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Research: Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals
- Daniel W. Bellott and
- David C. Page
Genome Res. February 2021 31: 198-210; Published in Advance January 21, 2021, doi:10.1101/gr.268516.120
...their counterparts on the Z and X Chromosomes and became subject to genetic decay (Charlesworth and Charlesworth 2000). In birds and mammals, Z and X Chromosomes retain >98% of the genes that were present on the ancestral autosomes (Bellott et al. 2010). In contrast, the chicken W Chromosome retains only 4...
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Research: Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals
- Antoine Molaro,
- Janet M. Young,
- and Harmit S. Malik
Genome Res. April 2018 28: 460-473; Published in Advance March 16, 2018, doi:10.1101/gr.229799.117
...H2A variants in eutherian mammalsTo gain a comprehensive understanding of the origins and evolution of mammalian short H2A variants, we scanned sequences from representative mammals (and chicken as an outgroup) using BLASTN and TBLASTN searches with human H2A.B, human H2A.P, and rat H2a.l sequences...
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Research: Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals
- Stefan Washietl,
- Manolis Kellis,
- and Manuel Garber
Genome Res. April 2014 24: 616-628; Published in Advance January 15, 2014, doi:10.1101/gr.165035.113
...of lincRNA expression levels and characterize their splicing patterns and tissue specificity across nine tissues in six mammals to directly evaluate whether lincRNA activity is evolutionarily constrained, despite their weak primary sequence conservation. We show that a significant subset of human linc...
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Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...), African Elephant (2n = 56) (Álvarez-González et al. 2022a), Tasmanian Devil (2n = 14) (Álvarez-González et al. 2022a), Platypus (2n = 52) (Zhou et al. 2021), Emu (2n = 78) (Liu et al. 2021), and chicken (2n = 70) (Fishman et al. 2019). As in birds and mammals, the diagonal of the heatmaps of Apalone...
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Research: Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance
- Yang Xi,
- Jingjing Qi,
- Zhao Yang,
- Yutian Zeng,
- Huicong Zhang,
- Qiuyu Tao,
- Mengru Xu,
- Anqi Huang,
- Shenqiang Hu,
- Chunchun Han,
- Lili Bai,
- Jiwei Hu,
- Jiwen Wang,
- Liang Li,
- Lingzhao Fang,
- and Hehe Liu
Genome Res. October 2025 35: 2211-2225; Published in Advance September 10, 2025, doi:10.1101/gr.280345.124
..., oviduct shell gland, and spleen, along with matched whole- sequencing data from 307 egg-laying ducks. We map cis-regulatory variants associated with gene expression (eQTL), alternative splicing (sQTL), and 3′ alternative polyadenylation (apaQTL), yielding 14,074, 6267, and 4994 genes with at least one...
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Research: Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
- Koichi Kitao,
- Kenji Ichiyanagi,
- and So Nakagawa
Genome Res. June 2025 35: 1287-1300; Published in Advance May 8, 2025, doi:10.1101/gr.280007.124
...examples of L1 co-option for vertebrate proteins have been reported. Here, we describe protein isoforms, in which the L1 retrotransposons are incorporated into host genes as protein-coding exons by alternative splicing. L1 ORF1 protein (ORF1p) is an RNA-binding protein that binds to L1 RNA and is required...
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LETTER: Characterization of intron loss events in mammals
- Jasmin Coulombe-Huntington and
- Jacek Majewski
Genome Res. January 2007 17: 23-32; Published in Advance November 15, 2006, doi:10.1101/gr.5703406
.... We found evidence for three independent losses of the ancestral intron 9 (dog, primate/rodent lineage, possum), and a total of nine losses that occurred in this gene in mammals ( Fig. 3 ). The fish, frog, chicken, elephant, and cow have retained the same ancestral structure. GAPDH is a known...
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Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
...rapidly evolved in specific lineages, and whether they contributed to adaptive evolution is still controversial. Here, using an increased number of sequenced s with high taxonomic coverage, we identified 2191 mammalian UCEs and 5938 avian UCEs from 95 mammal and 94 bird s, respectively. Our results show...
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LETTER: Differing patterns of selection in alternative and constitutive splice sites
- Kavita Garg and
- Phil Green
Genome Res. July 2007 17: 1015-1022; Published in Advance June 7, 2007, doi:10.1101/gr.6347907
...Open Access option. Copyright © 2007, Cold Spring Harbor Laboratory Press References ↵ Abril, J.F. , Castelo, R. , Guigo, R. ( 2005 ) Comparison of splice sites in mammals and chicken . Genome Res. 15 : 111 – 119 . ↵ Baek, D. , Green, P. ( 2005 ) Sequence conservation, relative isoform frequencies...
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RESOURCE: A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach
- Evgeny A. Glazov,
- Pauline A. Cottee,
- Wesley C. Barris,
- Robert J. Moore,
- Brian P. Dalrymple,
- and Mark L. Tizard
Genome Res. June 2008 18: 957-964; Published in Advance May 9, 2008, doi:10.1101/gr.074740.107
...identified in previous studies. Having identified 12 chicken mirtrons we extended our search to larger (&gt;200 nt) introns, looking for intronic sequence tags directly adjacent to splice sites. This search yielded another six mirtron candidates ( Fig. 1D ; Table 3 ; Supplemental Figs. S2m–S2r). Although we...

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