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Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
- Ursula Oggenfuss,
- Robert T. Todd,
- Natthapon Soisangwan,
- Bailey Kemp,
- Alison Guyer,
- Annette Beach,
- and Anna Selmecki
Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
...detect most SVs (Mahmoud et al. 2019). Short-read sequencing data underestimates SVs longer than the read length and has a limited ability in determining the genomic positions, zygosity, or allele frequencies of SVs. Additionally, mapping of short-read data to the reference has further limited...
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Research: C. elegans whole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency
- Bettina Meier,
- Susanna L. Cooke,
- Joerg Weiss,
- Aymeric P. Bailly,
- Ludmil B. Alexandrov,
- John Marshall,
- Keiran Raine,
- Mark Maddison,
- Elizabeth Anderson,
- Michael R. Stratton,
- Anton Gartner,
- and Peter J. Campbell
Genome Res. October 2014 24: 1624-1636; Published in Advance July 16, 2014, doi:10.1101/gr.175547.114
...C. elegans whole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency Bettina Meier 1 , 6 , Susanna L. Cooke 2 , 6 , Joerg Weiss 1 , Aymeric P. Bailly 1 , 3 , Ludmil B. Alexandrov...
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RESOURCE: Sequencing of natural strains of Arabidopsis thaliana with short reads
- Stephan Ossowski,
- Korbinian Schneeberger,
- Richard M. Clark,
- Christa Lanz,
- Norman Warthmann,
- and Detlef Weigel
Genome Res. December 2008 18: 2024-2033; Published in Advance September 25, 2008, doi:10.1101/gr.080200.108
...containing genomic DNA from species with larger s, de novo assembly with deep SBS read data is becoming practical ( Butler et al. 2008 ; Chaisson and Pevzner 2008 ; Hernandez et al. 2008 ; Zerbino and Birney 2008 ). In contrast, for larger s, complete de novo assembly with short single-end SBS reads...
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Resource: ECHO: A reference-free short-read error correction algorithm
- Wei-Chun Kao,
- Andrew H. Chan,
- and Yun S. Song
Genome Res. July 2011 21: 1181-1192; Published in Advance April 11, 2011, doi:10.1101/gr.111351.110
...-correction algorithm, called ECHO, is introduced for correcting base-call errors in short-reads, without the need of a reference genome. Unlike most previous methods, ECHO does not require the user to specify parameters of which optimal values are typically unknown a priori. ECHO automatically sets the parameters...
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Methods: A tale of two templates: Automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices
- Aaron E. Tenney,
- Jia Qian Wu,
- Laura Langton,
- Paul Klueh,
- Ralph Quatrano,
- and Michael R. Brent
Genome Res. February 2007 17: 212-218; Published in Advance January 8, 2007, doi:10.1101/gr.5661407
...). Localization of the insertion event to determine which, if any, gene has been disrupted involves amplifying and sequencing a short segment of genomic DNA that is adjacent to the insertion from universal primers. Ideally, there is only one insertion event and a clean single trace is obtained. If two insertion...
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Letter: Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production
- Juan Lucas Argueso,
- Marcelo F. Carazzolle,
- Piotr A. Mieczkowski,
- Fabiana M. Duarte,
- Osmar V.C. Netto,
- Silvia K. Missawa,
- Felipe Galzerani,
- Gustavo G.L. Costa,
- Ramon O. Vidal,
- Melline F. Noronha,
- Margaret Dominska,
- Maria G.S. Andrietta,
- Sílvio R. Andrietta,
- Anderson F. Cunha,
- Luiz H. Gomes,
- Flavio C.A. Tavares,
- André R. Alcarde,
- Fred S. Dietrich,
- John H. McCusker,
- Thomas D. Petes,
- and Gonçalo A.G. Pereira
Genome Res. December 2009 19: 2258-2270; Published in Advance October 7, 2009, doi:10.1101/gr.091777.109
...). Despite this high level of redundancy, because both of thesemethods generated relatively short sequence reads (<250 bp), we were still unable to assemble the into one single contiguous sequence per chromosome. Instead, our de novo assembly of the JAY291 resulted in 452 genomic fragments (contigs; Methods...
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Resource: Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment
- Martin Ebeling,
- Erich Küng,
- Angela See,
- Clemens Broger,
- Guido Steiner,
- Marco Berrera,
- Tobias Heckel,
- Leonardo Iniguez,
- Thomas Albert,
- Roland Schmucki,
- Hermann Biller,
- Thomas Singer,
- and Ulrich Certa
Genome Res. October 2011 21: 1746-1756; Published in Advance August 23, 2011, doi:10.1101/gr.123117.111
...power of primate experiments for humans, we determined the genome sequence of a Macaca fascicularis female of Mauritian origin using a whole-genome shotgun sequencing approach. We applied a template switch strategy that uses either the rhesus or the human genome to assemble sequence reads. The sixfold...
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Resource: The genome of the pear (Pyrus bretschneideri Rehd.)
- Jun Wu,
- Zhiwen Wang,
- Zebin Shi,
- Shu Zhang,
- Ray Ming,
- Shilin Zhu,
- M. Awais Khan,
- Shutian Tao,
- Schuyler S. Korban,
- Hao Wang,
- Nancy J. Chen,
- Takeshi Nishio,
- Xun Xu,
- Lin Cong,
- Kaijie Qi,
- Xiaosan Huang,
- Yingtao Wang,
- Xiang Zhao,
- Juyou Wu,
- Cao Deng,
- Caiyun Gou,
- Weili Zhou,
- Hao Yin,
- Gaihua Qin,
- Yuhui Sha,
- Ye Tao,
- Hui Chen,
- Yanan Yang,
- Yue Song,
- Dongliang Zhan,
- Juan Wang,
- Leiting Li,
- Meisong Dai,
- Chao Gu,
- Yuezhi Wang,
- Daihu Shi,
- Xiaowei Wang,
- Huping Zhang,
- Liang Zeng,
- Danman Zheng,
- Chunlei Wang,
- Maoshan Chen,
- Guangbiao Wang,
- Lin Xie,
- Valpuri Sovero,
- Shoufeng Sha,
- Wenjiang Huang,
- Shujun Zhang,
- Mingyue Zhang,
- Jiangmei Sun,
- Linlin Xu,
- Yuan Li,
- Xing Liu,
- Qingsong Li,
- Jiahui Shen,
- Junyi Wang,
- Robert E. Paull,
- Jeffrey L. Bennetzen,
- Jun Wang,
- and Shaoling Zhang
Genome Res. February 2013 23: 396-408; Published in Advance November 13, 2012, doi:10.1101/gr.144311.112
...to this work. Abstract The draft genome of the pear ( Pyrus bretschneideri ) using a combination of BAC-by-BAC and next-generation sequencing is reported. A 512.0-Mb sequence corresponding to 97.1% of the estimated genome size of this highly heterozygous species is assembled with 194× coverage. High...
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Method: A reduced representation approach to population genetic analyses and applications to human evolution
- Francesca Luca,
- Richard R. Hudson,
- David B. Witonsky,
- and Anna Di Rienzo
Genome Res. July 2011 21: 1087-1098; Published in Advance May 31, 2011, doi:10.1101/gr.119792.110
...decrease in sequencing costs, collecting whole-genome sequence data on a population scale is still prohibitive for many laboratories. We have implemented an inexpensive, reduced representation protocol for preparing resequencing targets, and we have developed the analytical tools necessary for making...
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Research: Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population
- Robert J. Schmitz,
- Yupeng He,
- Oswaldo Valdés-López,
- Saad M. Khan,
- Trupti Joshi,
- Mark A. Urich,
- Joseph R. Nery,
- Brian Diers,
- Dong Xu,
- Gary Stacey,
- and Joseph R. Ecker
Genome Res. October 2013 23: 1663-1674; Published in Advance June 5, 2013, doi:10.1101/gr.152538.112
...of differentially methylated regions (DMRs) revealed that DMRs mostly cosegregated with the genotype from which they were derived, but examples of the uncoupling of genotype and epigenotype were identified. Linkage mapping of methylation states assessed from whole-genome bisulfite sequencing of 83 RILs uncovered...

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