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Research: Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis
- Cristel G. Thomas,
- Wei Wang,
- Richard Jovelin,
- Rajarshi Ghosh,
- Tatiana Lomasko,
- Quang Trinh,
- Leonid Kruglyak,
- Lincoln D. Stein,
- and Asher D. Cutter
Genome Res. May 2015 25: 667-678; Published in Advance March 17, 2015, doi:10.1101/gr.187237.114
...-called “Tropical” circumglobal phylogeographic group (Supplemental Table 1), which excludes some genetically distinct strains also derived from low-latitude locations (Cutter et al. 2006; Félix et al. 2013). Polymorphisms in this Tropical sample showed a greater than fourfold enrichment on the chromosome arms...
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12 Drosophila Genomes/Letter: Genome-scale analysis of positionally relocated genes
- Arjun Bhutkar,
- Susan M. Russo,
- Temple F. Smith,
- and William M. Gelbart
Genome Res. December 2007 17: 1880-1887; Published in Advance November 7, 2007, doi:10.1101/gr.7062307
.... 39 : 715 – 720 . ↵ Coghlan, A. , Wolfe, K.H. ( 2002 ) Fourfold faster rate of rearrangement in nematodes than in Drosophila . Genome Res. 12 : 857 – 867 . ↵ Crosby, M.A. , Goodman, J.L. , Strelets, V.B. , Zhang, P. , Gelbart, W.M. ( 2007 ) FlyBase: Genomes by the dozen . Nucleic Acids Res. 35 : D486...
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Research: Fragile regions and not functional constraints predominate in shaping gene organization in the genus Drosophila
- Marcin von Grotthuss,
- Michael Ashburner,
- and José M. Ranz
Genome Res. August 2010 20: 1084-1096; Published in Advance July 2, 2010, doi:10.1101/gr.103713.109
...with the largest homologous collinear blocks (HCBs), since regions under no functional constraint would presumably have been disrupted. Likewise, highly rearranged s can show precisely how widespread breakpoint reuse is and to which genomic regions it is associated. The Drosophila is organized into six chromosomal...
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LETTER: Sex chromosome evolution: Molecular aspects of Y-chromosome degeneration in Drosophila
- Doris Bachtrog
Genome Res. October 2005 15: 1393-1401; Published in Advance September 16, 2005, doi:10.1101/gr.3543605
.... and Langley, C.H. 1989 . The population genetics of Drosophila transposable elements. Annu. Rev. Genet. 23 : 251 -287. ↵ Charlesworth, B., Sniegowski, P., and Stephan, W. 1994 . The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371 : 215 -220. ↵ Coghlan, A. and Wolfe, K. 2002 . Fourfold faster...
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ARTICLE: Extensive Exon Reshuffling Over Evolutionary Time Coupled to Trans-Splicing in Drosophila
- Mariano Labrador and
- Victor G. Corces
Genome Res. October 2003 13: 2220-2228; doi:10.1101/gr.1440703
...of the Drosophila melanogaster euchromatic sequence. Genome Biol. 3 : RESEARCH0079 . ↵ Coghlan, A. and Wolfe, K.H. 2002 . Fourfold faster rate of rearrangement in nematodes than in Drosophila . Genome Res. 12 : 857 -867. ↵ Dorn, R. and Krauss, V. 2003 . The modifier of mdg4 locus in Drosophila : Functional...
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Resource: RNA-seq analysis of the C. briggsae transcriptome
- Bora Uyar,
- Jeffrey S.C. Chu,
- Ismael A. Vergara,
- Shu Yi Chua,
- Martin R. Jones,
- Tammy Wong,
- David L. Baillie,
- and Nansheng Chen
Genome Res. August 2012 22: 1567-1580; Published in Advance July 6, 2012, doi:10.1101/gr.134601.111
.... The revised C. briggsae annotation represents a solid platform for comparative genomics analysis and evolutionary studies of Caenorhabditis species. [Supplemental material is available for this article.] The nematode Caenorhabditis briggsae is the most extensively studied sister species of the model organism...
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ARTICLE: The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint
- Cristian I. Castillo-Davis,
- Fyodor A. Kondrashov,
- Daniel L. Hartl,
- and Rob J. Kulathinal
Genome Res. May 2004 14: 802-811; doi:10.1101/gr.2195604
...by nonparametric bootstrap resampling with 1000 replicates). An accelerated mean rate of amino acid substitution is also seen in genes that are coexpressed in the ovary and uterus ( dN = 0.122, 95% CI [0.093, 0.151]; Fig. 2 ). Interestingly, genes that are thymus- or testis-specific seem to evolve faster ( dN = 0...
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Research: Accelerated rates of large-scale mutations in the presence of copper and nickel
- Frédéric J.J. Chain,
- Jullien M. Flynn,
- James K. Bull,
- and Melania E. Cristescu
Genome Res. January 2019 29: 64-73; Published in Advance November 28, 2018, doi:10.1101/gr.234724.118
...−6 per gene per generation), the presence of nickel and copper increased these rates fourfold. The realized mutation rate under selection was reduced to 0.4× that of control MA lines, providing evidence that CNVs contribute to mutational load. Our CNV breakpoint analysis revealed that nonhomologous...
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Research: Coordinated tissue-specific regulation of adjacent alternative 3′ splice sites in C. elegans
- James Matthew Ragle,
- Sol Katzman,
- Taylor F. Akers,
- Sergio Barberan-Soler,
- and Alan M. Zahler
Genome Res. July 2015 25: 982-994; Published in Advance April 28, 2015, doi:10.1101/gr.186783.114
...Gene Regulation, Stem Cells, and Cancer Program, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain Corresponding author: zahler@ucsc.edu ↵ 4 Present address: SomaGenics, Inc., Santa Cruz, CA 95060, USA Abstract Adjacent alternative 3′ splice sites...
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RESOURCE: genBlastA: Enabling BLAST to identify homologous gene sequences
- Rong She,
- Jeffrey S.-C. Chu,
- Ke Wang,
- Jian Pei,
- and Nansheng Chen
Genome Res. January 2009 19: 143-149; Published in Advance October 6, 2008, doi:10.1101/gr.082081.108
...biology and genomics . Nucleic Acids Res. 33 : D383 – D389 . ↵ Coghlan, A. , Wolfe, K.H. ( 2002 ) Fourfold faster rate of rearrangement in nematodes than in Drosophila . Genome Res. 12 : 857 – 867 . ↵ Consortium , 1998 Genome sequence of the nematode C. elegans : A platform for investigating biology...

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