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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...stability.With the ever-growing number of s made available for nonmodel organisms, biologists are now positioned to investigate the interplay between genomic evolution and species diversity. The genomic evolutionary history of some of the most rapidly diversifying lineages on the planet, such as African...
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Resource: Genetic features and genomic targets of human KRAB-zinc finger proteins
- Jonas de Tribolet-Hardy,
- Christian W. Thorball,
- Romain Forey,
- Evarist Planet,
- Julien Duc,
- Alexandre Coudray,
- Bara Khubieh,
- Sandra Offner,
- Cyril Pulver,
- Jacques Fellay,
- Michael Imbeault,
- Priscilla Turelli,
- and Didier Trono
Genome Res. August 2023 33: 1409-1423; Published in Advance September 20, 2023, doi:10.1101/gr.277722.123
...more than 400 million years ago. Previous work has revealed that many KZFPs recognize transposable element (TE)-embedded sequences as genomic targets, and that KZFPs facilitate the co-option of the regulatory potential of TEs for the benefit of the host. Here, we present a comprehensive survey...
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Research: Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain
- Christopher J. Playfoot,
- Julien Duc,
- Shaoline Sheppard,
- Sagane Dind,
- Alexandre Coudray,
- Evarist Planet,
- and Didier Trono
Genome Res. September 2021 31: 1531-1545; Published in Advance August 16, 2021, doi:10.1101/gr.275133.120
...of the developing human brain, we have analyzed two independent RNA-seq data sets encompassing 16 brain regions from eight weeks postconception into adulthood. We reveal a distinct KZFP:TE transcriptional profile defining the late prenatal to early postnatal transition, and the spatiotemporal and cell type...
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Resource: Coelacanth genomes reveal signatures for evolutionary transition from water to land
- Masato Nikaido,
- Hideki Noguchi,
- Hidenori Nishihara,
- Atsushi Toyoda,
- Yutaka Suzuki,
- Rei Kajitani,
- Hikoyu Suzuki,
- Miki Okuno,
- Mitsuto Aibara,
- Benjamin P. Ngatunga,
- Semvua I. Mzighani,
- Hassan W.J. Kalombo,
- Kawilarang W.A. Masengi,
- Josef Tuda,
- Sadao Nogami,
- Ryuichiro Maeda,
- Masamitsu Iwata,
- Yoshitaka Abe,
- Koji Fujimura,
- Masataka Okabe,
- Takanori Amano,
- Akiteru Maeno,
- Toshihiko Shiroishi,
- Takehiko Itoh,
- Sumio Sugano,
- Yuji Kohara,
- Asao Fujiyama,
- and Norihiro Okada
Genome Res. October 2013 23: 1740-1748; Published in Advance July 22, 2013, doi:10.1101/gr.158105.113
...Coelacanth genomes reveal signatures for evolutionary transition from water to land Masato Nikaido 1 , 14 , Hideki Noguchi 1 , 2 , 14 , Hidenori Nishihara 1 , 14 , Atsushi Toyoda 2 , 14 , Yutaka Suzuki 3 , 14 , Rei Kajitani...
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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
...2,3, Robert M. Waterhouse7,8, Yue Li2,3, Elspeth Bruford1,6, Jyoti S. Choudhary4, Adam Frankish1 and Manolis Kellis2,3 1European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom; 2MIT Computer Science and Artificial...
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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
...).Genome-wide patterns of conserved syntenyLamprey/gnathostome (human and chicken) comparative maps reveal relatively strong conservation of chromosome-scale synteny across deep evolutionary time (Fig 2; Supplemental Fig. S3; Supplemental Table S4). These comparative maps also bear the signatures of large...
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Perspective: Comparative genomics as a tool to understand evolution and disease
- Jessica Alföldi and
- Kerstin Lindblad-Toh
Genome Res. July 2013 23: 1063-1068; doi:10.1101/gr.157503.113
...the insights into evolution that can only come from comparative genomics. More recent analysis has demonstrated three different waves of genes that showed regulatory innovation in different eras of vertebrate evolutionary history. The investigators first identified CNEs on the s of five disparate vertebrates...
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Research: Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes
- Stephen R. Voss,
- D. Kevin Kump,
- Srikrishna Putta,
- Nathan Pauly,
- Anna Reynolds,
- Rema J. Henry,
- Saritha Basa,
- John A. Walker,
- and Jeramiah J. Smith
Genome Res. August 2011 21: 1306-1312; Published in Advance April 11, 2011, doi:10.1101/gr.116491.110
...: 612–616. Bogart JP, Balon EK, Bruton MN. 1994. The chromosomes of the living coelacanth and their remarkable similarity to those of one of the most ancient frogs. J Hered 85: 322–325. Burt DW. 2002. Origin of avian microchromosomes. Cytogenet Genome Res 96: 97–112. Dalloul RA, Long JA, Zimin AV, Aslam...
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LETTER: Bichir HoxA Cluster Sequence Reveals Surprising Trends in Ray-Finned Fish Genomic Evolution
- Chi-hua Chiu,
- Ken Dewar,
- Günter P. Wagner,
- Kazuhiko Takahashi,
- Frank Ruddle,
- Christina Ledje,
- Peter Bartsch,
- Jean-Luc Scemama,
- Edmund Stellwag,
- Claudia Fried,
- Sonja J. Prohaska,
- Peter F. Stadler,
- and Chris T. Amemiya
Genome Res. January 2004 14: 11-17; doi:10.1101/gr.1712904
...Bichir Hox A Cluster Sequence Reveals Surprising Trends in Ray-Finned Fish Genomic Evolution Chi-hua Chiu 1 , 2 , 13 , Ken Dewar 3 , Günter P. Wagner 4 , Kazuhiko Takahashi 4 , Frank Ruddle 5 , Christina Ledje 6 , Peter...
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REVIEW: Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health
- Victoria P. Belancio,
- Dale J. Hedges,
- and Prescott Deininger
Genome Res. March 2008 18: 343-358; Published in Advance February 6, 2008, doi:10.1101/gr.5558208
...Orleans, Louisiana 70112, USA Abstract Transposable elements (TEs) have shared an exceptionally long coexistence with their host organisms and have come to occupy a significant fraction of eukaryotic genomes. The bulk of the expansion occurring within mammalian genomes has arisen from...
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