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Research: Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response
- Yali Zhang,
- Yayi Zhou,
- Yangyang Chen,
- Xueyu Wang,
- Boyan Hu,
- Shahid Siddique,
- Romnick A. Latina,
- Veronica I. Casey,
- Dexin Bo,
- Yucheng Liao,
- Min Zhang,
- Ming Sun,
- Fengjuan Zhang,
- and Dadong Dai
Genome Res. April 2026 36: 726-739; Published in Advance March 23, 2026, doi:10.1101/gr.281016.125
...Illumina short-reads data to assemble the A. avenae . We assessed the ploidy of A. avenae and confirmed it to be diploid (Supplemental Fig. S2A). The haploid size was estimated to be ∼173 Mb (Supplemental Fig. S2B). Furthermore, k-mer–based analyses revealed a high level of genomic heterozygosity (∼6...
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Research: Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement
- Peter A. Audano and
- Christine R. Beck
Genome Res. January 2024 34: 7-19; Published in Advance January 4, 2024, doi:10.1101/gr.278203.123
.... 2020; Jebb et al. 2020; Mao et al. 2021; Ferraj et al. 2023; Li et al. 2023), which play fundamental roles in modern genomics.Variant discovery is largely based on aligning reads or assemblies to a reference to identify single-nucleotide variants (SNVs), small insertions and deletions (indels...
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Research: Evidence for selfing in a vertebrate from whole-genome sequencing
- Astrid Böhne,
- Zeynep Oğuzhan,
- Ioannis Chrysostomakis,
- Simon Vitt,
- Denis Meuthen,
- Sebastian Martin,
- Sandra Kukowka,
- and Timo Thünken
Genome Res. December 2023 33: 2133-2142; Published in Advance December 7, 2023, doi:10.1101/gr.277368.122
...reproducing ovophilic mouthbrooder from Western Africa. Our laboratory observations revealed that a wild-caught individual produced repeatedly viable offspring in absence of a mating partner. By analyzing -wide single-nucleotide polymorphism (SNP) data, we compare that individual and two of its offspring...
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Review: Genome graphs and the evolution of genome inference
- Benedict Paten,
- Adam M. Novak,
- Jordan M. Eizenga,
- and Erik Garrison
Genome Res. May 2017 27: 665-676; Published in Advance March 30, 2017, doi:10.1101/gr.214155.116
...–based assays, it is estimated that the average diploid human has between 4.1 and 5 million point mutations, either single nucleotide variants (SNVs), multinucleotide variants (MNVs), or short indels, which is only around 1 point variant every 1200–1450 bases of haploid sequence (The 1000Genomes Project...
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METHODS: Polymorphism Ratio Sequencing: A New Approach for Single Nucleotide Polymorphism Discovery and Genotyping
- Robert G. Blazej,
- Brian M. Paegel,
- and Richard A. Mathies
Genome Res. February 1, 2003 13: 287-293; doi:10.1101/gr.396203
..., Richard A RobertG Blazej 1549-5469 genome;13/2/287 10.1101/gr.396203 1088-9051 Polymorphism Ratio Sequencing: A New Approach for Single Nucleotide Polymorphism Discovery and Genotyping Polymorphism Ratio Sequencing: A New Approach for Single Nucleotide Polymorphism Discovery and Genotyping Robert G...
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Method: Bacterial genome reduction using the progressive clustering of deletions via yeast sexual cycling
- Yo Suzuki,
- Nacyra Assad-Garcia,
- Maxim Kostylev,
- Vladimir N. Noskov,
- Kim S. Wise,
- Bogumil J. Karas,
- Jason Stam,
- Michael G. Montague,
- Timothy J. Hanly,
- Nico J. Enriquez,
- Adi Ramon,
- Gregory M. Goldgof,
- R. Alexander Richter,
- Sanjay Vashee,
- Ray-Yuan Chuang,
- Elizabeth A. Winzeler,
- Clyde A. Hutchison III,
- Daniel G. Gibson,
- Hamilton O. Smith,
- John I. Glass,
- and J. Craig Venter
Genome Res. March 2015 25: 435-444; Published in Advance February 5, 2015, doi:10.1101/gr.182477.114
...strains. The first simultaneously lacked eight singly deletable regions of the genome, representing a total of 91 genes and ∼10% of the original genome. The second strain lacked seven of the eight regions, representing 84 genes. Growth assay data revealed an absence of genetic interactions among the 91...
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METHODS: High-Throughput Variation Detection and Genotyping Using Microarrays
- David J. Cutler,
- Michael E. Zwick,
- Minerva M. Carrasquillo,
- Christopher T. Yohn,
- Katherine P. Tobin,
- Carl Kashuk,
- Debra J. Mathews,
- Nila A. Shah,
- Evan E. Eichler,
- Janet A. Warrington,
- and Aravinda Chakravarti
Genome Res. November 1, 2001 11: 1913-1925; Published in Advance October 15, 2001, doi:10.1101/gr.197201
...individual VDA genotypes whether the site is polymorphic or not. It can be applied in experiments in which the target DNA sequences are either haploid or diploid. In effect, the ABACUS system allows an investigator using VDAs to determine the DNA sequence in a sample of interest. ABACUS has been implemented...
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Methods: Detection and Assignment of Mutations and Minihaplotypes in Human DNA Using Peptide Mass Signature Genotyping (PMSG): Application to the Human RDS/Peripherin Gene
- Cheryl A. Telmer,
- Adam R. Retchless,
- Ashley D. Kinsey,
- Yvette Conley,
- Brian Rigatti,
- Michael B. Gorin,
- and Jonathan W. Jarvik
Genome Res. August 2003 13: 1944-1951; doi:10.1101/gr.995103
.../peripherin genomic sequence (GenBank AL049843). Table 3 shows the exon 3 genotype of each of the 16 individuals analyzed. View this table: In this window In a new window Table 2. PMSG Mass Predictions Generated From the DNA Sequencing Results Showing Two Possible Bases at Four Positions in the DNA Being Analyzed...
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METHODS: Efficient Approach to Unique Single-Nucleotide Polymorphism Discovery
- Patricia Taillon-Miller,
- Ellen E. Piernot,
- and Pui-Yan Kwok
Genome Res. May 1, 1999 9: 499-505; doi:10.1101/gr.9.5.499
...Single-nucleotide polymorphisms (SNPs) are the most frequently found DNA sequence variations in the human genome. It has been argued that a dense set of SNP markers can be used to identify genetic factors associated with complex disease traits. Because all high-throughput genotyping methods require...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...alterations in transcriptomes or epis and cannot simultaneously capture genomic and epigenomic variations, which further hinders the phasing of methylation and the detection of allele-specific methylation (ASM).Addressing these challenges, long-read sequencing technologies, such as Pacific Biosciences (Pac...
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