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Research: Intron evolution in Neurospora: the role of mutational bias and selection
- Yu Sun,
- Carrie A. Whittle,
- Pádraic Corcoran,
- and Hanna Johannesson
Genome Res. January 2015 25: 100-110; Published in Advance October 23, 2014, doi:10.1101/gr.175653.114
...is likely to have been intron-rich (Csuros et al. 2011) and that intron losses have dominated inmany eukaryotic species; however, a few bursts of substantial intron gains have taken place, for example, during the origin ofmetazoan and land plants (Csuros et al. 2011; Rogozin et al. 2012). Among all...
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Resource: Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms
- José Carlos Montañés,
- Marta Huertas,
- Simone G. Moro,
- William R. Blevins,
- Mercè Carmona,
- José Ayté,
- Elena Hidalgo,
- and M. Mar Albà
Genome Res. June 2022 32: 1215-1227; Published in Advance May 26, 2022, doi:10.1101/gr.276516.121
...RNA to the fission yeast S. pombe, an intron-rich unicellular eukaryote that has become a very useful model to study splicing (Yan et al. 2015; Fair and Pleiss 2017). Our strategy was based on obtaining a very high coverage of the transcriptome to uncover alternative splice forms and lowly expressed transcripts. We...
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Research: Small chromosomal regions position themselves autonomously according to their chromatin class
- Harmen J.G. van de Werken,
- Josien C. Haan,
- Yana Feodorova,
- Dominika Bijos,
- An Weuts,
- Koen Theunis,
- Sjoerd J.B. Holwerda,
- Wouter Meuleman,
- Ludo Pagie,
- Katharina Thanisch,
- Parveen Kumar,
- Heinrich Leonhardt,
- Peter Marynen,
- Bas van Steensel,
- Thierry Voet,
- Wouter de Laat,
- Irina Solovei,
- and Boris Joffe
Genome Res. June 2017 27: 922-933; Published in Advance March 24, 2017, doi:10.1101/gr.213751.116
....6–97.8 Mb) and comprises three structurally different segments: (1) a gene-rich segment encompassing 19 protein coding genes (∼2.1 Mb); (2) a gene-poor segment (∼0.6 Mb) including the PTBP2 gene and part of the intron-rich gene DPYD; and (3) a gene desert (∼1.5 Mb) (Figs. 1, 2A). The three HAC segments also...
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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...
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LETTER: Very little intron loss/gain in Plasmodium: Intron loss/gain mutation rates and intron number
- Scott William Roy and
- Daniel L. Hartl
Genome Res. June 2006 16: 750-756; Published in Advance May 15, 2006, doi:10.1101/gr.4845406
...lamblia ( Venter et al. 2001 ; Aparicio et al. 2002 ; Nixon et al. 2002 ), and often even within eukaryotic groups. Traditional selection-based explanations ( Doolittle and Sapienza 1980 ; Gilbert 1987 ; Lynch 2002 ) do not predict recent findings of intron-rich early eukaryotes ( Fedorov et al. 2002...
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LETTER: Three distinct modes of intron dynamics in the evolution of eukaryotes
- Liran Carmel,
- Yuri I. Wolf,
- Igor B. Rogozin,
- and Eugene V. Koonin
Genome Res. July 2007 17: 1034-1044; Published in Advance May 10, 2007, doi:10.1101/gr.6438607
...level are presented in the accompanying paper ( Carmel et al. 2007 ). We demonstrate that ancestral eukaryotic forms were intron-rich and show that evolution of eukaryotic genes involved numerous gains and losses of introns, with losses being somewhat more common. We identify three distinct modalities...
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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
...sequenced to date ( Mourier and Jeffares 2003 ). According to this 5′ positional bias, introns are evenly distributed within the coding sequence of genes in intron-rich organisms, but are biased toward the 5′ ends of genes in intron-poor organisms. It has been proposed that this bias may have arisen...
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LETTER: Evolution of protein domain promiscuity in eukaryotes
- Malay Kumar Basu,
- Liran Carmel,
- Igor B. Rogozin,
- and Eugene V. Koonin
Genome Res. March 2008 18: 449-461; Published in Advance January 29, 2008, doi:10.1101/gr.6943508
...likelihood methods of evolutionary reconstruction yield substantially more intron-rich ancestors than parsimony methods ( Csuros 2005 ; Nguyen et al. 2005 ; Rogozin et al. 2005 ; Carmel et al. 2007 ). Thus, the parsimony estimates give the low bound of domain promiscuity in ancestral eukaryotic forms...
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LETTER: Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution
- Scott William Roy and
- David Penny
Genome Res. October 2006 16: 1270-1275; Published in Advance September 8, 2006, doi:10.1101/gr.5410606
...with the distantly related apicomplexan Theileria parva , whereas only 18.2% of introns in the more intron-rich T. parva are shared with P. falciparum . Comparison of 3305 pairs of orthologous genes between T. parva and Theileria annulata showed that 7089/7111 (99.7%) introns in conserved regions are shared...

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