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Method: Resolving the chromatin impact of mosaic variants with targeted Fiber-seq
- Stephanie C. Bohaczuk,
- Zachary J. Amador,
- Chang Li,
- Benjamin J. Mallory,
- Elliott G. Swanson,
- Jane Ranchalis,
- Mitchell R. Vollger,
- Katherine M. Munson,
- Tom Walsh,
- Morgan O. Hamm,
- Yizi Mao,
- Andre Lieber,
- and Andrew B. Stergachis
Genome Res. December 2024 34: 2269-2278; Published in Advance December 9, 2024, doi:10.1101/gr.279747.124
...fiber sequencing (Fiber-seq) achieves this, permitting single-molecule, long-read genomic, and epigenomic profiling across targeted >100 kb loci with ∼10-fold enrichment over untargeted sequencing. Targeted Fiber-seq reveals that pathogenic expansions of the DMPK CTG repeat that underlie Myotonic...
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RESOURCE: A global assembly of cotton ESTs
- Joshua A. Udall,
- Jordan M. Swanson,
- Karl Haller,
- Ryan A. Rapp,
- Michael E. Sparks,
- Jamie Hatfield,
- Yeisoo Yu,
- Yingru Wu,
- Caitriona Dowd,
- Aladdin B. Arpat,
- Brad A. Sickler,
- Thea A. Wilkins,
- Jin Ying Guo,
- Xiao Ya Chen,
- Jodi Scheffler,
- Earl Taliercio,
- Ricky Turley,
- Helen McFadden,
- Paxton Payton,
- Natalya Klueva,
- Randell Allen,
- Deshui Zhang,
- Candace Haigler,
- Curtis Wilkerson,
- Jinfeng Suo,
- Stefan R. Schulze,
- Margaret L. Pierce,
- Margaret Essenberg,
- HyeRan Kim,
- Danny J. Llewellyn,
- Elizabeth S. Dennis,
- David Kudrna,
- Rod Wing,
- Andrew H. Paterson,
- Cari Soderlund,
- and Jonathan F. Wendel
Genome Res. March 2006 16: 441-450; Published in Advance February 14, 2006, doi:10.1101/gr.4602906
...survey of ∼42,000 fiber ESTs based on a single fiber library from diploid G. arboreum (A ) proved extremely useful for identifying genes, and led to the development of a 70-mer oligonucleotide cotton fiber microarray. A more thorough description of the Gossypium transcriptome, involving a wide array...
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Method: DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools
- Anupama Jha,
- Stephanie C. Bohaczuk,
- Yizi Mao,
- Jane Ranchalis,
- Benjamin J. Mallory,
- Alan T. Min,
- Morgan O. Hamm,
- Elliott Swanson,
- Danilo Dubocanin,
- Connor Finkbeiner,
- Tony Li,
- Dale Whittington,
- William Stafford Noble,
- Andrew B. Stergachis,
- and Mitchell R. Vollger
Genome Res. November 2024 34: 1976-1986; Published in Advance June 7, 2024, doi:10.1101/gr.279095.124
...; Marks et al. 2012; Murray et al. 2012; Loman et al. 2015; https://github.com/PacificBiosciences/jasmine). Furthermore, using exogenous DNA methyltransferases to add DNA base modifications, such as in the context of single-molecule chromatin fiber sequencing (Abdulhay et al. 2020; Lee et al. 2020...
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Research: Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly
- Kang Du,
- Oliver Deusch,
- Ilja Bezrukov,
- Christa Lanz,
- Yann Guiguen,
- Margarete Hoffmann,
- Anette Habring,
- Detlef Weigel,
- Manfred Schartl,
- and Christine Dreyer
Genome Res. March 2025 35: 489-498; Published in Advance March 5, 2025, doi:10.1101/gr.279582.124
.... Genes that control the characteristic color traits could be genetically mapped on the X and Y Chromosomes (Winge 1922; Khoo et al. 1999; Lindholm and Breden 2002; Tripathi et al. 2009a). A genetic map based on EST- and BAC-derived markers was generated, and LG12 was identified as the sex chromosome...
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Research: Semiconservative transmission of DNA N⁶-adenine methylation in a unicellular eukaryote
- Yalan Sheng,
- Yuanyuan Wang,
- Wentao Yang,
- Xue Qing Wang,
- Jiuwei Lu,
- Bo Pan,
- Bei Nan,
- Yongqiang Liu,
- Fei Ye,
- Chun Li,
- Jikui Song,
- Yali Dou,
- Shan Gao,
- and Yifan Liu
Genome Res. May 2024 34: 740-756; Published in Advance May 14, 2024, doi:10.1101/gr.277843.123
...) are used to maximize 6mA calling accuracy (high number of passes of the DNA template), but at the cost of -wide coverage. SMRT CCS has also been applied to detect exogenously introduced 6mA in chromatin fiber sequencing, which exploits in vitro methylation by 6mA-specific MTases (e.g., M.EcoGII and Hia5...
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Resource: Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions
- Rodrigo P. Baptista,
- Yiran Li,
- Adam Sateriale,
- Mandy J. Sanders,
- Karen L. Brooks,
- Alan Tracey,
- Brendan R.E. Ansell,
- Aaron R. Jex,
- Garrett W. Cooper,
- Ethan D. Smith,
- Rui Xiao,
- Jennifer E. Dumaine,
- Peter Georgeson,
- Bernard J. Pope,
- Matthew Berriman,
- Boris Striepen,
- James A. Cotton,
- and Jessica C. Kissinger
Genome Res. January 2022 32: 203-213; Published in Advance November 11, 2021, doi:10.1101/gr.275325.121
..., (CpIRef), was assembled with a limited physical map (Abrahamsen et al. 2004) and a few hundred ESTs for training gene finders. Genomic, transcriptomic, and proteomic work has been lacking owing to the obligate quasi-intracellular nature of portions of the parasite's life cycle, the historical lack...
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Resource: Precision environmental health monitoring by longitudinal exposome and multi-omics profiling
- Peng Gao,
- Xiaotao Shen,
- Xinyue Zhang,
- Chao Jiang,
- Sai Zhang,
- Xin Zhou,
- Sophia Miryam Schüssler-Fiorenza Rose,
- and Michael Snyder
Genome Res. June 2022 32: 1199-1214; Published in Advance June 6, 2022, doi:10.1101/gr.276521.121
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Resource: The pig X and Y Chromosomes: structure, sequence, and evolution
- Benjamin M. Skinner,
- Carole A. Sargent,
- Carol Churcher,
- Toby Hunt,
- Javier Herrero,
- Jane E. Loveland,
- Matt Dunn,
- Sandra Louzada,
- Beiyuan Fu,
- William Chow,
- James Gilbert,
- Siobhan Austin-Guest,
- Kathryn Beal,
- Denise Carvalho-Silva,
- William Cheng,
- Daria Gordon,
- Darren Grafham,
- Matt Hardy,
- Jo Harley,
- Heidi Hauser,
- Philip Howden,
- Kerstin Howe,
- Kim Lachani,
- Peter J.I. Ellis,
- Daniel Kelly,
- Giselle Kerry,
- James Kerwin,
- Bee Ling Ng,
- Glen Threadgold,
- Thomas Wileman,
- Jonathan M.D. Wood,
- Fengtang Yang,
- Jen Harrow,
- Nabeel A. Affara,
- and Chris Tyler-Smith
Genome Res. January 2016 26: 130-139; Published in Advance November 11, 2015, doi:10.1101/gr.188839.114
...and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, 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
...identified 2190 genes (12% of the protein-coding ) with evidence of evolutionarily conserved alternative usage of similar exonic sequences (Fig. 6). The corresponding proteins tend to be involved in cell organization and muscle contraction (cytoskeleton, collagen, fibers, etc.), and in intercellular...
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LETTER: Prediction of Cell Type-Specific Gene Modules: Identification and Initial Characterization of a Core Set of Smooth Muscle-Specific Genes
- Sven Nelander,
- Petter Mostad,
- and Per Lindahl
Genome Res. August 2003 13: 1838-1854; Published in Advance July 17, 2003, doi:10.1101/gr.1197303
...-regulatory elements and a distinct set of transcription factors. Identifying such units is an important entry point to the molecular study of cell differentiation. We developed a general method to classify cell type-specific genes from expressed sequence tag (EST) data, and we optimized...

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