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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
...mtDNA observed in cnidarians consists of a set of 17 genes: the small and large ribosomal genes, methionine and tryptophan transfer RNA (tRNA) genes, and 13 energy pathway proteins (Bridge et al. 1992; Beagley et al. 1998). These genes are usually organized in the same transcriptional orientation...
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Research: The human ribosomal DNA array is composed of highly homogenized tandem clusters
- Yutaro Hori,
- Akira Shimamoto,
- and Takehiko Kobayashi
Genome Res. November 2021 31: 1971-1982; Published in Advance August 18, 2021, doi:10.1101/gr.275838.121
...of rDNA methylation works as a “clock” that tells the individual's age.To reveal the detailed structure and integrity in the human rDNA cluster at the DNA sequence level, we developed a method to analyze rDNA-derived long reads obtained by an Oxford Nanopore sequencer.ResultsLong sequence reads reveal...
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Research: The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible
- Yue Hao,
- Makenzie E. Mabry,
- Patrick P. Edger,
- Michael Freeling,
- Chunfang Zheng,
- Lingling Jin,
- Robert VanBuren,
- Marivi Colle,
- Hong An,
- R. Shawn Abrahams,
- Jacob D. Washburn,
- Xinshuai Qi,
- Kerrie Barry,
- Christopher Daum,
- Shengqiang Shu,
- Jeremy Schmutz,
- David Sankoff,
- Michael S. Barker,
- Eric Lyons,
- J. Chris Pires,
- and Gavin C. Conant
Genome Res. May 2021 31: 799-810; Published in Advance April 16, 2021, doi:10.1101/gr.270033.120
...dosage balance among highly interacting genes (Birchler et al. 2005; Hakes et al. 2007; Birchler and Veitia 2012, 2014; Conant et al. 2014). There are also genes that prefer not to be duplicated: genes for DNA repair and those targeted to organelles have returned to single copy rapidly after duplication...
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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
...transducers, specifically ion transport and kinase related terms; (3) DNA/RNA/protein metabolism; and (4) a group of catalytic terms (Fig. 6). Within the mouse, these broad groups show additional subdivision: Developmental terms cluster separately fromtranscription and metabolism; ion transport and kinase...
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LETTER: Ultraconserved elements in insect genomes: A highly conserved intronic sequence implicated in the control of homothorax mRNA splicing
- Evgeny A. Glazov,
- Michael Pheasant,
- Elizabeth A. McGraw,
- Gill Bejerano,
- and John S. Mattick
Genome Res. June 2005 15: 800-808; Published in Advance May 17, 2005, doi:10.1101/gr.3545105
...incidence of intron retention in hth pre-mRNA, suggesting that the conserved intronic element is critically important in the post-transcriptional regulation of hth expression in Diptera . Evolutionary conservation of DNA sequences between related or distant biological species is usually believed to reflect...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...dispersed throughout the The ribosomal-only contigs 19 to 29 (Fig. 2A) display a conserved structural pattern characterized by 45S rDNA genes (18S–5.8S–28S) flanked by a large array of tandemly repeated elements (Fig. 2B,C). We could identify other characteristic motifs: a 160 bp sequence at the 3′ end...
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Research: Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals
- Antoine Molaro,
- Janet M. Young,
- and Harmit S. Malik
Genome Res. April 2018 28: 460-473; Published in Advance March 16, 2018, doi:10.1101/gr.229799.117
...with their short tails, imply that they are among the shortest eukaryotic histones to be described to date. Furthermore, H2A.P and H2A.Q have lost two key conserved arginine (R) residues in Loop 1 and 2 that contact the DNA minor-groove. Loss of these arginine residues is predicted to further reduce the stability...
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Perspective: Short arms of human acrocentric chromosomes and the completion of the human genome sequence
- Stylianos E. Antonarakis
Genome Res. April 2022 32: 599-607; Published in Advance March 31, 2022, doi:10.1101/gr.275350.121
...elements, are located within dynamic chromosomal regions. Genes Dev 33: 1688–1701. doi:10.1101/gad.331892.119 ↵Wang M, Lemos B. 2019. Ribosomal DNA harbors an evolutionarily conserved clock of biological aging. Genome Res 29: 325–333. doi:10.1101/gr.241745.118 ↵Warner JR. 1999. The economics of ribosome...
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Research: Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control
- Todd P. Michael,
- Evan Ernst,
- Nolan Hartwick,
- Philomena Chu,
- Douglas Bryant,
- Sarah Gilbert,
- Stefan Ortleb,
- Erin L. Baggs,
- K. Sowjanya Sree,
- Klaus J. Appenroth,
- Joerg Fuchs,
- Florian Jupe,
- Justin P. Sandoval,
- Ksenia V. Krasileva,
- Ljudmylla Borisjuk,
- Todd C. Mockler,
- Joseph R. Ecker,
- Robert A. Martienssen,
- and Eric Lam
Genome Res. February 2021 31: 225-238; Published in Advance December 23, 2020, doi:10.1101/gr.266429.120
...of 126, 167, and 250 bp (Supplemental Fig. S3).Repeat sequence is a dominant driver of size differences in plants (Michael and VanBuren 2020). We looked at ribosomal DNA (rDNA) and long terminal repeat retrotransposon (LTR-RT) content in the W. australiana s to understand whether, as in Spirodela...
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Letter: Genome-wide mapping of alternative splicing in Arabidopsis thaliana
- Sergei A. Filichkin,
- Henry D. Priest,
- Scott A. Givan,
- Rongkun Shen,
- Douglas W. Bryant,
- Samuel E. Fox,
- Weng-Keen Wong,
- and Todd C. Mockler
Genome Res. January 2010 20: 45-58; Published in Advance October 26, 2009, doi:10.1101/gr.093302.109
...in favor of GT-AG and to a lesser extent GCAG introns among most ab initio gene prediction algorithms and the commonly used tools for alignment of EST/cDNA sequences to genomic sequences. Experimental validation of selected putative novel splicing events suggests that many of these unusual splicing events...

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