Intron evolution in <i>Neurospora</i>: the role of mutational bias and selection

Sun, Yu; Whittle, Carrie-Ann; Corcoran, Pádraic; Johannesson, Hanna

doi:10.1101/gr.175653.114

Cited by 9 publications

(7 citation statements)

References 84 publications

(124 reference statements)

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“…Thirteen positions show complex presence-absence patterns and a single position represents a single absence in a given species ( Fig 3E ). These results suggest a balanced number of putative intron gains and losses, consistent with previous intron gain and loss analyses in fungi [ 6 , 9 , 15 , 28 , 29 ].…”

Section: Resultssupporting

confidence: 90%

Novel Introner-Like Elements in fungi Are Involved in Parallel Gains of Spliceosomal Introns

et al. 2015

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Spliceosomal introns are key components of the eukaryotic gene structure. Although they contributed to the emergence of eukaryotes, their origin remains elusive. In fungi, they might originate from the multiplication of invasive introns named Introner-Like Elements (ILEs). However, so far ILEs have been observed in six fungal species only, including Fulvia fulva and Dothistroma septosporum (Dothideomycetes), arguing against ILE insertion as a general mechanism for intron gain. Here, we identified novel ILEs in eight additional fungal species that are phylogenetically related to F. fulva and D. septosporum using PCR amplification with primers derived from previously identified ILEs. The ILE content appeared unique to each species, suggesting independent multiplication events. Interestingly, we identified four genes each containing two gained ILEs. By analysing intron positions in orthologues of these four genes in Ascomycota, we found that three ILEs had inserted within a 15 bp window that contains regular spliceosomal introns in other fungal species. These three positions are not the result of intron sliding because ILEs are newly gained introns. Furthermore, the alternative hypothesis of an inferred ancestral gain followed by independent losses contradicts the observed degeneration of ILEs. These observations clearly indicate three parallel intron gains in four genes that were randomly identified. Our findings suggest that parallel intron gain is a phenomenon that has been highly underestimated in ILE-containing fungi, and likely in the whole fungal kingdom.

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Section: Resultssupporting

confidence: 90%

Novel Introner-Like Elements in fungi Are Involved in Parallel Gains of Spliceosomal Introns

et al. 2015

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“…We measured very fast rates of intron gain and loss at IPAP loci in Z. tritici , which have been suggested in Neurospora tetrasperma and Daphnia ( Li etal. 2014 ; Sun etal. 2015 ).…”

Section: Discussionmentioning

confidence: 99%

Origin and Spread of Spliceosomal Introns: Insights from the Fungal Clade Zymoseptoria

Macielog

Hao

2017

Genome Biology and Evolution

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Spliceosomal introns are a key feature of eukaryote genome architecture and have been proposed to originate from selfish group II introns from an endosymbiotic bacterium, that is, the ancestor of mitochondria. However, the mechanisms underlying the wide spread of spliceosomal introns across eukaryotic genomes have been obscure. In this study, we characterize the dynamic evolution of spliceosomal introns in the fungal genus Zymoseptoria at different evolutionary scales, that is, within a genome, among conspecific strains within species, and between different species. Within the genome, spliceosomal introns can proliferate in unrelated genes and intergenic regions. Among conspecific strains, spliceosomal introns undergo rapid turnover (gains and losses) and frequent sequence exchange between geographically distinct strains. Furthermore, spliceosomal introns could undergo introgression between distinct species, which can further promote intron invasion and proliferation. The dynamic invasion and proliferation processes of spliceosomal introns resemble the life cycles of mobile selfish (group I/II) introns, and these intron movements, at least in part, account for the dramatic processes of intron gain and intron loss during eukaryotic evolution.

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“…Paired-end library preparation and whole-genome sequencing was carried out at BGI HongKong using Illumina HiSeq 2000, which generated an average of 1.5 Gbp of paired 90-bp reads per strain (an average of 1.4 Gbp of sequenced reads after quality filtering) and an average coverage per strain of between 25 and 45× (Supplemental Table 1). The quality filtering of the FASTQ files was performed by BGI HongKong as described in Sun et al (2015). We performed both reference and de novo genome assemblies of the reads.…”

Section: Methodsmentioning

confidence: 99%

Introgression maintains the genetic integrity of the mating-type determining chromosome of the fungus Neurospora tetrasperma

et al. 2016

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Genome evolution is driven by a complex interplay of factors, including selection, recombination, and introgression. The regions determining sexual identity are particularly dynamic parts of eukaryotic genomes that are prone to molecular degeneration associated with suppressed recombination. In the fungus Neurospora tetrasperma, it has been proposed that this molecular degeneration is counteracted by the introgression of nondegenerated DNA from closely related species. In this study, we used comparative and population genomic analyses of 92 genomes from eight phylogenetically and reproductively isolated lineages of N. tetrasperma, and its three closest relatives, to investigate the factors shaping the evolutionary history of the genomes. We found that suppressed recombination extends across at least 6 Mbp (∼63%) of the mating-type (mat) chromosome in N. tetrasperma and is associated with decreased genetic diversity, which is likely the result primarily of selection at linked sites. Furthermore, analyses of molecular evolution revealed an increased mutational load in this region, relative to recombining regions. However, comparative genomic and phylogenetic analyses indicate that the mat chromosomes are temporarily regenerated via introgression from sister species; six of eight lineages show introgression into one of their mat chromosomes, with multiple Neurospora species acting as donors. The introgressed tracts have been fixed within lineages, suggesting that they confer an adaptive advantage in natural populations, and our analyses support the presence of selective sweeps in at least one lineage. Thus, these data strongly support the previously hypothesized role of introgression as a mechanism for the maintenance of mating-type determining chromosomal regions.

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Intron evolution in Neurospora: the role of mutational bias and selection

Cited by 9 publications

References 84 publications

Novel Introner-Like Elements in fungi Are Involved in Parallel Gains of Spliceosomal Introns

Novel Introner-Like Elements in fungi Are Involved in Parallel Gains of Spliceosomal Introns

Origin and Spread of Spliceosomal Introns: Insights from the Fungal Clade Zymoseptoria

Introgression maintains the genetic integrity of the mating-type determining chromosome of the fungus Neurospora tetrasperma

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