The intron landscape of the mtDNA
            <i>cytb</i>
            gene among the Ascomycota: introns and intron-encoded open reading frames

Guha, Tuhin Kumar; Wai, Alvan; Mullineux, Sahra-Taylor; Hausner, Georg

doi:10.1080/24701394.2017.1404042

Cited by 21 publications

(35 citation statements)

References 85 publications

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“…Twenty‐one species contained two or more HEG elements in a single intron. This nested HEG arrangement has the potential to drive alternative splicing (Guha et al, ), which in some lineages may foster gene regulatory divergence under variable environmental conditions, as has been demonstrated in diatoms (Rastogi et al, ).…”

Section: Discussionmentioning

confidence: 97%

“…Intron presence is well established in fungal mitochondrial genomes, but can vary widely among taxa (Giroux et al, 1994;Guha, Wai, Mullineux, & Hausner, 2017;Jeffares et al, 2006;Logsdon, 1998). Variation in intron number, which can occur even between different populations or strains of the same species, has the potential for widespread implications including impacting genome size and gene regulation or expression through alternative splicing mechanisms (Dibb, 1993;Jo & Choi, 2015;Lynch et al, 2006;Simmons et al, 2015;Wang et al, 2018).…”

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confidence: 99%

“…Variation in intron number, which can occur even between different populations or strains of the same species, has the potential for widespread implications including impacting genome size and gene regulation or expression through alternative splicing mechanisms (Dibb, 1993;Jo & Choi, 2015;Lynch et al, 2006;Simmons et al, 2015;Wang et al, 2018). Among fungi, species can vary remarkably in intron content as well as genome size (Hensgens, Bonen, Haan, Horst, & Grivell, 1983;van der Veen et al, 1986;Fink, 1987;Derr, Strathern, & Garfinkel, 1991;Nielsen, Friedman, Birren, Burge, & Galagan, 2004;Guha et al, 2017;Wang et al, 2018;e.g., 18.9 kbp in Schizosaccharomyces pombe; Anziano, Perlman, Lang, & Wolf, 1983 and 235 kbp in Rhizoctonia solani; Losada et al, 2014). However, the study of intron evolution in fungi has been limited primarily to nonlichenized systems (Derr et al, 1991;Fink, 1987;Guha et al, 2017;Hensgens et al, 1983;Nielsen et al, 2004;van der Veen et al, 1986), despite the fact that tens of thousands of species of fungi are lichenized and have symbiotic lifestyles (Hawksworth & Hill, 1984).…”

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confidence: 99%

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Genome streamlining via complete loss of introns has occurred multiple times in lichenized fungal mitochondria

Pogoda

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Nadiadi

et al. 2019

Ecology and Evolution

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Reductions in genome size and complexity are a hallmark of obligate symbioses. The mitochondrial genome displays clear examples of these reductions, with the ancestral alpha‐proteobacterial genome size and gene number having been reduced by orders of magnitude in most descendent modern mitochondrial genomes. Here, we examine patterns of mitochondrial evolution specifically looking at intron size, number, and position across 58 species from 21 genera of lichenized Ascomycete fungi, representing a broad range of fungal diversity and niches. Our results show that the cox1 gene always contained the highest number of introns out of all the mitochondrial protein‐coding genes, that high intron sequence similarity (>90%) can be maintained between different genera, and that lichens have undergone at least two instances of complete, genome‐wide intron loss consistent with evidence for genome streamlining via loss of parasitic, noncoding DNA, in Phlyctis boliviensis and Graphis lineola . Notably, however, lichenized fungi have not only undergone intron loss but in some instances have expanded considerably in size due to intron proliferation (e.g., Alectoria fallacina and Parmotrema neotropicum ), even between closely related sister species (e.g., Cladonia ). These results shed light on the highly dynamic mitochondrial evolution that is occurring in lichens and suggest that these obligate symbiotic organisms are in some cases undergoing recent, broad‐scale genome streamlining via loss of protein‐coding genes as well as noncoding, parasitic DNA elements.

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Section: Discussionmentioning

confidence: 97%

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confidence: 99%

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confidence: 99%

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Genome streamlining via complete loss of introns has occurred multiple times in lichenized fungal mitochondria

Pogoda

Keepers

Nadiadi

et al. 2019

Ecology and Evolution

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“…It is assumed that encoding a potentially essential gene ensures these introns are not subject to neutral evolution. Other introns for less obvious reason also appear to be observed at relative higher frequencies compared to other introns, such as cob393 and cob490 and possibly these introns may provide some means for gene regulation and therefore selection may favour their maintenance 57 . Rudan et al 58 recently presented data from S .…”

Section: Discussionmentioning

confidence: 99%

The mitochondrial genome of Endoconidiophora resinifera is intron rich

Zubaer

Wai

Hausner

2018

Sci Rep

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Endoconidiophora resinifera (=Ceratocystis resinifera) is a blue-stain fungus that occurs on conifers. The data showed that the Endoconidiophora resinifera mitochondrial genome is one of the largest mitochondrial genomes (>220 kb) so far reported among members of the Ascomycota. An exceptional large number of introns (81) were noted and differences among the four strains were restricted to minor variations in intron numbers and a few indels and single nucleotide polymorphisms. The major differences among the four strains examined are due to size polymorphisms generated by the absence or presence of mitochondrial introns. Also, these mitochondrial genomes encode the largest cytochrome oxidase subunit 1 gene (47.5 kb) reported so far among the fungi. The large size for this gene again can be attributed to the large number of intron insertions. This study reports the first mitochondrial genome for the genus Endoconidiophora, previously members of this genus were assigned to Ceratocystis. The latter genus has recently undergone extensive taxonomic revisions and the mitochondrial genome might provide loci that could be applied as molecular markers assisting in the identification of taxa within this group of economically important fungi. The large mitochondrial genome also may provide some insight on mechanisms that can lead to mitochondrial genome expansion.

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“…In all species except C. peziziformis that encoded cox1 as a single exon, introns in cox1 contained LAGLIDADG and GIY-YIG homing endonucleases. Presence of these selfish, parasitic elements in lichen mitochondrial genomes has been previously documented and they are thought to aid in the mobility of their host introns (Guha et al 2017). All species examined contained introns in mtLSU, and C. stipitata and C. leporina also contained introns in the mtSSU.…”

Section: Introns and Intergenic Spacer Regionsmentioning

confidence: 93%

Genomic insights into the mitochondria of 11 eastern North American species ofCladonia

Brigham

Allende

Shipley

et al. 2018

Mitochondrial DNA Part B

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Cladonia is among the most species-rich genera of lichens globally. Species in this lineage, commonly referred to as reindeer lichens, are ecologically important in numerous regions worldwide. In some locations, species of Cladonia can comprise the dominant groundcover, and are a major food source for caribou and other mammals. Additionally, many species are known to produce substances with antimicrobial properties or other characteristics with potentially important medical applications. This exceptional morphological and ecological variation contrasts sharply with the limited molecular divergence often observed among species. As a new resource to facilitate ongoing and future studies of these important species, we analyse here the sequences of 11 Cladonia mitochondrial genomes, including new mitochondrial genome assemblies and annotations representing nine species: C. apodocarpa, C. caroliniana, C. furcata, C. leporina, C. petrophila, C. peziziformis, C. robbinsii, C. stipitata, and C. subtenuis. These 11 genomes varied in size, intron content, and complement of tRNAs. Genes annotated within these mitochondrial genomes include 15 protein-coding genes, the large and small ribosomal subunits (mtLSU and mtSSU), and 23-26 tRNAs. All Cladonia mitochondrial genomes contained atp9, an important energy transport gene that has been lost evolutionarily in some lichen mycobiont mitochondria. Using a concatenated alignment of five mitochondrial genes (nad2, nad4, cox1, cox2, and cox3), a Bayesian phylogeny of relationships among species was inferred and was consistent with previously published phylogenetic relationships, highlighting the utility of these regions in reconstructing phylogenetic history.ARTICLE HISTORY

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The intron landscape of the mtDNA cytb gene among the Ascomycota: introns and intron-encoded open reading frames

Cited by 21 publications

References 85 publications

Genome streamlining via complete loss of introns has occurred multiple times in lichenized fungal mitochondria

Genome streamlining via complete loss of introns has occurred multiple times in lichenized fungal mitochondria

The mitochondrial genome of Endoconidiophora resinifera is intron rich

Genomic insights into the mitochondria of 11 eastern North American species ofCladonia

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