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Resource: Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize
- Laura E. Tibbs-Cortes,
- Tingting Guo,
- Carson M. Andorf,
- Xianran Li,
- and Jianming Yu
Genome Res. August 2024 34: 1253-1263; Published in Advance September 13, 2024, doi:10.1101/gr.279027.124
...for genes within 20 kb of significant markers from DTA slope and intercept GWASs. These identified genes included the known flowering genes cct103 and pebp8 for intercept, conz1 and cry3 for slope, and cct1 for both intercept and slope (Fig. 4). Major indel-based haplotypes of each gene from the 26 NAM...
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Research: Rates and spectra of de novo structural mutations in Chlamydomonas reinhardtii
- Eugenio López-Cortegano,
- Rory J. Craig,
- Jobran Chebib,
- Eniolaye J. Balogun,
- and Peter D. Keightley
Genome Res. January 2023 33: 45-60; Published in Advance December 12, 2022, doi:10.1101/gr.276957.122
..., duplications provide the raw material for gene family evolution via processes that include neo- and subfunctionalization (Kuzmin et al. 2022). Inversions may result in recombination suppression, and the subsequent evolutionary divergence of ancestral and inverted haplotypes has been implicated in local...
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Method: Epigenomic differences in the human and chimpanzee genomes are associated with structural variation
- Xiaoyu Zhuo,
- Alan Y. Du,
- Erica C. Pehrsson,
- Daofeng Li,
- and Ting Wang
Genome Res. February 2021 31: 279-290; Published in Advance December 10, 2020, doi:10.1101/gr.263491.120
...length on the x-axis and the number of indels of different lengths on the y-axis. Colors distinguish indels based on TE classification. (noTE) Not derived from a TE insertion. (C) The number of lineage-biased/invariant putative CNCC promoters, CNCC enhancers, and iPSC H3K9me3 heterochromatin regions...
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Research: Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans
- Yiguan Wang,
- Paul McNeil,
- Rashidatu Abdulazeez,
- Marta Pascual,
- Susan E. Johnston,
- Peter D. Keightley,
- and Darren J. Obbard
Genome Res. April 2023 33: 587-598; Published in Advance April 10, 2023, doi:10.1101/gr.277383.122
...on the simulation of synthetic mutations in raw reads (Supplemental Code), we estimate the median proportion of callable sites was 83.1% (range 78.3%–86.0%) for SNMs, and 78.3% (range 73.5%–80.1%) for short indels.Based on our wild-collected flies, the overall synonymous diversity (πS) was 1.27% in the West African...
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Method: Analyzing rare mutations in metagenomes assembled using long and accurate reads
- Marcus W. Fedarko,
- Mikhail Kolmogorov,
- and Pavel A. Pevzner
Genome Res. November/December 2022 32: 2119-2133; Published in Advance November 23, 2022, doi:10.1101/gr.276917.122
...our focus to substitution mutations because the substitution-based error rate in HiFi reads is an order of magnitude smaller than the indel-based error rate (Wenger et al. 2019).Given an alignment of reads to contigs (Supplemental Material, “Read alignment”), for each position pos in a contig, we...
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Research: Genome-wide evidence for speciation with gene flow in Heliconius butterflies
- Simon H. Martin,
- Kanchon K. Dasmahapatra,
- Nicola J. Nadeau,
- Camilo Salazar,
- James R. Walters,
- Fraser Simpson,
- Mark Blaxter,
- Andrea Manica,
- James Mallet,
- and Chris D. Jiggins
Genome Res. November 2013 23: 1817-1828; Published in Advance September 17, 2013, doi:10.1101/gr.159426.113
.../timareta samples, and 0.05 for outgroup silvaniform samples to allow mapping of reads from divergent species. To minimize false SNPs due to inconsistent mapping around indels, base alignment quality (BAQ) was considered duringmapping, and then local realignment around indels was performed using the Genome Analysis...
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Resource: A calibrated human Y-chromosomal phylogeny based on resequencing
- Wei Wei,
- Qasim Ayub,
- Yuan Chen,
- Shane McCarthy,
- Yiping Hou,
- Ignazio Carbone,
- Yali Xue,
- and Chris Tyler-Smith
Genome Res. February 2013 23: 388-395; Published in Advance October 4, 2012, doi:10.1101/gr.143198.112
...chromosomes to be distinguished. Five thousand eight hundred sixty-five (88.0%) of the variants identified were SNPs, 56 (0.8%) MNPs, and 741 (11.1%) indels. Based on the phylogeny, we found that 172 (2.9%) SNPs, five (9%) multi-nucleotide polymorphisms (MNPs), and 85 (11.5%) indels showed evidence...
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Method: Genome assembly quality: Assessment and improvement using the neutral indel model
- Stephen Meader,
- LaDeana W. Hillier,
- Devin Locke,
- Chris P. Ponting,
- and Gerton Lunter
Genome Res. May 2010 20: 675-684; Published in Advance March 19, 2010, doi:10.1101/gr.096966.109
...IGS histogram: The former increases the representation of long IGS (Fig. 1B), whereas the latter cause short IGS to becomemore prevalent than expected. Nevertheless, owing to the considerable divergence between human and mouse, the probability of a true indel greatly exceeds assembly indel error rates...
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Method: From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing
- Georgi K. Marinov,
- Brian A. Williams,
- Ken McCue,
- Gary P. Schroth,
- Jason Gertz,
- Richard M. Myers,
- and Barbara J. Wold
Genome Res. March 2014 24: 496-510; Published in Advance December 3, 2013, doi:10.1101/gr.161034.113
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Research: Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution
- Herwig Bachmann,
- Marjo J.C. Starrenburg,
- Douwe Molenaar,
- Michiel Kleerebezem,
- and Johan E.T. van Hylckama Vlieg
Genome Res. January 2012 22: 115-124; Published in Advance November 11, 2011, doi:10.1101/gr.121285.111
...as well as in the adapted strains NZ5521 and NZ5522. The reduced expression of sugar transport systems like Table 2. Identified insertions and deletions in the adapted strains Genome position Strain Feature INDEL type INDEL base Position relative to start codon Feature size in number of bases Description...

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