Searching journal content for articles similar to Farré et al. 29 (4): 576.

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Method: k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants
- Pengju Zhao,
- Jiayi He,
- Chen Peng,
- Yuelang Zhang,
- Chong Wang,
- Dongyou Yu,
- Lingzhao Fang,
- and Zhengguang Wang
Genome Res. March 23, 2026 gr.281289.125; Published in Advance March 23, 2026, doi:10.1101/gr.281289.125
...of both elements. Our goals were to elucidate their coevolutionary signatures and assess the 117 impact of TEs on gene regulation and structural variation, thereby advancing our 118 understanding of genomic evolution in ruminants (Fig. 1). 119 Results 120 The KZFP catalog and TE composition in ruminants...
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Research: Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation
- Xin Li,
- San-Gang He,
- Wen-Rong Li,
- Ling-Yun Luo,
- Ze Yan,
- Dong-Xin Mo,
- Xing Wan,
- Feng-Hua Lv,
- Ji Yang,
- Ya-Xi Xu,
- Juan Deng,
- Qiang-Hui Zhu,
- Xing-Long Xie,
- Song-Song Xu,
- Chen-Xi Liu,
- Xin-Rong Peng,
- Bin Han,
- Zhong-Hui Li,
- Lei Chen,
- Jian-Lin Han,
- Xue-Zhi Ding,
- Renqing Dingkao,
- Yue-Feng Chu,
- Jin-Yan Wu,
- Li-Min Wang,
- Ping Zhou,
- Ming-Jun Liu,
- and Meng-Hua Li
Genome Res. September 2022 32: 1669-1684; Published in Advance August 10, 2022, doi:10.1101/gr.276769.122
...molecular basis underlying the genomic recombination and chromosomal evolution.View larger version: In this window In a new window Figure 1. Research framework, hybridization scheme, karyotype and chromosomal painting, statistics of homologs and gene families, phylogenetic tree, and synteny landscape. (A...
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Resource: The pig X and Y Chromosomes: structure, sequence, and evolution
- Benjamin M. Skinner,
- Carole A. Sargent,
- Carol Churcher,
- Toby Hunt,
- Javier Herrero,
- Jane E. Loveland,
- Matt Dunn,
- Sandra Louzada,
- Beiyuan Fu,
- William Chow,
- James Gilbert,
- Siobhan Austin-Guest,
- Kathryn Beal,
- Denise Carvalho-Silva,
- William Cheng,
- Daria Gordon,
- Darren Grafham,
- Matt Hardy,
- Jo Harley,
- Heidi Hauser,
- Philip Howden,
- Kerstin Howe,
- Kim Lachani,
- Peter J.I. Ellis,
- Daniel Kelly,
- Giselle Kerry,
- James Kerwin,
- Bee Ling Ng,
- Glen Threadgold,
- Thomas Wileman,
- Jonathan M.D. Wood,
- Fengtang Yang,
- Jen Harrow,
- Nabeel A. Affara,
- and Chris Tyler-Smith
Genome Res. January 2016 26: 130-139; Published in Advance November 11, 2015, doi:10.1101/gr.188839.114
...-Y homologous pseudoautosomal region (PAR) that permits X-Y pairing during meiosis and within which there is obligate recombination between the sex chromosomes. The gene and sequence content of the PAR varies between species, reflecting processes of expansion and pruning of the PAR in different mammalian...
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LETTER: Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13)Svea36H Mouse
- Ann-Marie Mallon,
- Laurens Wilming,
- Joseph Weekes,
- James G.R. Gilbert,
- Jennifer Ashurst,
- Sandrine Peyrefitte,
- Lucy Matthews,
- Matthew Cadman,
- Richard McKeone,
- Chris A. Sellick,
- Ruth Arkell,
- Marc R.M. Botcherby,
- Mark A. Strivens,
- R. Duncan Campbell,
- Simon Gregory,
- Paul Denny,
- John M. Hancock,
- Jane Rogers,
- and Steve D.M. Brown
Genome Res. October 2004 14: 1888-1901; Published in Advance September 13, 2004, doi:10.1101/gr.2478604
...-9) are indicated. Note that on the human chromosome, the regions are split into two blocks, breaking in segment 5. Positions and relative sizes of regions are only approximate; human and mouse chromosomes are shown to different scales. ( B ) Del36H segment 5 has homology with human chromosome 6p25 and 6p22 at its...
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RESOURCE: A 1463 Gene Cattle–Human Comparative Map With Anchor Points Defined by Human Genome Sequence Coordinates
- Annelie Everts-van der Wind,
- Srinivas R. Kata,
- Mark R. Band,
- Mark Rebeiz,
- Denis M. Larkin,
- Robin E. Everts,
- Cheryl A. Green,
- Lei Liu,
- Shreedhar Natarajan,
- Tom Goldammer,
- Jun Heon Lee,
- Stephanie McKay,
- James E. Womack,
- and Harris A. Lewin
Genome Res. July 2004 14: 1424-1437; doi:10.1101/gr.2554404
...elements) would be compatible with a model of neutral evolution, whereas breakpoints at gene-rich sites could produce novel genes and regulatory elements by shuffling exons/regulatory elements that may be acted upon by selection. Breakpoints within duplicated regions may also create new gene families...
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Resource: Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set
- Joana Damas,
- Rebecca O'Connor,
- Marta Farré,
- Vasileios Panagiotis E. Lenis,
- Henry J. Martell,
- Anjali Mandawala,
- Katie Fowler,
- Sunitha Joseph,
- Martin T. Swain,
- Darren K. Griffin,
- and Denis M. Larkin
Genome Res. May 2017 27: 875-884; Published in Advance November 30, 2016, doi:10.1101/gr.213660.116
....02) (Supplemental Table S12). The -wide CNE density was 0.09, closer to the density observed in msHSBs. Of the ∼347 Mb of chicken found in the “zero CNE windows,” 0.5% was associated with EBRs and 15% with msHSBs. To investigate if these intervals are distributed differently in the breakpoint and synteny regions...
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Resource: Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
- Yang Zhou,
- Lv Yang,
- Xiaotao Han,
- Jiazheng Han,
- Yan Hu,
- Fan Li,
- Han Xia,
- Lingwei Peng,
- Clarissa Boschiero,
- Benjamin D. Rosen,
- Derek M. Bickhart,
- Shujun Zhang,
- Aizhen Guo,
- Curtis P. Van Tassell,
- Timothy P.L. Smith,
- Liguo Yang,
- and George E. Liu
Genome Res. August 2022 32: 1585-1601; Published in Advance August 17, 2022, doi:10.1101/gr.276550.122
.... The location of the black dot on the bar shows the frequency of the contig (log2(animal number)) in the 898 animals. The bars marked with triangles are the contigs with novel exons. Gene symbols with different colors represent protein-coding genes (purple), lncRNAs (pink), and pseudogenes (blue).Breakpoint...
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Resource: Analysis of copy number variations among diverse cattle breeds
- George E. Liu,
- Yali Hou,
- Bin Zhu,
- Maria Francesca Cardone,
- Lu Jiang,
- Angelo Cellamare,
- Apratim Mitra,
- Leeson J. Alexander,
- Luiz L. Coutinho,
- Maria Elena Dell'Aquila,
- Lou C. Gasbarre,
- Gianni Lacalandra,
- Robert W. Li,
- Lakshmi K. Matukumalli,
- Dan Nonneman,
- Luciana C. de A. Regitano,
- Tim P.L. Smith,
- Jiuzhou Song,
- Tad S. Sonstegard,
- Curt P. Van Tassell,
- Mario Ventura,
- Evan E. Eichler,
- Tara G. McDaneld,
- and John W. Keele
Genome Res. May 2010 20: 693-703; Published in Advance March 8, 2010, doi:10.1101/gr.105403.110
...that are significantly enriched for specific biological functions, such as immunity, lactation, reproduction, and rumination. Multiple gene families, including ULBP , have gone through ruminant lineage-specific gene amplification. We detected and confirmed marked differences in their CNV frequencies across diverse...
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ARTICLE: Zebrafish Comparative Genomics and the Origins of Vertebrate Chromosomes
- John H. Postlethwait,
- Ian G. Woods,
- Phuong Ngo-Hazelett,
- Yi-Lin Yan,
- Peter D. Kelly,
- Felicia Chu,
- Hui Huang,
- Alicia Hill-Force,
- and William S. Talbot
Genome Res. December 1, 2000 10: 1890-1902; doi:10.1101/gr.164800
...mechanisms of vertebrate genome evolution, we have compared zebrafish and tetrapod gene maps. It has been suggested that translocations are fixed more frequently than inversions in mammals. Gene maps showed that blocks of conserved syntenies between zebrafish and humans were large, but gene orders were...
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Method: Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome
- Cédric Howald,
- Andrea Tanzer,
- Jacqueline Chrast,
- Felix Kokocinski,
- Thomas Derrien,
- Nathalie Walters,
- Jose M. Gonzalez,
- Adam Frankish,
- Bronwen L. Aken,
- Thibaut Hourlier,
- Jan-Hinnerk Vogel,
- Simon White,
- Stephen Searle,
- Jennifer Harrow,
- Tim J. Hubbard,
- Roderic Guigó,
- and Alexandre Reymond
Genome Res. September 2012 22: 1698-1710; doi:10.1101/gr.134478.111
...RNAs) constitute the lion’s share of this ubiquitous transcription (Kapranov et al. 2002; Okazaki et al. 2002; The ENCODE Project Consortium 2007; Brawand et al. 2011). Some transcripts even shatter the conventional gene structure by joining exons of different well-established coding loci (Parra et al. 2006...
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