Global Characterization of Fungal Mitogenomes: New Insights on Genomic Diversity and Dynamism of Coding Genes and Accessory Elements

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...

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Autores principales:	Paula L. C. Fonseca, Ruth B. De-Paula, Daniel S. Araújo, Luiz Marcelo Ribeiro Tomé, Thairine Mendes-Pereira, Wenderson Felipe Costa Rodrigues, Luiz-Eduardo Del-Bem, Eric R. G. R. Aguiar, Aristóteles Góes-Neto
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	mitochondrial genome homing endonuclease intron size variation comparative genomics Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/d977fac8c76643e6a0bae5c6561066c3
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spelling	oai:doaj.org-article:d977fac8c76643e6a0bae5c6561066c32021-12-02T00:10:45ZGlobal Characterization of Fungal Mitogenomes: New Insights on Genomic Diversity and Dynamism of Coding Genes and Accessory Elements1664-302X10.3389/fmicb.2021.787283https://doaj.org/article/d977fac8c76643e6a0bae5c6561066c32021-12-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fmicb.2021.787283/fullhttps://doaj.org/toc/1664-302XFungi 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.Paula L. C. FonsecaPaula L. C. FonsecaRuth B. De-PaulaDaniel S. AraújoLuiz Marcelo Ribeiro ToméThairine Mendes-PereiraWenderson Felipe Costa RodriguesLuiz-Eduardo Del-BemLuiz-Eduardo Del-BemEric R. G. R. AguiarAristóteles Góes-NetoAristóteles Góes-NetoFrontiers Media S.A.articlemitochondrial genomehoming endonucleaseintronsize variationcomparative genomicsMicrobiologyQR1-502ENFrontiers in Microbiology, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	mitochondrial genome homing endonuclease intron size variation comparative genomics Microbiology QR1-502
spellingShingle	mitochondrial genome homing endonuclease intron size variation comparative genomics Microbiology QR1-502 Paula L. C. Fonseca Paula L. C. Fonseca Ruth B. De-Paula Daniel S. Araújo Luiz Marcelo Ribeiro Tomé Thairine Mendes-Pereira Wenderson Felipe Costa Rodrigues Luiz-Eduardo Del-Bem Luiz-Eduardo Del-Bem Eric R. G. R. Aguiar Aristóteles Góes-Neto Aristóteles Góes-Neto Global Characterization of Fungal Mitogenomes: New Insights on Genomic Diversity and Dynamism of Coding Genes and Accessory Elements
description	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.
format	article
author	Paula L. C. Fonseca Paula L. C. Fonseca Ruth B. De-Paula Daniel S. Araújo Luiz Marcelo Ribeiro Tomé Thairine Mendes-Pereira Wenderson Felipe Costa Rodrigues Luiz-Eduardo Del-Bem Luiz-Eduardo Del-Bem Eric R. G. R. Aguiar Aristóteles Góes-Neto Aristóteles Góes-Neto
author_facet	Paula L. C. Fonseca Paula L. C. Fonseca Ruth B. De-Paula Daniel S. Araújo Luiz Marcelo Ribeiro Tomé Thairine Mendes-Pereira Wenderson Felipe Costa Rodrigues Luiz-Eduardo Del-Bem Luiz-Eduardo Del-Bem Eric R. G. R. Aguiar Aristóteles Góes-Neto Aristóteles Góes-Neto
author_sort	Paula L. C. Fonseca
title	Global Characterization of Fungal Mitogenomes: New Insights on Genomic Diversity and Dynamism of Coding Genes and Accessory Elements
title_short	Global Characterization of Fungal Mitogenomes: New Insights on Genomic Diversity and Dynamism of Coding Genes and Accessory Elements
title_full	Global Characterization of Fungal Mitogenomes: New Insights on Genomic Diversity and Dynamism of Coding Genes and Accessory Elements
title_fullStr	Global Characterization of Fungal Mitogenomes: New Insights on Genomic Diversity and Dynamism of Coding Genes and Accessory Elements
title_full_unstemmed	Global Characterization of Fungal Mitogenomes: New Insights on Genomic Diversity and Dynamism of Coding Genes and Accessory Elements
title_sort	global characterization of fungal mitogenomes: new insights on genomic diversity and dynamism of coding genes and accessory elements
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/d977fac8c76643e6a0bae5c6561066c3
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Global Characterization of Fungal Mitogenomes: New Insights on Genomic Diversity and Dynamism of Coding Genes and Accessory Elements

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