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ARTICLE: A Phylogeny of Caenorhabditis Reveals Frequent Loss of Introns During Nematode Evolution
- Soochin Cho,
- Suk-Won Jin,
- Adam Cohen,
- and Ronald E. Ellis
Genome Res. July 2004 14: 1207-1220; doi:10.1101/gr.2639304
...A Phylogeny of Caenorhabditis Reveals Frequent Loss of Introns During Nematode Evolution Soochin Cho 1 , Suk-Won Jin 1 , Adam Cohen 1 , and Ronald E. Ellis 2 , 3 1 Department of Molecular, Cellular and Developmental Biology...
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LETTER: The chemoreceptor superfamily in the honey bee, Apis mellifera: Expansion of the odorant, but not gustatory, receptor family
- Hugh M. Robertson and
- Kevin W. Wanner
Genome Res. November 2006 16: 1395-1403; Published in Advance October 25, 2006, doi:10.1101/gr.5057506
..., and intron loss . Genome Res. 8 : 449 – 463 . Robertson, H.M. ( 2000 ) The large srh family of chemoreceptor genes in Caenorhabditis nematodes reveals processes of evolution involving large duplications and deletions and intron gains and losses . Genome Res. 10 : 192 – 203 . Robertson, H.M. , Thomas, J...
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Methods: Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization
- Jason S. Maydan,
- Stephane Flibotte,
- Mark L. Edgley,
- Joanne Lau,
- Rebecca R. Selzer,
- Todd A. Richmond,
- Nathan J. Pofahl,
- James H. Thomas,
- and Donald G. Moerman
Genome Res. March 2007 17: 337-347; Published in Advance January 31, 2007, doi:10.1101/gr.5690307
...chemoreceptor families. These four gene families are among those with the highest rates of birth–death evolution among Caenorhabditis species (J.H. Thomas, unpubl.). The correlation indicates that indel population diversity within the C. elegans species is related to long-term evolutionary stability in gene...
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LETTER: Genome Size Evolution in Pufferfish: A Comparative Analysis of Diodontid and Tetraodontid Pufferfish Genomes
- Daniel E. Neafsey and
- Stephen R. Palumbi
Genome Res. May 1, 2003 13: 821-830; doi:10.1101/gr.841703
...as Determinants of Genome Size The small size of introns and intergenic spaces in the F. rubripes has long been thought to have been generated by a higher rate of DNA loss in this fish compared with humans ( Brenner et al. 1993 ; Aparicio et al. 2002 ). This hypothesis is supported by our study. Although Graur et...
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REPORT: Classification of Transmembrane Protein Families in the Caenorhabditis elegans Genome and Identification of Human Orthologs
- Maido Remm and
- Erik Sonnhammer
Genome Res. November 1, 2000 10: 1679-1689; Published in Advance November 8, 2000, doi:10.1101/gr.GR-1491R
..., and intron loss. Genome Res. 8 : 449 – 463 . ↵ ( 2000 ) The large srh family of chemoreceptor genes in Caenorhabditis nematodes reveals processes of evolution involving large duplications and deletions and intron gains and losses. Genome Res. 10 : 192 – 203 , ibid . ↵ Schuler G.D. ( 1997 ) Pieces...
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LETTER: Millions of Years of Evolution Preserved: A Comprehensive Catalog of the Processed Pseudogenes in the Human Genome
- Zhaolei Zhang,
- Paul M. Harrison,
- Yin Liu,
- and Mark Gerstein
Genome Res. December 2003 13: 2541-2558; doi:10.1101/gr.1429003
...such as intron-absence, frame-disruption, polyadenylation, and truncation. This has enabled us to identify in recent genome drafts ∼8000 processed pseudogenes (distributed from http://pseudogene.org ). Overall, processed pseudogenes are very similar to their closest corresponding human gene, being 94% complete...
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LETTER: Evidence Suggesting That a Fifth of Annotated Caenorhabditis elegans Genes May Be Pseudogenes
- Andrew Mounsey,
- Petra Bauer,
- and Ian A. Hope
Genome Res. May 1, 2002 12: 770-775; Published in Advance April 12, 2002, doi:10.1101/gr208802
...in Caenorhabditis nematodes reveals processes of evolution involving large duplications and deletions and intron gains and losses. Genome Res. 10 : 192 – 203 . ↵ Schmid K.J. , Aquadro C.F. ( 2001 ) The evolutionary analysis of “orphans”. from the Drosophila identifies rapidly diverging and incorrectly annotated...
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LETTER: Genome-Wide Analysis of the Odorant-Binding Protein Gene Family in Drosophila melanogaster
- Daria S. Hekmat-Scafe,
- Charles R. Scafe,
- Aimee J. McKinney,
- and Mark A. Tanouye
Genome Res. September 1, 2002 12: 1357-1369; doi:10.1101/gr.239402
...). Duplication and Divergence of the Drosophila Obp Gene Family The genomic clustering, sequence conservation, and common intron insertion sites of the 51 Drosophila Obp genes summarized in Figure 5 reflect a complicated history of gene duplication and divergence for this large gene family. Expansion...
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Methods: Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations
- Gennifer E. Merrihew,
- Colleen Davis,
- Brent Ewing,
- Gary Williams,
- Lukas Käll,
- Barbara E. Frewen,
- William Stafford Noble,
- Phil Green,
- James H. Thomas,
- and Michael J. MacCoss
Genome Res. October 2008 18: 1660-1669; Published in Advance July 24, 2008, doi:10.1101/gr.077644.108
...annotation of the putative seven-pass chemoreceptor family revealed a substantial number of probable new genes and correction of a large number of gene predictions ( Robertson 2000 , 2001 ). Short single-exon genes also present problems for prediction and, lacking strong support from experimental evidence...
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RESOURCE: WormBase as an Integrated Platform for the C. elegans ORFeome
- Nansheng Chen,
- Daniel Lawson,
- Keith Bradnam,
- Todd W. Harris,
- and Lincoln D. Stein
Genome Res. October 15, 2004 14: 2155-2161; doi:10.1101/gr.2521304
...-scale protein expression. Nat. Genet. 34 : 35 -41. ↵ Robertson, H.M. 2000 . The large srh family of chemoreceptor genes in Caenorhabditis nematodes reveals processes of evolution involving large duplications and deletions and intron gains and losses. Genome Res. 10 : 192 -203. ↵ ____. 2001 . Updating the str...

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