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Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
- Yuan Lu,
- Edward Rice,
- Kang Du,
- Susanne Kneitz,
- Magali Naville,
- Corentin Dechaud,
- Jean-Nicolas Volff,
- Mikki Boswell,
- William Boswell,
- LaDeana Hillier,
- Chad Tomlinson,
- Kremitzki Milin,
- Ronald B. Walter,
- Manfred Schartl,
- and Wesley C. Warren
Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
...) to align the X. maculatus scaffolds to the genetic linkage map (Amores et al. 2014) and then assigned chromosome coordinates. Using default parameter settings, Chromonomer attempts to find the best set of nonconflicting markers that maximizes the number of scaffolds in the map while minimizing ordering...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...Pan analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility Dongying Xie1,2,3, Pohao Ye1,3, Yiming Ma1 and Zhongying Zhao1 1Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China; 2Institute for Research...
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Research: Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
- Yang Liu,
- João Botelho,
- and Jaime Iranzo
Genome Res. February 2025 35: 268-278; Published in Advance January 10, 2025, doi:10.1101/gr.279300.124
...produce similar effects on HGT. Although reasonable, this grouping criterion may not be optimal in systems in which subtypes markedly differ in their eco-evolutionary dynamics and linkage with MGEs. Moreover, fine-grain dissection of highly abundant systems, such as RM and DMS, could help improve...
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Method: Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome
- Yueying He,
- Yue Xue,
- Jingyao Wang,
- Yupeng Huang,
- Lu Liu,
- Yanyi Huang,
- and Yi Qin Gao
Genome Res. August 2023 33: 1354-1368; Published in Advance July 25, 2023, doi:10.1101/gr.277737.123
...of the . CTG aims to recover a steady genomic structural geometry excluding any stochastic sources.One way to test whether a sequencing-based method such as Hi-C can faithfully reproduce geometric structure information is to make a comparison with fluorescence in situ hybridization (FISH) imaging data (Su et...
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Resource: Haplotype-resolved 3D chromatin architecture of the hybrid pig
- Yu Lin,
- Jing Li,
- Yiren Gu,
- Long Jin,
- Jingyi Bai,
- Jiaman Zhang,
- Yujie Wang,
- Pengliang Liu,
- Keren Long,
- Mengnan He,
- Diyan Li,
- Can Liu,
- Ziyin Han,
- Yu Zhang,
- Xiaokai Li,
- Bo Zeng,
- Lu Lu,
- Fanli Kong,
- Ying Sun,
- Yongliang Fan,
- Xun Wang,
- Tao Wang,
- An'an Jiang,
- Jideng Ma,
- Linyuan Shen,
- Li Zhu,
- Yanzhi Jiang,
- Guoqing Tang,
- Xiaolan Fan,
- Qingyou Liu,
- Hua Li,
- Jinyong Wang,
- Li Chen,
- Liangpeng Ge,
- Xuewei Li,
- Qianzi Tang,
- and Mingzhou Li
Genome Res. February 2024 34: 310-325; Published in Advance March 13, 2024, doi:10.1101/gr.278101.123
..., skeletal muscle, and brain of F1 hybrids were collected for multi-omic assays (for details, see Supplemental Fig. S1). F1i and F1r denote the F1 hybrids of initial and reverse crosses, respectively. (B) Allele assignment of in situ Hi-C contacts in F1 hybrids. A total of about 48.95 billion valid Hi...
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Method: Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network
- Xingyan Liu,
- Qunlun Shen,
- and Shihua Zhang
Genome Res. January 2023 33: 96-111; Published in Advance December 16, 2022, doi:10.1101/gr.276868.122
...-type assignment, a traditional approach includes three steps: clustering single cells, performing differentially expression analysis to find cluster-specific genes, and matching these genes with known markers. However, this strategy fails when clustering different cell types into one group and when analyzing many...
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Research: Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice
- Hongru Wang,
- Filipe G. Vieira,
- Jacob E. Crawford,
- Chengcai Chu,
- and Rasmus Nielsen
Genome Res. June 2017 27: 1029-1038; Published in Advance April 6, 2017, doi:10.1101/gr.204800.116
...to be substantially admixed and thus could not be assigned to a single ancestry group, suggesting a complicated history of hybridization and differentiation among wild rice. Among the identified clusters, four components (Or-A, Or-B, Or-C, andOr-D) are unique to wild rice. TheOr-A component is the first to emerge...
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Method: Characterization of meiotic recombination intermediates through gene knockouts in founder hybrid mice
- Benjamin Davies,
- Gang Zhang,
- Daniela Moralli,
- Samy Alghadban,
- Daniel Biggs,
- Chris Preece,
- Peter Donnelly,
- and Anjali Gupta Hinch
Genome Res. November 2023 33: 2018-2027; Published in Advance November 17, 2023, doi:10.1101/gr.278024.123
..., and RAD51 to single-stranded DNA substrates. High-resolution in vivo binding maps of these proteins provide insights into the underlying molecular mechanisms. When assayed in F1-hybrid mice, these maps can distinguish the broken chromosome from the chromosome used as template for repair, revealing more...
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Method: Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
- Nicholas H. Putnam,
- Brendan L. O'Connell,
- Jonathan C. Stites,
- Brandon J. Rice,
- Marco Blanchette,
- Robert Calef,
- Christopher J. Troll,
- Andrew Fields,
- Paul D. Hartley,
- Charles W. Sugnet,
- David Haussler,
- Daniel S. Rokhsar,
- and Richard E. Green
Genome Res. March 2016 26: 342-350; Published in Advance February 4, 2016, doi:10.1101/gr.193474.115
...suited to the characterization of short-range sequence contiguity and genomic variation. Achieving long-range linkage and haplotype phasing requires either the ability to directly and accurately read long (i.e., tens of kilobase) sequences or the capture of linkage and phase relationships through paired...
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Research: The subgenomes show asymmetric expression of alleles in hybrid lineages of Megalobrama amblycephala × Culter alburnus
- Li Ren,
- Wuhui Li,
- Qinbo Qin,
- He Dai,
- Fengming Han,
- Jun Xiao,
- Xin Gao,
- Jialin Cui,
- Chang Wu,
- Xiaojing Yan,
- Guoliang Wang,
- Guiming Liu,
- Jia Liu,
- Jiaming Li,
- Zhong Wan,
- Conghui Yang,
- Chun Zhang,
- Min Tao,
- Jing Wang,
- Kaikun Luo,
- Shi Wang,
- Fangzhou Hu,
- Rurong Zhao,
- Xuming Li,
- Min Liu,
- Hongkun Zheng,
- Rong Zhou,
- Yuqin Shu,
- Yude Wang,
- Qinfeng Liu,
- Chenchen Tang,
- Wei Duan,
- and Shaojun Liu
Genome Res. November 2019 29: 1805-1815; Published in Advance October 24, 2019, doi:10.1101/gr.249805.119
...in this study is shown in Figure 1. BSB and TC were used as the parents in the reciprocal cross hybrids to form two types of hybrid lineages. In the first cross group, a BSB (♀) × TC (♂) cross was performed to produce F1 hybrids (BT, 2n = 48). Then, the intercrossing within F1 females and males produce F2...
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