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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...prior to the WGD. Analysis of individual TE insertions, however, revealed enrichment of TE-CREs originating from WGD-associated TE activity, particularly for the DTT (Tc1-Mariner) DNA elements. Furthermore, coexpression analyses supported the presence of TE-driven gene regulatory network evolution...
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Research: An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication
- Elise Parey,
- Alexandra Louis,
- Jérôme Montfort,
- Yann Guiguen,
- Hugues Roest Crollius,
- and Camille Berthelot
Genome Res. September 2022 32: 1685-1697; Published in Advance August 12, 2022, doi:10.1101/gr.276953.122
...a fundamental gap in the interpretation of their functional evolution. As a result of the whole- duplication, identifying orthologous and paralogous genomic regions across teleosts is challenging, hindering -wide investigations into their polyploid history. Here, we combine tailored gene phylogeny methodology...
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Resource: Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci
- Jonathan M. Mudge,
- Irwin Jungreis,
- Toby Hunt,
- Jose Manuel Gonzalez,
- James C. Wright,
- Mike Kay,
- Claire Davidson,
- Stephen Fitzgerald,
- Ruth Seal,
- Susan Tweedie,
- Liang He,
- Robert M. Waterhouse,
- Yue Li,
- Elspeth Bruford,
- Jyoti S. Choudhary,
- Adam Frankish,
- and Manolis Kellis
Genome Res. December 2019 29: 2073-2087; Published in Advance September 19, 2019, doi:10.1101/gr.246462.118
...predate vertebrate evolution, although orthology is presumptive owing to lack of synteny beyond coelacanth. The gene has at best weak expression data in all species examined, but all but one of the mouse splice junctions is supported by minimal ENCODE RNA-seq data from pooled sources, and all splice sites...
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Resource: Alignathon: a competitive assessment of whole-genome alignment methods
- Dent Earl,
- Ngan Nguyen,
- Glenn Hickey,
- Robert S. Harris,
- Stephen Fitzgerald,
- Kathryn Beal,
- Igor Seledtsov,
- Vladimir Molodtsov,
- Brian J. Raney,
- Hiram Clawson,
- Jaebum Kim,
- Carsten Kemena,
- Jia-Ming Chang,
- Ionas Erb,
- Alexander Poliakov,
- Minmei Hou,
- Javier Herrero,
- William James Kent,
- Victor Solovyev,
- Aaron E. Darling,
- Jian Ma,
- Cedric Notredame,
- Michael Brudno,
- Inna Dubchak,
- David Haussler,
- and Benedict Paten
Genome Res. December 2014 24: 2077-2089; Published in Advance October 1, 2014, doi:10.1101/gr.174920.114
...-like’’ s, i.e., haploid s. EVOLVER models DNA sequence evolution with sequence annotations; a gene model; a base-level evolutionary constraint model; chromosome evolution, including inter- and intrachromosomal rearrangements; tandem and segmental duplications; and mobile element insertions, movements...
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Resource: Automated identification of conserved synteny after whole-genome duplication
- Julian M. Catchen,
- John S. Conery,
- and John H. Postlethwait
Genome Res. August 2009 19: 1497-1505; Published in Advance May 22, 2009, doi:10.1101/gr.090480.108
...for the investigation of individual gene families in multiple lineages and can detect chromosomal inversions and translocations as well as ohnologs (paralogs derived by whole-genome duplication) gone missing. To demonstrate the utility of the system, we present a case study of gene family evolution, investigating...
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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
...and gene expression evolution, our work demonstrated that lineage-specific regulatory elements colocalized with gross chromosome rearrangements may have provided valuable functional modifications that helped to shape ruminant evolution.The extent that chromosome rearrangements provide a substrate...
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Resource: Multiple whole-genome alignments without a reference organism
- Inna Dubchak,
- Alexander Poliakov,
- Andrey Kislyuk,
- and Michael Brudno
Genome Res. April 2009 19: 682-689; Published in Advance January 28, 2009, doi:10.1101/gr.081778.108
..., and Centre for Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5R 3G4, Canada Abstract Multiple sequence alignments have become one of the most commonly used resources in genomics research. Most algorithms for multiple alignment of whole genomes rely either...
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Research: Allelic diversification after transposable element exaptation promoted gsdf as the master sex determining gene of sablefish
- Amaury Herpin,
- Manfred Schartl,
- Alexandra Depincé,
- Yann Guiguen,
- Julien Bobe,
- Aurélie Hua-Van,
- Edward S. Hayman,
- Anna Octavera,
- Goro Yoshizaki,
- Krista M. Nichols,
- Giles W. Goetz,
- and J. Adam Luckenbach
Genome Res. August 2021 31: 1366-1380; Published in Advance June 28, 2021, doi:10.1101/gr.274266.120
...diversification, the transcriptional context clearly changed between the two gsdf variants (see Fig. 2B). To obtain insights into the sequence evolution of the cis-regulatory regions of the gsdfX and gsdfY genes, their upstream regions were analyzed in detail (Fig. 4A).View larger version: In this window In a new...
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Methods: Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human
- Michael Brudno,
- Alexander Poliakov,
- Asaf Salamov,
- Gregory M. Cooper,
- Arend Sidow,
- Edward M. Rubin,
- Victor Solovyev,
- Serafim Batzoglou,
- and Inna Dubchak
Genome Res. April 2004 14: 685-692; doi:10.1101/gr.2067704
...downloaded. ↵ http://pipeline.lbl.gov/downloads.shtml ; Download page for whole alignments and other materials. ↵ http://www.softberry.com/berry.phtml?topic=human-mouse-rat ; Three-way gene-based synteny. Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human Michael Brudno 1 , Alexander Poliakov...
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LETTER: Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data
- Austen R.D. Ganley and
- Takehiko Kobayashi
Genome Res. February 2007 17: 184-191; Published in Advance January 2, 2007, doi:10.1101/gr.5457707
...evolution over birth-and-death evolution for many large repeat arrays. Here we use whole-genome shotgun sequence data from the genome projects of five fungal species to reveal absolute levels of sequence variation within the ribosomal RNA gene repeats (rDNA). The level of sequence variation is remarkably...

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