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Research: Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates
- Étienne Fafard-Couture,
- Pierre-Étienne Jacques,
- and Michelle S. Scott
Genome Res. April 2023 33: 525-540; Published in Advance April 18, 2023, doi:10.1101/gr.277483.122
...that snoRNAs rely on conserved motifs, a stable global structure and terminal stem, and a transcribed locus to be expressed. We observe that these features explain well the varying abundance of snoRNAs embedded within the same host gene. By predicting the expression status of snoRNAs across several...
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Method: Assessing conservation of alternative splicing with evolutionary splicing graphs
- Diego Javier Zea,
- Sofya Laskina,
- Alexis Baudin,
- Hugues Richard,
- and Elodie Laine
Genome Res. August 2021 31: 1462-1473; Published in Advance June 15, 2021, doi:10.1101/gr.274696.120
...show a good overall agreement, many subpaths are contributed solely by RNA-seq in platypus, cow, and zebrafish (Fig. 2B).View larger version: In this window In a new window Figure 2. Conservation and tissue regulation of a set of documented AS events. (A) Each event is designated by the name...
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Research: Historical RNA expression profiles from the extinct Tasmanian tiger
- Emilio Mármol-Sánchez,
- Bastian Fromm,
- Nikolay Oskolkov,
- Zoé Pochon,
- Panagiotis Kalogeropoulos,
- Eli Eriksson,
- Inna Biryukova,
- Vaishnovi Sekar,
- Erik Ersmark,
- Björn Andersson,
- Love Dalén,
- and Marc R. Friedländer
Genome Res. August 2023 33: 1299-1316; Published in Advance July 18, 2023, doi:10.1101/gr.277663.123
...et al. 2022). It is well established that tissue-specific miRNA expression patterns are conserved across evolution; therefore, we hypothesized that our historical miRNA profiles should cluster according to tissues rather than to their species identity. Only shared miRNAs among the four species...
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Platypus Special/Letter: Retroposed SNOfall—A mammalian-wide comparison of platypus snoRNAs
- Jürgen Schmitz,
- Anja Zemann,
- Gennady Churakov,
- Heiner Kuhl,
- Frank Grützner,
- Richard Reinhardt,
- and Jürgen Brosius
Genome Res. June 2008 18: 1005-1010; Published in Advance May 7, 2008, doi:10.1101/gr.7177908
...to that of certain vertebrate populations of miRNAs ( Tanzer and Stadler 2006 ). View larger version: In this window In a new window Figure 1. snoRNA representation in the of platypus. ( A ) snoRNAs with corresponding paralogs distributed by cis - or trans -duplication (trans). (Red lettering) snoRNAs conserved...
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Platypus Special/Letter: Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes
- Frédéric Veyrunes,
- Paul D. Waters,
- Pat Miethke,
- Willem Rens,
- Daniel McMillan,
- Amber E. Alsop,
- Frank Grützner,
- Janine E. Deakin,
- Camilla M. Whittington,
- Kyriena Schatzkamer,
- Colin L. Kremitzki,
- Tina Graves,
- Malcolm A. Ferguson-Smith,
- Wes Warren,
- and Jennifer A. Marshall Graves
Genome Res. June 2008 18: 965-973; Published in Advance May 7, 2008, doi:10.1101/gr.7101908
..., comparative mapping shows that, contrary to earlier reports, there is no homology between the platypus and therian X chromosomes. Orthologs of genes in the conserved region of the human X (including SOX3 , the gene from which SRY evolved) all map to platypus chromosome 6, which therefore represents...
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Platypus Special/Letter: Defensins and the convergent evolution of platypus and reptile venom genes
- Camilla M. Whittington,
- Anthony T. Papenfuss,
- Paramjit Bansal,
- Allan M. Torres,
- Emily S.W. Wong,
- Janine E. Deakin,
- Tina Graves,
- Amber Alsop,
- Kyriena Schatzkamer,
- Colin Kremitzki,
- Chris P. Ponting,
- Peter Temple-Smith,
- Wesley C. Warren,
- Philip W. Kuchel,
- and Katherine Belov
Genome Res. June 2008 18: 986-994; Published in Advance May 7, 2008, doi:10.1101/gr.7149808
...through a bite, as do snakes and shrews, male platypuses have venomous spurs on each hind leg. The platypus genome sequence provides a unique opportunity to unravel the evolutionary history of many of these interesting features. While searching the platypus genome for the sequences of antimicrobial...
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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
...conserved) (Simakov et al. 2013; Li et al. 2022).We used KaKs_Calculator (v2.0) (Zhang 2022) to calculate the Ka/Ks ratios of paralogous gene pairs between macrochromosomes and microchromosomes, and gene expression values for L. osseus RNA-seq data were calculated using featureCounts (v2.0.2) (Liao et al...
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Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
...the APGs. MHC-I genes exhibit lineage-specific duplications and signs of concerted evolution, resulting in poorly resolved phylogenies. In contrast, MHC-II genes are more conserved and exhibit extensive trans-species polymorphism. Expression and polymorphism patterns identify putative nonclassical MHC...
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Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...diversity of vertebrate chromatin conformation, here we generate de novo assemblies for two cryptodiran (hidden-neck) turtles via Illumina sequencing, chromosome conformation capture, and RNA-seq: Apalone spinifera (ZZ/ZW, 2n = 66) and Staurotypus triporcatus (XX/XY, 2n = 54). We detected differences...
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Methods: Multigenome DNA sequence conservation identifies Hox cis-regulatory elements
- Steven G. Kuntz,
- Erich M. Schwarz,
- John A. DeModena,
- Tristan De Buysscher,
- Diane Trout,
- Hiroaki Shizuya,
- Paul W. Sternberg,
- and Barbara J. Wold
Genome Res. December 2008 18: 1955-1968; Published in Advance November 3, 2008, doi:10.1101/gr.085472.108
...-13 and lin-39 orthologs, HOXA1 and HOXA5, respectively. Scans of the HOXA clusters in dog, opossum, platypus, and frog also revealed this pairing ( Fig. 6A ). Among the vertebrates alone, sequence conservation was high, indicating that these hits were located in functionally important DNA ( Fig. 6B...

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