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Research: Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles
- Xuejing Wang and
- Gerald Heckel
Genome Res. June 2024 34: 851-862; Published in Advance July 2, 2024, doi:10.1101/gr.278487.123
...al. 2018). Combining tests for multiple signatures of selection in different categories which are nearly uncorrelated in the way they are affected by variation of recombination rate and genetic drift in neutral genomic regions, for example LD based XP-EHH and derived allele frequency, allows to boost...
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Research: Unexpectedly low recombination rates and presence of hotspots in termite genomes
- Turid Everitt,
- Tilman Rönneburg,
- Daniel Elsner,
- Anna Olsson,
- Yuanzhen Liu,
- Tuuli Larva,
- Judith Korb,
- and Matthew T. Webster
Genome Res. May 2025 35: 1124-1137; Published in Advance March 20, 2025, doi:10.1101/gr.279180.124
...average recombination rate that is observed in honey bees.View larger version: In this window In a new window Figure 1. Genome-wide decay of LD measured as r2 versus distance (base pairs) between SNPs for the two termite species (M. bellicosus, dark red; C. secundus, yellow) and honey bees (A. mellifera...
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Research: Extreme heterochiasmy and high rates of sex-reversed recombination result in large yet homomorphic sex chromosomes in the Emei moustache toad
- Siyu Xie,
- Jun Li,
- Wanyan Chen,
- Lydia J.M. Fong,
- Chunhua Huang,
- Yan Feng,
- Qingbo Ai,
- Mian Zhao,
- Judith E. Mank,
- and Hua Wu
Genome Res. June 2025 35: 1325-1336; Published in Advance April 24, 2025, doi:10.1101/gr.280161.124
...al. 2021), with chromosomes only paired at their terminal region during male meiosis (Morescalchi and Galgano 1973; Miura 1994), similar to what we observed in L. boringii. Genomic regions with sex-specific recombination rates may be important in sex chromosome divergence (Wright et al. 2016...
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Method: Fast inference of genetic recombination rates in biobank scale data
- Ardalan Naseri,
- William Yue,
- Shaojie Zhang,
- and Degui Zhi
Genome Res. July 2023 33: 1015-1022; Published in Advance June 22, 2023, doi:10.1101/gr.277676.123
...,000 subsets (s1, s2, s3, and s4) out of the 200,000 sample in the 34- to 35-MB genomic region at 10-kb resolution are depicted in C. The minimum cutoff was set to l = 0.5 cM. s* denotes the recombination rates in the simulated data. (D) The running time increases linearly with the sample size. The error rates...
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Method: Genome-wide TOP2A DNA cleavage is biased toward translocated and highly transcribed loci
- Xiang Yu,
- James W. Davenport,
- Karen A. Urtishak,
- Marie L. Carillo,
- Sager J. Gosai,
- Christos P. Kolaris,
- Jo Ann W. Byl,
- Eric F. Rappaport,
- Neil Osheroff,
- Brian D. Gregory,
- and Carolyn A. Felix
Genome Res. July 2017 27: 1238-1249; Published in Advance April 6, 2017, doi:10.1101/gr.211615.116
...were DSBs and the remainder were SSNs (Supplemental Table S1; Supplemental Fig. S2). Genome-wide characterization of TOP2A cleavage cluster regions The KMT2A bcr analyses suggested a clustering of reads (Fig. 1C) and TOP2A cleavage sites (Fig. 1D; Supplemental Figs. S3, S4) in compact genomic regions...
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Research: Genome-wide A-to-I RNA editing in fungi independent of ADAR enzymes
- Huiquan Liu,
- Qinhu Wang,
- Yi He,
- Lingfeng Chen,
- Chaofeng Hao,
- Cong Jiang,
- Yang Li,
- Yafeng Dai,
- Zhensheng Kang,
- and Jin-Rong Xu
Genome Res. April 2016 26: 499-509; Published in Advance March 2, 2016, doi:10.1101/gr.199877.115
...were edited to UG1831GUG1834G. Genome-wide analysis identified 26,056 perithecium-specific A-to-I editing sites. Unlike those in animals, 70.5% of A-to-I editing sites in F. graminearum occur in coding regions, and more than two-thirds of them result in amino acid changes, including editing of 69...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...and the density of different classes of transposable elements, most notably a significant enrichment of short interspersed nucleotide elements in genomic regions with higher recombination rate. Finally, the analyses unveiled significant enrichment of genes involved in farnesyltranstransferase activity...
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Research: Genome-wide signals of positive selection in human evolution
- David Enard,
- Philipp W. Messer,
- and Dmitri A. Petrov
Genome Res. June 2014 24: 885-895; Published in Advance March 11, 2014, doi:10.1101/gr.164822.113
...populations of the 1000 Genomes Phase 1 project (SupplementalMaterial). In Europe andAsia, absolute values of iHS correlate positively with ERE density (Fig. 7B,C), but the correlation is more subtle in Africa, where it becomes positive only in low recombination regions (Fig. 7A). The correlation is notably...
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Resource: Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization
- Cory Gardner,
- Junhao Chen,
- Christina Hadfield,
- Zhaolian Lu,
- David Debruin,
- Yu Zhan,
- Maureen J. Donlin,
- Tae-Hyuk Ahn,
- and Zhenguo Lin
Genome Res. November 2024 34: 2133-2146; Published in Advance September 17, 2024, doi:10.1101/gr.279364.124
...(Supplemental Fig. S7). In addition, the Pearson correlation coefficient for the percentages of genomic content is 0.99 (Supplemental Table S4), supporting the robustness of our inference of the origin of genomic regions.We identified a total of 55 major recombination breakpoints in the 16 pairs of CBS380...
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Research: Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species
- Charles Plessy,
- Michael J. Mansfield,
- Aleksandra Bliznina,
- Aki Masunaga,
- Charlotte West,
- Yongkai Tan,
- Andrew W. Liu,
- Jan Grašič,
- María Sara del Río Pisula,
- Gaspar Sánchez-Serna,
- Marc Fabrega-Torrus,
- Alfonso Ferrández-Roldán,
- Vittoria Roncalli,
- Pavla Navratilova,
- Eric M. Thompson,
- Takeshi Onuma,
- Hiroki Nishida,
- Cristian Cañestro,
- and Nicholas M. Luscombe
Genome Res. March 2024 34: 426-440; Published in Advance April 15, 2024, doi:10.1101/gr.278295.123
...pseudoautosomal region (PAR) connected to sex-specific regions by a ribosomal DNA locus (Denoeud et al. 2010; Bliznina et al. 2021). The Y-specific region is repeat-rich and gene-poor and differs from all other genomic regions. Chromosome contact analysis of O. dioica suggests that there is relatively little...
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