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Research: Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection–related chromatin reorganization
- Cyril Matthey-Doret,
- Morgan J. Colp,
- Pedro Escoll,
- Agnès Thierry,
- Pierrick Moreau,
- Bruce Curtis,
- Tobias Sahr,
- Matt Sarrasin,
- Michael W. Gray,
- B. Franz Lang,
- John M. Archibald,
- Carmen Buchrieser,
- and Romain Koszul
Genome Res. September 2022 32: 1698-1710; Published in Advance September 15, 2022, doi:10.1101/gr.276375.121
...using Oxford Nanopore long reads. To account for the error-prone nature of long reads, we polished the first draft assemblies with paired-end shotgun Illumina sequences using HyPo (Kundu et al. 2019). The polished assemblies were then scaffolded with long-range Hi-C contacts using our probabilistic...
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Resource: A chromosome-scale assembly of the axolotl genome
- Jeramiah J. Smith,
- Nataliya Timoshevskaya,
- Vladimir A. Timoshevskiy,
- Melissa C. Keinath,
- Drew Hardy,
- and S. Randal Voss
Genome Res. February 2019 29: 317-324; Published in Advance January 24, 2019, doi:10.1101/gr.241901.118
.... Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res 26: 342–350. doi:10.1101/gr.193474.115 ↵Reiß C, Olsson L, Hossfeld U. 2015. The history of the oldest self-sustaining laboratory animal: 150 years of axolotl research. J Exp Zool B Mol Dev Evol 324: 393–404. doi:10...
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Resource: An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations
- Bernardo J. Clavijo,
- Luca Venturini,
- Christian Schudoma,
- Gonzalo Garcia Accinelli,
- Gemy Kaithakottil,
- Jonathan Wright,
- Philippa Borrill,
- George Kettleborough,
- Darren Heavens,
- Helen Chapman,
- James Lipscombe,
- Tom Barker,
- Fu-Hao Lu,
- Neil McKenzie,
- Dina Raats,
- Ricardo H. Ramirez-Gonzalez,
- Aurore Coince,
- Ned Peel,
- Lawrence Percival-Alwyn,
- Owen Duncan,
- Josua Trösch,
- Guotai Yu,
- Dan M. Bolser,
- Guy Namaati,
- Arnaud Kerhornou,
- Manuel Spannagl,
- Heidrun Gundlach,
- Georg Haberer,
- Robert P. Davey,
- Christine Fosker,
- Federica Di Palma,
- Andrew L. Phillips,
- A. Harvey Millar,
- Paul J. Kersey,
- Cristobal Uauy,
- Ksenia V. Krasileva,
- David Swarbreck,
- Michael W. Bevan,
- and Matthew D. Clark
Genome Res. May 2017 27: 885-896; Published in Advance April 18, 2017, doi:10.1101/gr.217117.116
...al. 2014). Recent innovations in sequence library preparation, assembly algorithms, and long-range scaffolding have dramatically improved whole- shotgun assemblies from short-read sequences. These include PCR-free library preparation to reduce bias (Aird et al. 2011), longer sequence reads...
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Research: Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling
- Edward S. Rice,
- Satomi Kohno,
- John St. John,
- Son Pham,
- Jonathan Howard,
- Liana F. Lareau,
- Brendan L. O'Connell,
- Glenn Hickey,
- Joel Armstrong,
- Alden Deran,
- Ian Fiddes,
- Roy N. Platt II,
- Cathy Gresham,
- Fiona McCarthy,
- Colin Kern,
- David Haan,
- Tan Phan,
- Carl Schmidt,
- Jeremy R. Sanford,
- David A. Ray,
- Benedict Paten,
- Louis J. Guillette, Jr.,
- and Richard E. Green
Genome Res. May 2017 27: 686-696; Published in Advance January 30, 2017, doi:10.1101/gr.213595.116
...of estrogen receptor alpha binding sites are distal enhancers—that is, they are far from the genes they regulate (Carroll et al. 2006; Lin et al. 2007; Welboren et al. 2009). A majority of estrogen receptor binding events are associated with long-range intrachromosomal chromatin interactions...
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Method: Phased nanopore assembly with Shasta and modular graph phasing with GFAse
- Ryan Lorig-Roach,
- Melissa Meredith,
- Jean Monlong,
- Miten Jain,
- Hugh E. Olsen,
- Brandy McNulty,
- David Porubsky,
- Tessa G. Montague,
- Julian K. Lucas,
- Chris Condon,
- Jordan M. Eizenga,
- Sissel Juul,
- Sean K. McKenzie,
- Sara E. Simmonds,
- Jimin Park,
- Mobin Asri,
- Sergey Koren,
- Evan E. Eichler,
- Richard Axel,
- Bruce Martin,
- Paolo Carnevali,
- Karen H. Miga,
- and Benedict Paten
Genome Res. March 2024 34: 454-468; Published in Advance April 16, 2024, doi:10.1101/gr.278268.123
...to perform phased de novo assembly. As a step toward reducing the cost and complexity of this type of analysis, we describe new methods for accurately phasing Oxford Nanopore Technologies (ONT) sequence data with the Shasta assembler and a modular tool for extending phasing to the chromosome scale called...
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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
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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
...) Syntenic dot plots comparing H. symbiolongicarpus with four cnidarian species: H. echinata, C. hemisphaerica, H. vulgaris, and Nematostella vectensis. Colored boxes indicate linkage groups. (D) Stacked bar chart showing proportions of different transposable element classes in each Hydractinia using Repeat...
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Research: Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation
- David C.H. Metzger,
- Imogen Porter,
- Brendan Mobley,
- Benjamin A. Sandkam,
- Lydia J.M. Fong,
- Andrew P. Anderson,
- and Judith E. Mank
Genome Res. November 2023 33: 1917-1931; Published in Advance November 21, 2023, doi:10.1101/gr.278127.123
...–dependent binding affinity of the YY1 transcription factor could then result in sex-specific differences in the formation of long-range regulatory regions, such as altering 3D chromatin structure and the formation of insulated regions, resulting in global dosage compensation.Recent expansion of repetitive elements...
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Method: Chromosome assembly of large and complex genomes using multiple references
- Mikhail Kolmogorov,
- Joel Armstrong,
- Brian J. Raney,
- Ian Streeter,
- Matthew Dunn,
- Fengtang Yang,
- Duncan Odom,
- Paul Flicek,
- Thomas M. Keane,
- David Thybert,
- Benedict Paten,
- and Son Pham
Genome Res. November 2018 28: 1720-1732; Published in Advance October 19, 2018, doi:10.1101/gr.236273.118
...transformed three sets of contigs (generated using PacBio reads only) into chromosome-scale assemblies with accuracy comparable to chromosome assemblies generated in the original study using BioNano maps, Hi-C, BAC clones, and FISH.The year 2001 marked an important step in biology with the release...
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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
...-quality reference of emu, including the repetitive Chr W, we produced 70-fold genomic coverage of Pacific Biosciences (PacBio) reads (subread N50 length 15.5 kb), and long-range linkage data of 124-fold 10x Genomics linked reads, 154-fold Dovetail Chicago data, and 46-fold Hi-C data from three female emu...

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