large subunit of nuclear ribosomal DNA (LSU) and the second subunit of RNA polymerase II (RPB2). The P. djamor complex shows high intraspecific polymorphism evidenced by sequence divergence and genetic distance values, presents a cosmopolitan distribution and also comprises material initially identified as P. flabellatus, P. opuntiae, P. ostreatoroseus, P. parsonsiae and P. salmoneostramineus. An ITS tree including representative specimens from all major Pleurotus species is provided for the first time and ambiguous taxa are discussed in the context of new findings.
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Affiliation(s)
- Georgios I Zervakis
- Agricultural University of Athens, Laboratory of General and Agricultural Microbiology, Iera Odos 75, 11855 Athens, Greece.
| | - Giuseppe Venturella
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze, Bldg 4, I-90128 Palermo, Italy.
| | - Vassiliki Fryssouli
- Agricultural University of Athens, Laboratory of General and Agricultural Microbiology, Iera Odos 75, 11855 Athens, Greece
| | - Paolo Inglese
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze, Bldg 4, I-90128 Palermo, Italy
| | - Elias Polemis
- Agricultural University of Athens, Laboratory of General and Agricultural Microbiology, Iera Odos 75, 11855 Athens, Greece
| | - Maria Letizia Gargano
- Department of Earth and Marine Sciences, University of Palermo, Viale delle Scienze, Bldg 5, I-90128 Palermo, Italy
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Avin FA, Subha B, Tan Y, Braukmann TWA, Vikineswary S, Hebert PDN. Escaping introns in COI through cDNA barcoding of mushrooms: Pleurotus as a test case. Ecol Evol 2017; 7:6972-6980. [PMID: 28904776 PMCID: PMC5587487 DOI: 10.1002/ece3.3049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 03/31/2017] [Accepted: 04/02/2017] [Indexed: 01/28/2023] Open
Abstract
DNA barcoding involves the use of one or more short, standardized DNA fragments for the rapid identification of species. A 648-bp segment near the 5' terminus of the mitochondrial cytochrome c oxidase subunit I (COI) gene has been adopted as the universal DNA barcode for members of the animal kingdom, but its utility in mushrooms is complicated by the frequent occurrence of large introns. As a consequence, ITS has been adopted as the standard DNA barcode marker for mushrooms despite several shortcomings. This study employed newly designed primers coupled with cDNA analysis to examine COI sequence diversity in six species of Pleurotus and compared these results with those for ITS. The ability of the COI gene to discriminate six species of Pleurotus, the commonly cultivated oyster mushroom, was examined by analysis of cDNA. The amplification success, sequence variation within and among species, and the ability to design effective primers was tested. We compared ITS sequences to their COI cDNA counterparts for all isolates. ITS discriminated between all six species, but some sequence results were uninterpretable, because of length variation among ITS copies. By comparison, a complete COI sequences were recovered from all but three individuals of Pleurotus giganteus where only the 5' region was obtained. The COI sequences permitted the resolution of all species when partial data was excluded for P. giganteus. Our results suggest that COI can be a useful barcode marker for mushrooms when cDNA analysis is adopted, permitting identifications in cases where ITS cannot be recovered or where it offers higher resolution when fresh tissue is. The suitability of this approach remains to be confirmed for other mushrooms.
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Affiliation(s)
- Farhat A. Avin
- Mushroom Research Centre (MRC)University of MalayaKuala LumpurMalaysia
- Department of BiotechnologyFaculty of ScienceLincoln University College47301 Petaling JayaMalaysia
| | - Bhassu Subha
- Centre for Biotechnology in Agriculture Research (CEBAR)Division of Genetics and Molecular BiologyUniversity of MalayaKuala LumpurMalaysia
- Institute of Biological SciencesFaculty of ScienceUniversity of MalayaKuala LumpurMalaysia
| | - Yee‐Shin Tan
- Mushroom Research Centre (MRC)University of MalayaKuala LumpurMalaysia
- Institute of Biological SciencesFaculty of ScienceUniversity of MalayaKuala LumpurMalaysia
| | | | - Sabaratnam Vikineswary
- Mushroom Research Centre (MRC)University of MalayaKuala LumpurMalaysia
- Institute of Biological SciencesFaculty of ScienceUniversity of MalayaKuala LumpurMalaysia
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