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Research: The genomic consequences and persistence of sociality in spiders
- Jilong Ma,
- Jesper Bechsgaard,
- Anne Aagaard,
- Palle Villesen,
- Trine Bilde,
- and Mikkel Heide Schierup
Genome Res. March 2025 35: 499-511; Published in Advance February 20, 2025, doi:10.1101/gr.279503.124
...et al. 2020) estimation on our s reveal k-mer completeness ranging from 97.65% to 99.41% and a consensus quality QV ranging from 62.54 to 73.86, which is higher than the Vertebrate Genomes Project (VGP) benchmarking recommendations of QV > 40 and k-mer completeness > 95% (Rhie et al. 2021). When...
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Research: Worldwide patterns of genomic variation and admixture in gray wolves
- Zhenxin Fan,
- Pedro Silva,
- Ilan Gronau,
- Shuoguo Wang,
- Aitor Serres Armero,
- Rena M. Schweizer,
- Oscar Ramirez,
- John Pollinger,
- Marco Galaverni,
- Diego Ortega Del-Vecchyo,
- Lianming Du,
- Wenping Zhang,
- Zhihe Zhang,
- Jinchuan Xing,
- Carles Vilà,
- Tomas Marques-Bonet,
- Raquel Godinho,
- Bisong Yue,
- and Robert K. Wayne
Genome Res. February 2016 26: 163-173; Published in Advance December 17, 2015, doi:10.1101/gr.197517.115
...s of nine individual wolves, one coyote, and one golden jackal at 9–28× coverage using the Illumina HiSeq 2000 platform to geographically complement existing canine sequences. Combined with published s, we assemble a data set with 34 canid s to (1) assess relationshippatternsacross theentire...
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LETTER: The genome-wide determinants of human and chimpanzee microsatellite evolution
- Yogeshwar D. Kelkar,
- Svitlana Tyekucheva,
- Francesca Chiaromonte,
- and Kateryna D. Makova
Genome Res. January 2008 18: 30-38; Published in Advance November 21, 2007, doi:10.1101/gr.7113408
...in chimpanzee and/or (3) different repeated motifs at orthologous locations in human and chimpanzee and/or (4) neighboring microsatellites within 10 bp (because adjacent microsatellites might affect each other’s mutation rates) ( Almeida and Penha-Goncalves 2004 ) and/or (5) fewer than nine repeats...
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LETTER: Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias
- Mikael Brandström and
- Hans Ellegren
Genome Res. June 2008 18: 881-887; Published in Advance March 20, 2008, doi:10.1101/gr.075242.107
...genomic sequences of nine species . Genome Res. 13 : 2242 – 2251 . ↵ Ellegren, H. ( 2000 ) Heterogeneous mutation processes in human microsatellite DNA sequences . Nat. Genet. 24 : 400 – 402 . ↵ Ellegren, H. , Primmer, C.R. , Sheldon, B.C. ( 1995 ) Microsatellite 'evolution': Directionality or bias? Nat...
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Research: Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species
- Phillip A. Morin,
- Frederick I. Archer,
- Andrew D. Foote,
- Julia Vilstrup,
- Eric E. Allen,
- Paul Wade,
- John Durban,
- Kim Parsons,
- Robert Pitman,
- Lewyn Li,
- Pascal Bouffard,
- Sandra C. Abel Nielsen,
- Morten Rasmussen,
- Eske Willerslev,
- M. Thomas P. Gilbert,
- and Timothy Harkins
Genome Res. July 2010 20: 908-916; Published in Advance April 22, 2010, doi:10.1101/gr.102954.109
...–5217), the assembly was unreliable, so the regions were shortened to a fixed set of nine Cs and seven As, respectively, for phylogenetic analysis to avoid introducing potentially erroneous variation. Eight samples were sequenced twice and analyzed for differences between replicates. Sequence alignments of other...
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Method: Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes
- Michael F. Lin,
- Pouya Kheradpour,
- Stefan Washietl,
- Brian J. Parker,
- Jakob S. Pedersen,
- and Manolis Kellis
Genome Res. November 2011 21: 1916-1928; Published in Advance October 12, 2011, doi:10.1101/gr.108753.110
...to the inferred ancestral sequence; (dark green) conservative amino acid substitutions; (red) other nonsynonymous substitutions. The estimated parameter ls ome denotes the rate of synonymous substitution within these selected windows relative to -wide averages. For example, the nine-codon window starting at codon...
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Perspective: Constructing genomic maps of positive selection in humans: Where do we go from here?
- Joshua M. Akey
Genome Res. May 2009 19: 711-722; doi:10.1101/gr.086652.108
...), the type of selection acting upon LCT (Bersaglieri et al. 2004; Tishkoff et al. 2007). The integrated map of positive selection across these nine -wide scans is shown in Figure 2. In total, 5110 distinct regions were identified in one or more study. These regions encompass ;409 Mb of sequence (;14...
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Methods: Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization
- Jason S. Maydan,
- Stephane Flibotte,
- Mark L. Edgley,
- Joanne Lau,
- Rebecca R. Selzer,
- Todd A. Richmond,
- Nathan J. Pofahl,
- James H. Thomas,
- and Donald G. Moerman
Genome Res. March 2007 17: 337-347; Published in Advance January 31, 2007, doi:10.1101/gr.5690307
...of the nine genes targeted by the deletion. Duplications of sequences flanking the deletion are indicated by positive log 2 ratios. Adjacent 50-mer probes in this region overlap by as much as 44 bp. Using the same X:II array design, we next examined whether oaCGH could detect a smaller homozygous deletion...
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Methods: High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping
- Daniel A. Peiffer,
- Jennie M. Le,
- Frank J. Steemers,
- Weihua Chang,
- Tony Jenniges,
- Francisco Garcia,
- Kirt Haden,
- Jiangzhen Li,
- Chad A. Shaw,
- John Belmont,
- Sau Wai Cheung,
- Richard M. Shen,
- David L. Barker,
- and Kevin L. Gunderson
Genome Res. September 2006 16: 1136-1148; Published in Advance August 9, 2006, doi:10.1101/gr.5402306
...chromosomes were detected on the 317K BeadChip. The 72-kb duplication was detected on the 109K primarily because of the split of the heterozygous cluster. The 109K array detected nine out of 10 aberrations ( Fig. 4F ), and the 317K detected the aberration missed by the 109K array (a 115-kb deletion) ( Fig. 4G...
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REPORT: MHC Class II Pseudogene and Genomic Signature of a 32-kb Cosmid in the House Finch (Carpodacus mexicanus)
- Christopher M. Hess,
- Joe Gasper,
- Hopi E. Hoekstra,
- Christopher E. Hill,
- and Scott V. Edwards
Genome Res. May 1, 2000 10: 613-623; doi:10.1101/gr.10.5.613
...), and a “nonclassical” class II chicken gene (n=3). These comparisons were made with a number of chicken sequences downloaded from GenBank ( Zoorob et al. 1993 ) and the nine inferred haplotypes from house finches obtained through PCR amplification, direct sequencing, and analysis using HAPINFER as described in text...

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