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Research: Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus
- Eli Rodgers-Melnick,
- Shrinivasrao P. Mane,
- Palitha Dharmawardhana,
- Gancho T. Slavov,
- Oswald R. Crasta,
- Steven H. Strauss,
- Amy M. Brunner,
- and Stephen P. DiFazio
Genome Res. January 2012 22: 95-105; Published in Advance October 5, 2011, doi:10.1101/gr.125146.111
...compared gene duplicates resulting from a recent whole genome duplication to a set of tandemly duplicated genes in the model forest tree Populus trichocarpa . We used a combination of microarray expression analyses of a diverse set of tissues and functional annotation to assess factors related...
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Research: Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication
- Andrew J. Heidel,
- Hajara M. Lawal,
- Marius Felder,
- Christina Schilde,
- Nicholas R. Helps,
- Budi Tunggal,
- Francisco Rivero,
- Uwe John,
- Michael Schleicher,
- Ludwig Eichinger,
- Matthias Platzer,
- Angelika A. Noegel,
- Pauline Schaap,
- and Gernot Glöckner
Genome Res. November 2011 21: 1882-1891; Published in Advance July 14, 2011, doi:10.1101/gr.121137.111
...the relationship between genotypic and phenotypic change on a wide scale is complicated by the large number of loci involved and the range of phenotypic change. Comparative genomics is the tool of choice to define common gene sets and the first occurrence of genetic changes that may have caused phenotypic...
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Research: The motif composition of variable number tandem repeats impacts gene expression
- Tsung-Yu Lu,
- Paulina N. Smaruj,
- Geoffrey Fudenberg,
- Nicholas Mancuso,
- and Mark J.P. Chaisson
Genome Res. April 2023 33: 511-524; Published in Advance April 10, 2023, doi:10.1101/gr.276768.122
.... 2017; Narzisi et al. 2018). Furthermore, this formulation groups all occurrences of repetitive k-mers across input sequences by construction, which can be a particularly desirable property when studying the biological implication of VNTR motifs.By leveraging the advantages of PGG and dBG, genotyping...
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Research: Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
- Marta Farré,
- Jaebum Kim,
- Anastasia A. Proskuryakova,
- Yang Zhang,
- Anastasia I. Kulemzina,
- Qiye Li,
- Yang Zhou,
- Yingqi Xiong,
- Jennifer L. Johnson,
- Polina L. Perelman,
- Warren E. Johnson,
- Wesley C. Warren,
- Anna V. Kukekova,
- Guojie Zhang,
- Stephen J. O'Brien,
- Oliver A. Ryder,
- Alexander S. Graphodatsky,
- Jian Ma,
- Harris A. Lewin,
- and Denis M. Larkin
Genome Res. April 2019 29: 576-589; Published in Advance February 13, 2019, doi:10.1101/gr.239863.118
...S2). The EBRs were classified using our previously published method (Farré et al. 2016) utilizing a phylogenetic tree that was constructed on the basis of genomic data from this study (Fig. 1; Supplemental Fig. S1). A total of 1699 EBRs were assigned to all phylogenetic nodes, of which 78 and 33...
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Resource: Phenotypic diversity and genotypic flexibility of Burkholderia cenocepacia during long-term chronic infection of cystic fibrosis lungs
- Amy Huei-Yi Lee,
- Stephane Flibotte,
- Sunita Sinha,
- Adrianna Paiero,
- Rachel L. Ehrlich,
- Sergey Balashov,
- Garth D. Ehrlich,
- James E.A. Zlosnik,
- Joshua Chang Mell,
- and Corey Nislow
Genome Res. April 2017 27: 650-662; Published in Advance March 21, 2017, doi:10.1101/gr.213363.116
...The retrospective nature of this study constrained our ability to associate genotype with phenotype. Building phylogenetic trees of each RAPD type based on their specific core gene orthologs and mapping the phenotypes of the corresponding strains to each tree (Fig. 5; Supplemental Fig. S10) can, however, illuminate...
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Research: Polymerase theta-mediated end joining of replication-associated DNA breaks in C. elegans
- Sophie F. Roerink,
- Robin van Schendel,
- and Marcel Tijsterman
Genome Res. June 2014 24: 954-962; Published in Advance March 10, 2014, doi:10.1101/gr.170431.113
..., and their contribution to genome evolution largely unexplored. Here, through whole-genome sequencing of animal populations that were clonally propagated for more than 50 generations, we identify a distinct class of deletions that spontaneously accumulate in C. elegans strains lacking translesion synthesis (TLS...
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LETTER: Prokaryotic phylogenies inferred from protein structural domains
- Eric J. Deeds,
- Hooman Hennessey,
- and Eugene I. Shakhnovich
Genome Res. March 2005 15: 393-402; doi:10.1101/gr.3033805
.... The structural domains used in this work also have advantages when compared with structural information that has been used to infer phylogenies in previous studies ( Wolf et al. 1999 ; Lin and Gerstein 2000 ). These studies were based on the “fold” level of structural classification, which correspond to clusters...
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Letter: Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization
- Xiyin Wang,
- Haibao Tang,
- John E. Bowers,
- and Andrew H. Paterson
Genome Res. June 2009 19: 1026-1032; Published in Advance April 16, 2009, doi:10.1101/gr.087288.108
...produces massive duplicated blocks in plant genomes. Sharing appreciable sequence similarity, duplicated blocks may have been affected by illegitimate recombination. However, large-scale evaluation of illegitimate recombination in plant genomes has not been possible previously. Here, based on comparative...
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Research: Genome sequencing reveals complex speciation in the Drosophila simulans clade
- Daniel Garrigan,
- Sarah B. Kingan,
- Anthony J. Geneva,
- Peter Andolfatto,
- Andrew G. Clark,
- Kevin R. Thornton,
- and Daven C. Presgraves
Genome Res. August 2012 22: 1499-1511; Published in Advance April 13, 2012, doi:10.1101/gr.130922.111
...Center for Comparative and Population Genomics, Cornell University, Ithaca, New York 14853, USA; 4 Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California 92697, USA Abstract The three species of the Drosophila simulans clade...
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LETTER: Many or most genes in Arabidopsis transposed after the origin of the order Brassicales
- Michael Freeling,
- Eric Lyons,
- Brent Pedersen,
- Maqsudul Alam,
- Ray Ming,
- and Damon Lisch
Genome Res. December 2008 18: 1924-1937; Published in Advance October 3, 2008, doi:10.1101/gr.081026.108
...in the Brassicales. We used the CoGe comparative genomics system to perform and visualize multiple orthologous chromosomal alignments. Using this tool, we found large differences between different categories of genes. Ten of the gene families examined, including genes in most transcription factor families, exhibited...

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