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Research: Introgression maintains the genetic integrity of the mating-type determining chromosome of the fungus Neurospora tetrasperma
- Pádraic Corcoran,
- Jennifer L. Anderson,
- David J. Jacobson,
- Yu Sun,
- Peixiang Ni,
- Martin Lascoux,
- and Hanna Johannesson
Genome Res. April 2016 26: 486-498; Published in Advance February 18, 2016, doi:10.1101/gr.197244.115
...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...
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LETTER: Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data
- Austen R.D. Ganley and
- Takehiko Kobayashi
Genome Res. February 2007 17: 184-191; Published in Advance January 2, 2007, doi:10.1101/gr.5457707
...standard procedures ( Sambrook and Russell 2001 ) and rDNA bands were detected using a probe from a conserved region of the LSU derived from S. cerevisiae . Nucleotide diversity Sequences of the polyubiquitin repeat (poly-u repeats) arrays (after removal of introns; monomer ubiquitin sequences were...
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Research: Rates and spectra of de novo structural mutations in Chlamydomonas reinhardtii
- Eugenio López-Cortegano,
- Rory J. Craig,
- Jobran Chebib,
- Eniolaye J. Balogun,
- and Peter D. Keightley
Genome Res. January 2023 33: 45-60; Published in Advance December 12, 2022, doi:10.1101/gr.276957.122
...to the independent underlying mechanisms of mutation compared with other SMs. Approximately 22% of TRMs occurred in microsatellites (defined as tandem repeats with monomers <10 bp), and most of the remainder occurred in satellite DNA. The C. reinhardtii contains many introns featuring tandem repeats (Craig et al...
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Research: Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control
- Daniel E. Neafsey,
- Bridget M. Barker,
- Thomas J. Sharpton,
- Jason E. Stajich,
- Daniel J. Park,
- Emily Whiston,
- Chiung-Yu Hung,
- Cody McMahan,
- Jared White,
- Sean Sykes,
- David Heiman,
- Sarah Young,
- Qiandong Zeng,
- Amr Abouelleil,
- Lynne Aftuck,
- Daniel Bessette,
- Adam Brown,
- Michael FitzGerald,
- Annie Lui,
- J. Pendexter Macdonald,
- Margaret Priest,
- Marc J. Orbach,
- John N. Galgiani,
- Theo N. Kirkland,
- Garry T. Cole,
- Bruce W. Birren,
- Matthew R. Henn,
- John W. Taylor,
- and Steven D. Rounsley
Genome Res. July 2010 20: 938-946; Published in Advance June 1, 2010, doi:10.1101/gr.103911.109
...are the most biased, with a 16-fold higher mutation rate in repeats. In Neurospora and several other fungi, CpA dinucleotides are the preferred mutational target of RIP, but in Coccidioides we see a pronounced effect onCpGdinucleotides—a context that has also been reported in other fungi (Galagan and Selker...
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Letter: Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression
- Jesse D. Hollister and
- Brandon S. Gaut
Genome Res. August 2009 19: 1419-1428; Published in Advance May 28, 2009, doi:10.1101/gr.091678.109
...to ensure that our data set contained only TEs belonging to well-defined, multicopy families (see Methods). Consistent with prior investigations (Wright et al. 2003), 85.7% of the TEs in our data set occupied intergenic regions; i.e., they were not within exons, introns, or untranslated regions (UTRs...
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Letter: Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives
- Thomas J. Sharpton,
- Jason E. Stajich,
- Steven D. Rounsley,
- Malcolm J. Gardner,
- Jennifer R. Wortman,
- Vinita S. Jordar,
- Rama Maiti,
- Chinnappa D. Kodira,
- Daniel E. Neafsey,
- Qiandong Zeng,
- Chiung-Yu Hung,
- Cody McMahan,
- Anna Muszewska,
- Marcin Grynberg,
- M. Alejandra Mandel,
- Ellen M. Kellner,
- Bridget M. Barker,
- John N. Galgiani,
- Marc J. Orbach,
- Theo N. Kirkland,
- Garry T. Cole,
- Matthew R. Henn,
- Bruce W. Birren,
- and John W. Taylor
Genome Res. October 2009 19: 1722-1731; Published in Advance August 28, 2009, doi:10.1101/gr.087551.108
...1441 1824 1433 1305 Mean intron length 101 85 98 143 GC% 46 46.6 48.2 42.8 GC% coding 49.9 49.7 50.9 49.8 GC% noncoding 46.2 45.8 46.6 43.7 Mean intron number per gene 2.3 2.3 2 2.5 Mean exon number per gene 3.4 3.3 3 2.5 Table 2. Distribution of repetitive genomic content Genome Total repetitive...
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LETTER: Evolutionarily conserved genes preferentially accumulate introns
- Liran Carmel,
- Igor B. Rogozin,
- Yuri I. Wolf,
- and Eugene V. Koonin
Genome Res. July 2007 17: 1045-1050; Published in Advance May 10, 2007, doi:10.1101/gr.5978207
...evolution includes a neutral component, which is manifest in the positive correlation between the gain and loss rates and a selection-driven component as reflected in the links between intron gain and loss and sequence evolution. The increased intron gain and decreased intron loss in evolutionarily...
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LETTER: Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes
- Schraga Schwartz,
- João Silva,
- David Burstein,
- Tal Pupko,
- Eduardo Eyras,
- and Gil Ast
Genome Res. January 2008 18: 88-103; Published in Advance November 21, 2007, doi:10.1101/gr.6818908
...splicing signals underwent extensive changes during evolution, in parallel with considerable changes in terms of exon-intron architecture and domain structure of the splicing regulators. These changes were presumably shaped by the lifestyle of the organism, selective pressure on maintaining multi-intron...
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PERSPECTIVE: Genomics of the fungal kingdom: Insights into eukaryotic biology
- James E. Galagan,
- Matthew R. Henn,
- Li-Jun Ma,
- Christina A. Cuomo,
- and Bruce Birren
Genome Res. December 2005 15: 1620-1631; doi:10.1101/gr.3767105
...5-6 introns per gene in basidiomycetes such as Cryptococcus neoformans ( Loftus et al. 2005 ), to one to two introns per gene on average for many recently sequenced ascomycetes (e.g., Neurospora, Magnaporthe ) ( Galagan et al. 2003 ; Borkovich et al. 2004 ; Dean et al. 2005 ) to &lt;300 introns...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
.... Original annotations for TEs are indicated in parentheses. Promoters include [−1 kb; +100 bp] around the transcription start site; Terminators include [−100 bp; +1 kb] around the transcription termination site; Genes include both exons and introns. MBD1 peaks were shuffled in the to generate a random set...

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