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Research: The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications
- Jeramiah J. Smith and
- Melissa C. Keinath
Genome Res. August 2015 25: 1081-1090; Published in Advance June 5, 2015, doi:10.1101/gr.184135.114
...: In this window In a new window Figure 3. Distribution of individual orthologous genes across paralogous chicken and lamprey chromosomes. (A) Orthologs from chicken chromosomes GG14 and GG18 are distributed across five lamprey LGs (the complete set of lamprey linkage groups with significant enrichment...
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ARTICLE: Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis
- Gayle K. McEwen,
- Adam Woolfe,
- Debbie Goode,
- Tanya Vavouri,
- Heather Callaway,
- and Greg Elgar
Genome Res. April 2006 16: 451-465; Published in Advance March 13, 2006, doi:10.1101/gr.4143406
..., that are highly conserved within and between vertebrate genomes. In 74% of cases, we were able to assign a specific set of paralogous genes with annotation relating to transcriptional regulation and/or development to each family, thus removing much of the ambiguity in identifying associated genes. We find...
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Letter: Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention
- Andrew L. Hufton,
- Susanne Mathia,
- Helene Braun,
- Udo Georgi,
- Hans Lehrach,
- Martin Vingron,
- Albert J. Poustka,
- and Georgia Panopoulou
Genome Res. November 2009 19: 2036-2051; Published in Advance August 24, 2009, doi:10.1101/gr.093237.109
...used to identify these PCNEs were chosen to maximize sensitivity while maintaining an acceptably low error rate. We estimated our false-positive rate by replacing each gene in the original gene families with random substitute genes from within the same , thereby creating sets of genomic regions...
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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
..., revealing how the ancestral teleost became tetraploid.ResultsConstruction of TGD-aware teleost gene treesWe collected a data set of 101 vertebrate s, including 74 teleost fish, two nonteleost fish (bowfin and spotted gar, which did not undergo the teleost duplication or TGD), 20 other vertebrates of which...
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Research: Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera
- Peter O. Mulhair,
- Liam Crowley,
- Douglas H. Boyes,
- Amber Harper,
- Owen T. Lewis,
- Darwin Tree of Life Consortium,
- and Peter W.H. Holland
Genome Res. January 2023 33: 32-44; Published in Advance December 8, 2022, doi:10.1101/gr.277118.122
...generally comprises 10 homeobox genes arranged in a specific order reflecting their evolutionary origin by tandem gene duplication: lab, pb, zen, Dfd, Scr, Antp, ftz, Ubx, abd-A, and Abd-B. The cluster may be split, as in many Drosophila species (Duboule 2007; Negre and Ruiz 2007), individual genes may...
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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...2012; Wang et al. 2014; Attig et al. 2019) or as a result of intron retention events (Zaghlool et al. 2013). In such cases, it can be challenging to determine if a TE-mapping read originates from a gene promoter or a TE promoter (Lanciano and Cristofari 2020). To address this issue, we categorized...
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Perspective: Insights into neural crest development and evolution from genomic analysis
- Marcos Simões-Costa and
- Marianne E. Bronner
Genome Res. July 2013 23: 1069-1080; doi:10.1101/gr.157586.113
...this process. Furthermore, comparative genomic analyses are providing important insights about the evolution of the neural crest and the origins of the vertebrate clade. Here, we will present a synopsis of the current state of the field of neural crest biology from a gene regulatory perspective and will also...
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Research: Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints
- Manuel Irimia,
- Juan J. Tena,
- Maria S. Alexis,
- Ana Fernandez-Miñan,
- Ignacio Maeso,
- Ozren Bogdanović,
- Elisa de la Calle-Mustienes,
- Scott W. Roy,
- José L. Gómez-Skarmeta,
- and Hunter B. Fraser
Genome Res. December 2012 22: 2356-2367; Published in Advance June 21, 2012, doi:10.1101/gr.139725.112
...a final set of 795 unique groups of gene pairs (or three or more gene clusters) (Supplemental Table S2). Due to high duplication rates, precise orthology and paralogy relationships could not be established for 89/795 groups. These included previously described examples, such as the histone clusters...
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PERSPECTIVE: Unraveling genomic regulatory networks in the simple chordate, Ciona intestinalis
- Weiyang Shi,
- Michael Levine,
- and Brad Davidson
Genome Res. December 2005 15: 1668-1674; doi:10.1101/gr.3768905
.... and Holland, P.W. 2004 . Amphioxus and ascidian Dmbx homeobox genes give clues to the vertebrate origins of midbrain development. Development 131 : 3285 -3294. ↵ Takahashi, H., Hotta, K., Erives, A., Di Gregorio, A., Zeller, R.W., Levine, M., and Satoh, N. 1999 . Brachyury downstream notochord differentiation...

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