Internally Symmetrical Stwintrons and Related Canonical Introns in Hypoxylaceae Species

Fekete, Erzsébet; Pénzes, Fruzsina; Scazzocchio, Claudio; Flipphi, Michel; Karaffa, Levente

doi:10.3390/jof7090710

Cited by 3 publications

(22 citation statements)

References 73 publications

(126 reference statements)

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“…Some algal Introners appear to be MITE TEs based on observation of target site duplications (TSDs), terminal inverted repeats (TIRs), and biased insertion into nucleosome linker regions ( 12 ). In contrast, fungal Introners lack TSDs and TIRs and are highly biased towards gene regions (insertion into nucleosome linkers was not studied), and have been interpreted as novel RNA-based elements that propagate through reverse-splicing of RNA copies of spliced Introners ( 14, 16 ).…”

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…Introners have only been described in 5 eukaryotic lineages, and even among these cases, the precise molecular mechanisms remain obscure. Some Introner families show clear signatures of DNA TEs ( 12, 15 ) while others may be novel RNA-propagated elements ( 14, 16 ). More importantly, determining the extent to which introners are a primary source of ongoing intron gain is essential for interpreting the evolution of genome structure and function, and requires a broad survey that spans the eukaryotic tree of life.…”

Section: Introductionmentioning

confidence: 99%

“…In addition to these ad hoc intron creation mechanisms, the intron-generating transposable elements (TEs) known as Introners represent a mechanism that could explain the high and episodic frequency and genome-wide scale of intron gains observed across eukaryotic lineages. These poorly understood TEs create introns de novo through insertion into exons (12)(13)(14)(15)(16)(17). Introners have only been described in 5 eukaryotic lineages, and even among these cases, the precise molecular mechanisms remain obscure.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Transposable elements drive intron gain in diverse eukaryotes

Gozashti

Roy

Thornlow

et al. 2022

Preprint

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There is massive variation in intron numbers across eukaryotic genomes, yet the major drivers of intron content during evolution remain elusive. Rapid intron loss and gain in some lineages contrasts with long term evolutionary stasis in others. Episodic intron gain could be explained by recently discovered specialized transposons called Introners, but so far introners are only known from a handful of species. Here, we performed a systematic search across 3,325 eukaryotic genomes and identified 27,563 Introner-derived introns in 175 genomes (5.2%). Species with introners span remarkable phylogenetic diversity, from animals to basal protists, representing lineages whose last common ancestor dates to over 1.7 billion years ago. Marine organisms were 6.5 times more likely to contain Introners than their terrestrial counterparts. Introners exhibit mechanistic diversity but most are consistent with DNA transposition, indicating that Introners have evolved convergently hundreds of times from autonomous transposable elements. Transposable elements and marine taxa are associated with high rates of horizontal gene transfer, suggesting that this combination of factors may explain the punctuated and biased diversity of species containing Introners. More generally our data suggest that Introners may explain the episodic nature of intron gain across the eukaryotic tree of life. These results illuminate the major source of ongoing intron creation in eukaryotic genomes.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Transposable elements drive intron gain in diverse eukaryotes

Gozashti

Roy

Thornlow

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…In addition to these ad hoc intron creation mechanisms, the intron-generating transposable elements (TEs) known as Introners represent a mechanism that could explain the high and episodic frequency and genome-wide scale of intron gains observed across eukaryotic lineages. These poorly understood TEs create introns de novo through insertion into exons ( 12 – 17 ). Introners have only been described in five eukaryotic lineages, and even among these cases, the precise molecular mechanisms remain obscure.…”

mentioning

confidence: 99%

Transposable elements drive intron gain in diverse eukaryotes

Gozashti

Roy

Thornlow

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

There is massive variation in intron numbers across eukaryotic genomes, yet the major drivers of intron content during evolution remain elusive. Rapid intron loss and gain in some lineages contrast with long-term evolutionary stasis in others. Episodic intron gain could be explained by recently discovered specialized transposons called Introners, but so far Introners are only known from a handful of species. Here, we performed a systematic search across 3,325 eukaryotic genomes and identified 27,563 Introner-derived introns in 175 genomes (5.2%). Species with Introners span remarkable phylogenetic diversity, from animals to basal protists, representing lineages whose last common ancestor dates to over 1.7 billion years ago. Aquatic organisms were 6.5 times more likely to contain Introners than terrestrial organisms. Introners exhibit mechanistic diversity but most are consistent with DNA transposition, indicating that Introners have evolved convergently hundreds of times from nonautonomous transposable elements. Transposable elements and aquatic taxa are associated with high rates of horizontal gene transfer, suggesting that this combination of factors may explain the punctuated and biased diversity of species containing Introners. More generally, our data suggest that Introners may explain the episodic nature of intron gain across the eukaryotic tree of life. These results illuminate the major source of ongoing intron creation in eukaryotic genomes.

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Unique and Repeated Stwintrons (Spliceosomal Twin Introns) in the Hypoxylaceae

Pénzes

Fekete

Ág-Rácz

et al. 2022

JoF

Self Cite

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Introns are usually non-coding sequences interrupting open reading frames in pre-mRNAs [D1,2]. Stwintrons are nested spliceosomal introns, where an internal intron splits a second donor sequence into two consecutive splicing reactions leading to mature mRNA. In Hypoxylon sp. CO27-5, 36 highly sequence-similar [D1,2] stwintrons are extant (sister stwintrons). An additional 81 [D1,2] sequence-unrelated stwintrons are described here. Most of them are located at conserved gene positions rooted deep in the Hypoxylaceae. Absence of exonic sequence bias at the exon–stwintron junctions and a very similar phase distribution were noted for both groups. The presence of an underlying sequence symmetry in all 117 stwintrons was striking. This symmetry, more pronounced near the termini of most of the full-length sister stwintrons, may lead to a secondary structure that brings into close proximity the most distal splice sites, the donor of the internal and the acceptor of the external intron. The Hypoxylon stwintrons were overwhelmingly excised by consecutive splicing reactions precisely removing the whole intervening sequence, whereas one excision involving the distal splice sites led to a frameshift. Alternative (mis)splicing took place for both sister and uniquely occurring stwintrons. The extraordinary symmetry of the sister stwintrons thus seems dispensable for the infrequent, direct utilisation of the distal splice sites.

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Internally Symmetrical Stwintrons and Related Canonical Introns in Hypoxylaceae Species

Cited by 3 publications

References 73 publications

Transposable elements drive intron gain in diverse eukaryotes

Transposable elements drive intron gain in diverse eukaryotes

Transposable elements drive intron gain in diverse eukaryotes

Unique and Repeated Stwintrons (Spliceosomal Twin Introns) in the Hypoxylaceae

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