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LETTER: Genomic analysis of the immune gene repertoire of amphioxus reveals extraordinary innate complexity and diversity
- Shengfeng Huang,
- Shaochun Yuan,
- Lei Guo,
- Yanhong Yu,
- Jun Li,
- Tao Wu,
- Tong Liu,
- Manyi Yang,
- Kui Wu,
- Huiling Liu,
- Jin Ge,
- Yingcai Yu,
- Huiqing Huang,
- Meiling Dong,
- Cuiling Yu,
- Shangwu Chen,
- and Anlong Xu
Genome Res. July 2008 18: 1112-1126; Published in Advance June 18, 2008, doi:10.1101/gr.069674.107
...Genomic analysis of the immune gene repertoire of amphioxus reveals extraordinary innate complexity and diversity Shengfeng Huang , Shaochun Yuan , Lei Guo , Yanhong Yu , Jun Li , Tao Wu , Tong Liu , Manyi Yang...
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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
...the ARNTL gene family in the genomes of Ciona intestinalis , amphioxus, zebrafish, and human. Footnotes ↵ 3 Corresponding author. E-mail jpostle@uoneuro.uoregon.edu ; fax (541) 346-4548. [Supplemental material is available online at www.genome.org . The Synteny Database is freely...
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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: 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
...to 15 Hox genes in amphioxus and 14 in the common ancestor of vertebrates (Powers and Amemiya 2004; Holland et al. 2008). Genome duplications during vertebrate evolution increased the total number of Hox genes; for example, human and mouse have 39 Hox genes, the African butterfly fish Pantodon buchholzi...
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Research: Evolution of a genomic regulatory domain: The role of gene co-option and gene duplication in the Enhancer of split complex
- Elizabeth J. Duncan and
- Peter K. Dearden
Genome Res. July 2010 20: 917-928; Published in Advance May 10, 2010, doi:10.1101/gr.104794.109
...Evolution of a genomic regulatory domain: The role of gene co-option and gene duplication in the Enhancer of split complex Elizabeth J. Duncan and Peter K. Dearden 1 Laboratory for Evolution and Development, Genetics Otago and the National Research Centre...
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ARTICLE: A Genetic Linkage Map for Zebrafish: Comparative Analysis and Localization of Genes and Expressed Sequences
- Michael A. Gates,
- Lisa Kim,
- Elizabeth S. Egan,
- Timothy Cardozo,
- Howard I. Sirotkin,
- Scott T. Dougan,
- Deval Lashkari,
- Ruben Abagyan,
- Alexander F. Schier,
- and William S. Talbot
Genome Res. April 1, 1999 9: 334-347; doi:10.1101/gr.9.4.334
...1996 ). Analysis of chordate s reveals a fourfold increase in the number of genes and members of gene families in mammals relative to the cephalochordate amphioxus. For example, tetrapods have four paralogous Hox complexes whereas amphioxus has only one (excluding the ParaHox complex, which is thought...
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ERRATUM: Errata Genome Res. August 2008 18: 1380

...genome;18/8/1380 1088-9051 Errata Errata Genome Research 18: 1100–1111 (2008) The amphioxus illuminates vertebrate origins and cephalochordate biology Linda Z. Holland, Ricard Albalat, Kaoru Azumi, Èlia Benito-Gutiérrez, Matthew J. Blow, Marianne Bronner-Fraser, Frederic Brunet, Thomas Butts...
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Letter: Domain shuffling and the evolution of vertebrates
- Takeshi Kawashima,
- Shuichi Kawashima,
- Chisaki Tanaka,
- Miho Murai,
- Masahiko Yoneda,
- Nicholas H. Putnam,
- Daniel S. Rokhsar,
- Minoru Kanehisa,
- Nori Satoh,
- and Hiroshi Wada
Genome Res. August 2009 19: 1393-1403; Published in Advance May 14, 2009, doi:10.1101/gr.087072.108
..., Benito-Gutie´rrez E, Blow MJ, BronnerFraser M, Brunet F, Butts T, Candiani S, Dishaw LJ, et al. 2008. The amphioxus illuminates vertebrate origins and cephalochordate biology. Genome Res 18: 1100–1111. Huang S, Yuan S, Guo L, Yu Y, Li J, Wu T, Liu T, Yang M, Wu K, Liu H, et al. 2008. Genomic analysis...

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