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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
..., such as telomeres, pose well-known challenges for phasing during assembly. In the Hi-C anchoring step, most telomere sequences generate signals on both chromosomes simultaneously, yet they are ultimately assigned to only one chromosome (Supplemental Fig. S10). To further explore the genomic landscape of A. avenae...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...and ran RepeatMasker (Tarailo-Graovac and Chen 2009) with parameters -a -s -c -gccalc to calculate Kimura values for all identified TEs using the script calcDivergenceFromAlign.pl. We then generated TE landscapes using the script createRepeatLandscape.pl. In addition, because our repetitive sequence...
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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
...chromosomes over large genomic regions.The evolution of sex chromosomes represents one of the major innovations of inheritance and plays a core role in sexual evolution in the animal kingdom (Charlesworth 1991; Wright et al. 2016). In species with genetic sex determination mechanisms, sex chromosomes carry...
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Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
- Ursula Oggenfuss,
- Robert T. Todd,
- Natthapon Soisangwan,
- Bailey Kemp,
- Alison Guyer,
- Annette Beach,
- and Anna Selmecki
Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
...-read sequencing reveals dynamic -wide SVs in three clinical isolates. (A) Genome-wide genomic landscape: Gene content and TE content in 5000 bp windows of the C. albicans reference . Distribution of SVs in SC5314, L26, and P75063. Colors indicate the SV type in comparison with the reference : green...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...insertions) only the Nimb retrotransposon superfamily was an exception to this pattern, for which 18% of the copies were found in promoter regions (Fig. 1D).View larger version: In this window In a new window Figure 1. Overview of the genomic TE landscape. (A) Superfamily level overview of TE annotations...
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Research: Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation
- David C.H. Metzger,
- Imogen Porter,
- Brendan Mobley,
- Benjamin A. Sandkam,
- Lydia J.M. Fong,
- Andrew P. Anderson,
- and Judith E. Mank
Genome Res. November 2023 33: 1917-1931; Published in Advance November 21, 2023, doi:10.1101/gr.278127.123
...evolution of a novel dosage compensation system. In this study, we examine the genomic and epigenomic landscape of P. picta to identify sex-specific patterns consistent with X Chromosome dosage compensation, embedded within a comparative framework with related species.View larger version: In this window...
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Resource: High-quality sika deer omics data and integrative analysis reveal genic and cellular regulation of antler regeneration
- Zihe Li,
- Ziyu Xu,
- Lei Zhu,
- Tao Qin,
- Jinrui Ma,
- Zhanying Feng,
- Huishan Yue,
- Qing Guan,
- Botong Zhou,
- Ge Han,
- Guokun Zhang,
- Chunyi Li,
- Shuaijun Jia,
- Qiang Qiu,
- Dingjun Hao,
- Yong Wang,
- and Wen Wang
Genome Res. January 2025 35: 188-201; Published in Advance November 14, 2024, doi:10.1101/gr.279448.124
...value (QV) using Merqury (Rhie et al. 2020). In addition, we performed a BUSCO (Waterhouse et al. 2018) assessment of the sequences using the certa_odb10 database.Genome annotationRepeatMasker (Tarailo-Graovac and Chen 2009) was first used to detect and mask the repetitive region. Then, we integrated...
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Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
- Wenyu Zhang,
- Anja Guenther,
- Yuanxiao Gao,
- Kristian Ullrich,
- Bruno Huettel,
- Aftab Ahmad,
- Lei Duan,
- Kaizong Wei,
- and Diethard Tautz
Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
...Differences, Max Planck Institute for Evolutionary Biology, Ploen 24306, Germany; 5School of Mathematics and Data Science, Shaanxi University of Science and Technology, Xi'an 710021, China; 6Max-Planck-Genome-Centre Cologne, MPI for Plant Breeding Research, Cologne 50829, Germany Corresponding authors...
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Method: High-fidelity, large-scale targeted profiling of microsatellites
- Caitlin A. Loh,
- Danielle A. Shields,
- Adam Schwing,
- and Gilad D. Evrony
Genome Res. July 2024 34: 1008-1026; Published in Advance July 16, 2024, doi:10.1101/gr.278785.123
...–6 bp) sequence motifs. Microsatellite loci vary widely in length and number of repeats, and there are more than one million microsatellite loci in the human (Ellegren 2004). The repetitive structure of microsatellites makes them highly mutable relative to other genomic sequences. The estimated de novo...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...to spindle microtubules during cell division. Notably, although centromeres maintain a conserved function in chromosome segregation, the underlying DNA sequences are diverse both within and between species and are predominantly repetitive in nature. The repeat content of centromeres includes high-copy tandem...
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