scholarly journals First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5963 ◽  
Author(s):  
Balázs Brankovics ◽  
Tomasz Kulik ◽  
Jakub Sawicki ◽  
Katarzyna Bilska ◽  
Hao Zhang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Fusarium Graminearum ◽  
Population Analysis ◽  
Gene Copy ◽  
Sequence Length ◽  
Length Variation ◽  
Group I Introns ◽  
Group I ◽  
Pooled Sequencing ◽  
Mitochondrial Introns

There is a gradual shift from representing a species’ genome by a single reference genome sequence to a pan-genome representation. Pan-genomes are the abstract representations of the genomes of all the strains that are present in the population or species. In this study, we employed a pan-genomic approach to analyze the intraspecific mitochondrial genome diversity of Fusarium graminearum. We present an improved reference mitochondrial genome for F. graminearum with an intron-exon annotation that was verified using RNA-seq data. Each of the 24 studied isolates had a distinct mitochondrial sequence. Length variation in the F. graminearum mitogenome was found to be largely due to variation of intron regions (99.98%). The “intronless” mitogenome length was found to be quite stable and could be informative when comparing species. The coding regions showed high conservation, while the variability of intergenic regions was highest. However, the most important variable parts are the intron regions, because they contain approximately half of the variable sites, make up more than half of the mitogenome, and show presence/absence variation. Furthermore, our analyses show that the mitogenome of F. graminearum is recombining, as was previously shown in F. oxysporum, indicating that mitogenome recombination is a common phenomenon in Fusarium. The majority of mitochondrial introns in F. graminearum belongs to group I introns, which are associated with homing endonuclease genes (HEGs). Mitochondrial introns containing HE genes may spread within populations through homing, where the endonuclease recognizes and cleaves the recognition site in the target gene. After cleavage of the “host” gene, it is replaced by the gene copy containing the intron with HEG. We propose to use introns unique to a population for tracking the spread of the given population, because introns can spread through vertical inheritance, recombination as well as via horizontal transfer. We demonstrate how pooled sequencing of strains can be used for mining mitogenome data. The usage of pooled sequencing offers a scalable solution for population analysis and for species level comparisons studies. This study may serve as a basis for future mitochondrial genome variability studies and representations.

scholarly journals First steps towards mitochondrial pan-genomics: Detailed analysis of Fusarium graminearum mitogenomes

2018 ◽  
Author(s):  
Balázs Brankovics ◽  
Tomasz Kulik ◽  
Jakub Sawicki ◽  
Katarzyna Bilska ◽  
Hao Zhang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Fusarium Graminearum ◽  
Population Analysis ◽  
Gene Copy ◽  
Sequence Length ◽  
Length Variation ◽  
Group I Introns ◽  
Group I ◽  
Pooled Sequencing ◽  
Mitochondrial Introns

There is a gradual shift from representing a species’ genome by a single reference genome sequence to a pan-genome representation. Pan-genomes are the abstract representations of the genomes of all the strains that are present in the population or species. In this study, we employed a pan-genomic approach to analyze the intraspecific mitochondrial genome diversity of Fusarium graminearum. We present an improved reference mitochondrial genome for F. graminearum with an intron-exon annotation that was verified using RNA-seq data. Each of the 24 studied isolates had a distinct mitochondrial sequence. Length variation in the F. graminearum mitogenome was found to be largely due to variation of intron regions (99.98%). The “intronless” mitogenome length was found to be quite stable and could be informative when comparing species. The coding regions showed high conservation, while the variability of intergenic regions was highest. However, the most important variable parts are the intron regions, because they contain approximately half of the variable sites, make up more than half of the mitogenome, and show presence/absence variation. Furthermore, our analyses show that the mitogenome of F. graminearum is recombining, as was previously shown in F. oxysporum, indicating that mitogenome recombination is a common phenomenon in Fusarium. The majority of mitochondrial introns in F. graminearum belongs to group I introns, which are associated with homing endonuclease genes (HEGs). Mitochondrial introns containing HE genes may spread within populations through homing, where the endonuclease recognizes and cleaves the recognition site in the target gene. After cleavage of the “host” gene, it is replaced by the gene copy containing the intron with HEG. We propose to use introns unique to a population for tracking the spread of the given population, because introns can spread through vertical inheritance, recombination as well as via horizontal transfer. We demonstrated how pooled sequencing of strains can be used for mining mitogenome data. The usage of pooled sequencing offers a scalable solution for population analysis and for species level comparisons studies. This study may serve as a basis for future mitochondrial genome variability studies and representations.

scholarly journals First steps towards mitochondrial pan-genomics: Detailed analysis of Fusarium graminearum mitogenomes

2018 ◽  
Author(s):  
Balázs Brankovics ◽  
Tomasz Kulik ◽  
Jakub Sawicki ◽  
Katarzyna Bilska ◽  
Hao Zhang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Fusarium Graminearum ◽  
Population Analysis ◽  
Gene Copy ◽  
Sequence Length ◽  
Length Variation ◽  
Group I Introns ◽  
Group I ◽  
Pooled Sequencing ◽  
Mitochondrial Introns

There is a gradual shift from representing a species’ genome by a single reference genome sequence to a pan-genome representation. Pan-genomes are the abstract representations of the genomes of all the strains that are present in the population or species. In this study, we employed a pan-genomic approach to analyze the intraspecific mitochondrial genome diversity of Fusarium graminearum. We present an improved reference mitochondrial genome for F. graminearum with an intron-exon annotation that was verified using RNA-seq data. Each of the 24 studied isolates had a distinct mitochondrial sequence. Length variation in the F. graminearum mitogenome was found to be largely due to variation of intron regions (99.98%). The “intronless” mitogenome length was found to be quite stable and could be informative when comparing species. The coding regions showed high conservation, while the variability of intergenic regions was highest. However, the most important variable parts are the intron regions, because they contain approximately half of the variable sites, make up more than half of the mitogenome, and show presence/absence variation. Furthermore, our analyses show that the mitogenome of F. graminearum is recombining, as was previously shown in F. oxysporum, indicating that mitogenome recombination is a common phenomenon in Fusarium. The majority of mitochondrial introns in F. graminearum belongs to group I introns, which are associated with homing endonuclease genes (HEGs). Mitochondrial introns containing HE genes may spread within populations through homing, where the endonuclease recognizes and cleaves the recognition site in the target gene. After cleavage of the “host” gene, it is replaced by the gene copy containing the intron with HEG. We propose to use introns unique to a population for tracking the spread of the given population, because introns can spread through vertical inheritance, recombination as well as via horizontal transfer. We demonstrated how pooled sequencing of strains can be used for mining mitogenome data. The usage of pooled sequencing offers a scalable solution for population analysis and for species level comparisons studies. This study may serve as a basis for future mitochondrial genome variability studies and representations.

scholarly journals Proposal of a new nomenclature for introns in protein-coding genes in fungal mitogenomes

IMA Fungus ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Shu Zhang ◽  
Yong-Jie Zhang
Keyword(s):  
Insertion Site ◽  
Mitochondrial Protein ◽  
Host Gene ◽  
Rrna Genes ◽  
Group I Introns ◽  
Protein Coding ◽  
Standard Nomenclature ◽  
Protein Coding Genes ◽  
Group I ◽  
Mitochondrial Introns

Abstract Fungal mitochondrial genes are often invaded by group I or II introns, which represent an ideal marker for understanding fungal evolution. A standard nomenclature of mitochondrial introns is needed to avoid confusion when comparing different fungal mitogenomes. Currently, there has been a standard nomenclature for introns present in rRNA genes, but there is a lack of a standard nomenclature for introns present in protein-coding genes. In this study, we propose a new nomenclature system for introns in fungal mitochondrial protein-coding genes based on (1) three-letter abbreviation of host scientific name, (2) host gene name, (3), one capital letter P (for group I introns), S (for group II introns), or U (for introns with unknown types), and (4) intron insertion site in the host gene according to the cyclosporin-producing fungus Tolypocladium inflatum. The suggested nomenclature was proved feasible by naming introns present in mitogenomes of 16 fungi of different phyla, including both basal and higher fungal lineages although minor adjustment of the nomenclature is needed to fit certain special conditions. The nomenclature also had the potential to name plant/protist/animal mitochondrial introns. We hope future studies follow the proposed nomenclature to ensure direct comparison across different studies.

scholarly journals Group I introns in the liverwort mitochondrial genome: the gene coding for subunit 1 of cytochrome oxidase shares five intron positions with its fungal counterparts

1993 ◽  
Vol 21 (5) ◽  
pp. 1297-1305 ◽  
Author(s):  
Eiji Ohta ◽  
Kenji Oda ◽  
Katsuyuki Yamato ◽  
Yasukazu Nakamura ◽  
Miho Takemura ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Cytochrome Oxidase ◽  
Group I Introns ◽  
Group I ◽  
Gene Coding

scholarly journals The Mitochondrial Genome of the Prasinophyte Prasinoderma coloniale Reveals Two Trans-Spliced Group I Introns in the Large Subunit rRNA Gene

PLoS ONE ◽  
2013 ◽  
Vol 8 (12) ◽  
pp. e84325 ◽  
Author(s):  
Jean-François Pombert ◽  
Christian Otis ◽  
Monique Turmel ◽  
Claude Lemieux
Keyword(s):  
Mitochondrial Genome ◽  
Large Subunit ◽  
Rrna Gene ◽  
Group I Introns ◽  
Group I ◽  
Large Subunit Rrna

scholarly journals The mitochondrial genome of the arbuscular mycorrhizal fungusGigaspora margaritareveals two unsuspectedtrans-splicing events of group I introns

2012 ◽  
Vol 194 (3) ◽  
pp. 836-845 ◽  
Author(s):  
Adrian Pelin ◽  
Jean-François Pombert ◽  
Alessandra Salvioli ◽  
Linda Bonen ◽  
Paola Bonfante ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Arbuscular Mycorrhizal ◽  
Group I Introns ◽  
Group I
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