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Research: Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
- Matthias H. Weissensteiner,
- Andy W.C. Pang,
- Ignas Bunikis,
- Ida Höijer,
- Olga Vinnere-Petterson,
- Alexander Suh,
- and Jochen B.W. Wolf
Genome Res. May 2017 27: 697-708; Published in Advance March 30, 2017, doi:10.1101/gr.215095.116
...the exception among assemblies. Promising examples of approaches using long-range information (Bickhart et al. 2016; Steinberg et al. 2016) and a combination of comparative genomics and universal probes (Damas et al. 2017) illustrate the rapid development of high-quality assemblies for nonmodel organisms...
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Research: Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events
- Marin Volarić,
- Evelin Despot-Slade,
- Damira Veseljak,
- Brankica Mravinac,
- and Nevenka Meštrović
Genome Res. November 2024 34: 1878-1894; Published in Advance October 22, 2024, doi:10.1101/gr.279225.124
...-depth analyses of the dominant satDNA fraction in euchromatin. The second aim was to disclose the chromosome distribution, genomic environment, evolutionary trends, and mechanisms of propagation of the dominant euchromatic satDNAs.ResultsChromosome-scale ONT- assembly and repetitive element identification...
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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
...and sequenced both Hydractinia s using a combination of Pacific Biosciences (PacBio) SMRT long-read and Illumina short-read sequence data (for details, see Supplemental Material; Supplemental Table S2). These PacBio data were then used to generate primary contig assemblies using the diploid-aware assembler Canu...
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Resource: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
- Ran Li,
- Mian Gong,
- Xinmiao Zhang,
- Fei Wang,
- Zhenyu Liu,
- Lei Zhang,
- Qimeng Yang,
- Yuan Xu,
- Mengsi Xu,
- Huanhuan Zhang,
- Yunfeng Zhang,
- Xuelei Dai,
- Yuanpeng Gao,
- Zhuangbiao Zhang,
- Wenwen Fang,
- Yuta Yang,
- Weiwei Fu,
- Chunna Cao,
- Peng Yang,
- Zeinab Amiri Ghanatsaman,
- Niloufar Jafarpour Negari,
- Hojjat Asadollahpour Nanaei,
- Xiangpeng Yue,
- Yuxuan Song,
- Xianyong Lan,
- Weidong Deng,
- Xihong Wang,
- Chuanying Pan,
- Ruidong Xiang,
- Eveline M. Ibeagha-Awemu,
- Pat (J.S.) Heslop-Harrison,
- Benjamin D. Rosen,
- Johannes A. Lenstra,
- Shangquan Gan,
- and Yu Jiang
Genome Res. March 2023 33: 463-477; Published in Advance April 3, 2023, doi:10.1101/gr.277372.12
...was measured using Illumina short reads sequenced to 24× on average (Table 1), which showed higher values for all the primary and phased assemblies than obtained for the reference (QV = 42.5), except for WDU1 (QV = 41.7).SV discovery from PacBio HiFi reads and the ovine graphThe SVs from the 15 individuals...
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Resource: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
- Ran Li,
- Mian Gong,
- Xinmiao Zhang,
- Fei Wang,
- Zhenyu Liu,
- Lei Zhang,
- Qimeng Yang,
- Yuan Xu,
- Mengsi Xu,
- Huanhuan Zhang,
- Yunfeng Zhang,
- Xuelei Dai,
- Yuanpeng Gao,
- Zhuangbiao Zhang,
- Wenwen Fang,
- Yuta Yang,
- Weiwei Fu,
- Chunna Cao,
- Peng Yang,
- Zeinab Amiri Ghanatsaman,
- Niloufar Jafarpour Negari,
- Hojjat Asadollahpour Nanaei,
- Xiangpeng Yue,
- Yuxuan Song,
- Xianyong Lan,
- Weidong Deng,
- Xihong Wang,
- Chuanying Pan,
- Ruidong Xiang,
- Eveline M. Ibeagha-Awemu,
- Pat (J.S.) Heslop-Harrison,
- Benjamin D. Rosen,
- Johannes A. Lenstra,
- Shangquan Gan,
- and Yu Jiang
Genome Res. March 27, 2023 ; Published in Advance March 27, 2023, doi:10.1101/gr.277372.122
...; Supplemental Table S2). The quality value (QV) of the assemblies was measured using Illumina short reads sequenced to 24× on average (Table 1), which showedhigher values for all the primary and phased assemblies than obtained for the reference (QV= 42.5), except for WDU1 (QV=41.7). SV discovery from PacBio Hi...
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Research: Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
- Marta Farré,
- Jaebum Kim,
- Anastasia A. Proskuryakova,
- Yang Zhang,
- Anastasia I. Kulemzina,
- Qiye Li,
- Yang Zhou,
- Yingqi Xiong,
- Jennifer L. Johnson,
- Polina L. Perelman,
- Warren E. Johnson,
- Wesley C. Warren,
- Anna V. Kukekova,
- Guojie Zhang,
- Stephen J. O'Brien,
- Oliver A. Ryder,
- Alexander S. Graphodatsky,
- Jian Ma,
- Harris A. Lewin,
- and Denis M. Larkin
Genome Res. April 2019 29: 576-589; Published in Advance February 13, 2019, doi:10.1101/gr.239863.118
...about the evolution of chromosome structures, gene expression, and phenotypes. However, studies on other clades, involving chromosome-level assemblies and expression data from multiple tissues, are required to prove that our findings are indeed a general pattern of mammalian evolution.MethodsGenome data...
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Methods: High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing
- Emily Hodges,
- Andrew D. Smith,
- Jude Kendall,
- Zhenyu Xuan,
- Kandasamy Ravi,
- Michelle Rooks,
- Michael Q. Zhang,
- Kenny Ye,
- Arindam Bhattacharjee,
- Leonardo Brizuela,
- W. Richard McCombie,
- Michael Wigler,
- Gregory J. Hannon,
- and James B. Hicks
Genome Res. September 2009 19: 1593-1605; Published in Advance July 6, 2009, doi:10.1101/gr.095190.109
...methylation, we randomly selected 324 islands between 300 and 2000 bp representing 258,895 bases of genomic space and 25,000 CpG sites (;0.1% of all CpG sites in the ). The set was distributed among all autosomes and chromosome X, including 170 islands located within 1500 bp upstream of annotated protein...
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Research: Allelic diversification after transposable element exaptation promoted gsdf as the master sex determining gene of sablefish
- Amaury Herpin,
- Manfred Schartl,
- Alexandra Depincé,
- Yann Guiguen,
- Julien Bobe,
- Aurélie Hua-Van,
- Edward S. Hayman,
- Anna Octavera,
- Goro Yoshizaki,
- Krista M. Nichols,
- Giles W. Goetz,
- and J. Adam Luckenbach
Genome Res. August 2021 31: 1366-1380; Published in Advance June 28, 2021, doi:10.1101/gr.274266.120
...has prominent phenotypic consequences, or if many consecutive alterations in the DNA over longer time periods lead to phenotypic divergence. In the marine teleost, sablefish (Anoplopoma fimbria), complementary genomic and genetic studies led to the identification of a sex locus on the Y Chromosome...
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Method: Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations
- Anand Patel,
- Richard Schwab,
- Yu-Tsueng Liu,
- and Vineet Bafna
Genome Res. February 2014 24: 318-328; Published in Advance December 4, 2013, doi:10.1101/gr.161497.113
..., University of California San Diego, La Jolla, California 92093, USA; 2Moores Cancer Center, La Jolla, California 92093, USA; 3Department of Computer Science, University of California San Diego, La Jolla, California 92093, USA Deletion of tumor-suppressor genes as well as other genomic rearrangements pervade...

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