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Research: Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
- Nikolaos Vakirlis and
- Anne Kupczok
Genome Res. June 2024 34: 888-903; Published in Advance July 8, 2024, doi:10.1101/gr.278977.124
...; and they are more aggregation-prone, have a higher biosynthetic cost, and a higher isoelectric point (the latter was also observed for de novo genes in yeast and fly) (Blevins et al. 2021; Montañés et al. 2023). All these differences hold when considering each taxonomic class individually (Supplemental Fig. S8...
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Methods: OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
- Li Li,
- Christian J. Stoeckert, Jr.,
- and David S. Roos
Genome Res. September 2003 13: 2178-2189; doi:10.1101/gr.1224503
...window Table 1. Comparison of Ortholog Groups Identified by OrthoMCL vs. INPARANOID OrthoMCL Performance on a Three-Species Data Set (Yeast, Worm, Fly) A serious limitation to the general application of INPARANOID for comparative genomics applications is that this algorithm can only be employed...
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Methods: Comprehensive Analysis of Orthologous Protein Domains Using the HOPS Database
- Christian E.V. Storm and
- Erik L.L. Sonnhammer
Genome Res. October 2003 13: 2353-2362; doi:10.1101/gr1305203
.... Genome Res. 6 : 846 -857. ↵ Mushegian, A.R., Garey, J.R., Martin, J., and Liu, L.X. 1998 . Large-scale taxonomic profiling of eukaryotic model organisms: A comparison of orthologous proteins encoded by the human, fly, nematode, and yeast s. Genome Res. 8 : 590 -598. ↵ Page, R.D.M. 1994 . Maps between...
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ARTICLE: Large-Scale Comparison of Fungal Sequence Information: Mechanisms of Innovation in Neurospora crassa and Gene Loss in Saccharomyces cerevisiae
- Edward L. Braun,
- Aaron L. Halpern,
- Mary Anne Nelson,
- and Donald O. Natvig
Genome Res. April 1, 2000 10: 416-430; doi:10.1101/gr.10.4.416
...analyses of the ascomycete yeast S. cerevisiae have been nearly as successful in finding homologs in other organisms, with standard homology searches resulting in the identification of homologs for &gt;60% of the genes ( Koonin et al. 1994 ; Goffeau et al. 1996 ). However, genomic analysis of other...
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Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
...only one gene, CG43744, which encodes an RNA-binding protein that binds to the EDEN element and mediates maternal mRNA translational repression (FlyBase) (Gramates et al. 2022). This gene shows a dS value superior to 0.6 in all lines except FI and DK. We also looked at the polymorphism of established...
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LETTER: Coelomata and Not Ecdysozoa: Evidence From Genome-Wide Phylogenetic Analysis
- Yuri I. Wolf,
- Igor B. Rogozin,
- and Eugene V. Koonin
Genome Res. January 2004 14: 29-36; doi:10.1101/gr.1347404
...analyses of Noctuoidea (Insecta: Lepidoptera). Syst. Biol. 49 : 202 -224. ↵ Mushegian, A.R., Garey, J.R., Martin, J., and Liu, L.X. 1998 . Large-scale taxonomic profiling of eukaryotic model organisms: A comparison of orthologous proteins encoded by the human, fly, nematode, and yeast s. Genome Res. 8...
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LETTER: The Basic Helix-Loop-Helix Protein Family: Comparative Genomics and Phylogenetic Analysis
- Valérie Ledent and
- Michel Vervoort
Genome Res. May 1, 2001 11: 754-770; doi:10.1101/gr.177001
...and animals. In addition, we identified two bHLH motifs present only in yeast, and four that are present only in plants; however, the latter number is certainly an underestimate. Most animal families (35/38) comprise fly, nematode, and vertebrate genes, suggesting that their common ancestor, which lived...
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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
...taxonomic profiling of eukaryotic model organisms: A comparison of orthologous proteins encoded by the human, fly, nematode, and yeast s. Genome Res. 8 : 590 – 598 . ↵ Park J. , Karplus K. , Barrett C. , Hughey R. , Haussler D. , Hubbard T. , Chothia C. ( 1998 ) Sequence comparisons using multiple sequences...
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ARTICLE: Fourfold Faster Rate of Genome Rearrangement in Nematodes Than in Drosophila
- Avril Coghlan and
- Kenneth H. Wolfe
Genome Res. June 1, 2002 12: 857-867; doi:10.1101/gr.172702
...pair of congeneric eukaryotes. Such a big sample has a high power for detecting -wide trends. For example, the breakpoints of reciprocal translocations and inversions are frequently near repetitive DNA. This has been observed in bacteria ( Romero et al. 1999 ), yeast ( Fischer et al. 2000 ), insects...
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ARTICLE: Novel Protein Domains and Repeats in Drosophila melanogaster: Insights into Structure, Function, and Evolution
- Chris P. Ponting,
- Richard Mott,
- Peer Bork,
- and Richard R. Copley
Genome Res. December 1, 2001 11: 1996-2008; Published in Advance November 12, 2001, doi:10.1101/gr.198701
.... For this study the complete set of predicted proteins (the ‘proteome’) of the fruit fly Drosophila melanogaster ( Adams et al. 2000 ) was targeted for analysis. The s of model organisms, including Drosophila , promise valuable insights into biology that extend far beyond narrow phyletic bounds. Genes...

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