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Review: Accurate and complete genomes from metagenomes
- Lin-Xing Chen,
- Karthik Anantharaman,
- Alon Shaiber,
- A. Murat Eren,
- and Jillian F. Banfield
Genome Res. March 2020 30: 315-333; Published in Advance March 18, 2020, doi:10.1101/gr.258640.119
...published relatively early in the microbial genomics era, Fraser et al. (2002) stated “you get what you pay for.” The investigators argued the lower scientific value of draft (partial) versus complete s, noting for example higher error rates, potential contaminant sequences, loss of information about gene...
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Research: Less effective selection leads to larger genomes
- Tristan Lefébure,
- Claire Morvan,
- Florian Malard,
- Clémentine François,
- Lara Konecny-Dupré,
- Laurent Guéguen,
- Michèle Weiss-Gayet,
- Andaine Seguin-Orlando,
- Luca Ermini,
- Clio Der Sarkissian,
- N. Pierre Charrier,
- David Eme,
- Florian Mermillod-Blondin,
- Laurent Duret,
- Cristina Vieira,
- Ludovic Orlando,
- and Christophe Jean Douady
Genome Res. June 2017 27: 1016-1028; Published in Advance April 19, 2017, doi:10.1101/gr.212589.116
...time) represents the proportion of the terminal branches estimated to be subterranean using the opsin gene, it is equal to timecolonization/timespeciation. aP-value <0.05. bP-value <0.01. Lefe´bure et al. 1018 Genome Research www..org Subterranean species share multiple convergent regressive phenotypes...
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Research: Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality
- Daniel F. Simola,
- Lothar Wissler,
- Greg Donahue,
- Robert M. Waterhouse,
- Martin Helmkampf,
- Julien Roux,
- Sanne Nygaard,
- Karl M. Glastad,
- Darren E. Hagen,
- Lumi Viljakainen,
- Justin T. Reese,
- Brendan G. Hunt,
- Dan Graur,
- Eran Elhaik,
- Evgenia V. Kriventseva,
- Jiayu Wen,
- Brian J. Parker,
- Elizabeth Cash,
- Eyal Privman,
- Christopher P. Childers,
- Monica C. Muñoz-Torres,
- Jacobus J. Boomsma,
- Erich Bornberg-Bauer,
- Cameron R. Currie,
- Christine G. Elsik,
- Garret Suen,
- Michael A.D. Goodisman,
- Laurent Keller,
- Jürgen Liebig,
- Alan Rawls,
- Danny Reinberg,
- Chris D. Smith,
- Chris R. Smith,
- Neil Tsutsui,
- Yannick Wurm,
- Evgeny M. Zdobnov,
- Shelley L. Berger,
- and Jürgen Gadau
Genome Res. August 2013 23: 1235-1247; Published in Advance May 1, 2013, doi:10.1101/gr.155408.113
...Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality Daniel F. Simola 1 , 2 , 20 , Lothar Wissler 3 , 20 , Greg Donahue 1 , 2 , Robert M. Waterhouse 4...
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Research: Analysis of gene expression from the Wolbachia genome of a filarial nematode supports both metabolic and defensive roles within the symbiosis
- Alistair C. Darby,
- Stuart D. Armstrong,
- Germanus S. Bah,
- Gaganjot Kaur,
- Margaret A. Hughes,
- Suzanne M. Kay,
- Pia Koldkjær,
- Lucille Rainbow,
- Alan D. Radford,
- Mark L. Blaxter,
- Vincent N. Tanya,
- Alexander J. Trees,
- Richard Cordaux,
- Jonathan M. Wastling,
- and Benjamin L. Makepeace
Genome Res. December 2012 22: 2467-2477; Published in Advance August 23, 2012, doi:10.1101/gr.138420.112
...Analysis of gene expression from the Wolbachia genome of a filarial nematode supports both metabolic and defensive roles within the symbiosis Alistair C. Darby 1 , Stuart D. Armstrong 2 , Germanus S. Bah 2 , 3 , Gaganjot Kaur 4 , Margaret A...
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LETTER: Evolutionary Conservation of Regulatory Elements in Vertebrate Hox Gene Clusters
- Simona Santini,
- Jeffrey L. Boore,
- and Axel Meyer
Genome Res. June 2003 13: 1111-1122; doi:10.1101/gr.700503
...of functional divergence of duplicated genes. Footnotes [Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to GenBank under accession no. AF538976.] Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr...
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Resource: The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals
- Christine E. Schnitzler,
- E. Sally Chang,
- Justin Waletich,
- Gonzalo Quiroga-Artigas,
- Wai Yee Wong,
- Anh-Dao Nguyen,
- Sofia N. Barreira,
- Liam B. Doonan,
- Paul Gonzalez,
- Sergey Koren,
- James M. Gahan,
- Steven M. Sanders,
- Brian Bradshaw,
- Timothy Q. DuBuc,
- Febrimarsa,
- Danielle de Jong,
- Eric P. Nawrocki,
- Alexandra Larson,
- Samantha Klasfeld,
- Sebastian G. Gornik,
- R. Travis Moreland,
- Tyra G. Wolfsberg,
- Adam M. Phillippy,
- James C. Mullikin,
- Oleg Simakov,
- Paulyn Cartwright,
- Matthew Nicotra,
- Uri Frank,
- and Andreas D. Baxevanis
Genome Res. March 2024 34: 498-513; Published in Advance March 20, 2024, doi:10.1101/gr.278382.123
...hydroid that shows remarkable biological properties, including the capacity to regenerate its entire body throughout its lifetime, a process made possible by its adult migratory stem cells, known as i-cells. Here, we provide an in-depth characterization of the genomic structure and gene content of two...
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Research: The genomic basis of evolutionary differentiation among honey bees
- Bertrand Fouks,
- Philipp Brand,
- Hung N. Nguyen,
- Jacob Herman,
- Francisco Camara,
- Daniel Ence,
- Darren E. Hagen,
- Katharina J. Hoff,
- Stefanie Nachweide,
- Lars Romoth,
- Kimberly K.O. Walden,
- Roderic Guigo,
- Mario Stanke,
- Giuseppe Narzisi,
- Mark Yandell,
- Hugh M. Robertson,
- Nikolaus Koeniger,
- Panuwan Chantawannakul,
- Michael C. Schatz,
- Kim C. Worley,
- Gene E. Robinson,
- Christine G. Elsik,
- and Olav Rueppell
Genome Res. July 2021 31: 1203-1215; Published in Advance May 4, 2021, doi:10.1101/gr.272310.120
...et al. 2021).The evolution of complex insect societies represents one of the major evolutionary transitions (Maynard Smith and Szathmáry 1995). Genomic signatures of this transition share few commonalities across taxa, except for an increase in gene regulatory capacity (Gadau et al. 2012; Simola et...
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RESEARCH: The Comparative Genomic Structure and Sequence of the Surfeit Gene Homologs in the Puffer Fish Fugu rubripes and their Association with CpG-Rich Islands
- Niall Armes,
- Jonathan Gilley,
- and Mike Fried
Genome Res. December 1, 1997 7: 1138-1152; doi:10.1101/gr.7.12.1138
...Fugu and mouse Surfeit gene homolog. The genomic distance between the initiator codon and the termination codon of the Fugu Surf-4, Surf-5, and Surf-6 gene homologs is much reduced with respect to the mouse Surf-4, Surf-5, and Surf-6 genes, the Fugu genes being ∼7, 3.5, and 2.5 times smaller...
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Research: Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers
- Valer Gotea,
- Axel Visel,
- John M. Westlund,
- Marcelo A. Nobrega,
- Len A. Pennacchio,
- and Ivan Ovcharenko
Genome Res. May 2010 20: 565-577; Published in Advance April 2, 2010, doi:10.1101/gr.104471.109
...of human cis-regulatory modules and suggest that they play an important role in gene regulation in the human and other vertebrate s. [Supplemental material is available online at http://www..org.] The completion of the sequencing of the human (International Human Genome Sequencing Consortium 2001; Venter...
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Resource: A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes
- Jing Liu,
- Zongji Wang,
- Jing Li,
- Luohao Xu,
- Jiaqi Liu,
- Shaohong Feng,
- Chunxue Guo,
- Shengchan Chen,
- Zhanjun Ren,
- Jinpeng Rao,
- Kai Wei,
- Yuezhou Chen,
- Erich D. Jarvis,
- Guojie Zhang,
- and Qi Zhou
Genome Res. March 2021 31: 497-511; Published in Advance January 6, 2021, doi:10.1101/gr.271569.120
...shark (Venkatesh et al. 2014) , dating the likely existence of microchromosomes at least to the ancestor of jawed vertebrates.Chicken microchromosomes tend to be gene-rich and have higher recombination rate and GC content than macrochromosomes (International Chicken Genome Sequencing Consortium 2004...

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