Searching journal content for articles similar to Cordero et al..

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  1. 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
    ...opposite scenarios by quantifying the association between defense systems, MGE abundance, and gene acquisition rates in a phylogeny-aware comparative study of 197 prokaryotic species.Our results shed light on previous, apparently contradictory findings concerning the effect of CRISPR-Cas on evolution...
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  2. Methods: Reconstructing ancestral gene content by coevolution
    • Tamir Tuller,
    • Hadas Birin,
    • Uri Gophna,
    • Martin Kupiec,
    • and Eytan Ruppin
    Genome Res. January 2010 20: 122-132; Published in Advance November 30, 2009, doi:10.1101/gr.096115.109
    ...Reconstructing ancestral gene content by coevolution Tamir Tuller 1 , 2 , 3 , 4 , 5 , Hadas Birin 1 , 4 , Uri Gophna 2 , Martin Kupiec 2 and Eytan Ruppin 1 , 3 1 School of Computer Sciences, Tel Aviv University...
  3. Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
    • Jacopo Martelossi,
    • Jacopo Vujovic,
    • Yue Huang,
    • Alessia Tatti,
    • Kaiwei Xu,
    • Federico Puliga,
    • Yuanxue Chen,
    • Omar Rota Stabelli,
    • Fabrizio Ghiselli,
    • Xiaoping Zhang,
    • and Alessandra Zambonelli
    Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
    ...-existing Chromoviridae-related Gypsy clades independently expanded in different truffle lineages, leading to increased size and high gene-family turnover rates, but without resulting in highly rearranged s. Additionally, we uncover a significant enrichment of ECM-induced gene families stemming from ancestral duplication...
  4. Research: Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths
    • Fangyuan Yang,
    • Li-Jun Cao,
    • Petr Nguyen,
    • Zhong-Zheng Ma,
    • Jin-Cui Chen,
    • Wei Song,
    • and Shu-Jun Wei
    Genome Res. January 2025 35: 66-77; Published in Advance January 6, 2025, doi:10.1101/gr.279569.124
    ...islands) were identified by the values of FST and Da (Fig. 4B, gray bar; Supplemental Fig. S9). In these islands, we identified multiple genes or gene families related to host adaptation (for the longest 14 chromosomes, see Fig. 4B; Supplemental Table S7) such as the ABCC4 transporter on M17 that was also...
  5. Resource: The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation
    • Zhengcao Li,
    • Xiaohong Liu,
    • Chen Wang,
    • Zhenyang Li,
    • Bo Jiang,
    • Ruifeng Zhang,
    • Lu Tong,
    • Youping Qu,
    • Sheng He,
    • Haifan Chen,
    • Yafei Mao,
    • Qingnan Li,
    • Torsten Pook,
    • Yu Wu,
    • Yanjun Zan,
    • Hui Zhang,
    • Lu Li,
    • Keying Wen,
    • and Yaosheng Chen
    Genome Res. October 2023 33: 1833-1847; Published in Advance November 1, 2023, doi:10.1101/gr.277638.122
    ...features of the pig mobilome that contained 490,480 transposable element insertion polymorphisms (TIPs) resulting from recent mobilization of 970 TE families, and investigated their population dynamics along with influences on population differentiation and gene expression. In addition, several candidate...
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  6. Research: Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera
    • Peter O. Mulhair,
    • Liam Crowley,
    • Douglas H. Boyes,
    • Amber Harper,
    • Owen T. Lewis,
    • Darwin Tree of Life Consortium,
    • and Peter W.H. Holland
    Genome Res. January 2023 33: 32-44; Published in Advance December 8, 2022, doi:10.1101/gr.277118.122
    ...order of insects. Here we analyze an extensive data set of high-quality s to characterize the number and organization of all homeobox genes in 123 species of Lepidoptera from 23 taxonomic families. We find most Lepidoptera have around 100 homeobox loci, including an unusual Hox gene cluster in which...
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  7. 12 Drosophila Genomes/Letter: Sequence variation within the rRNA gene loci of 12 Drosophila species
    • Deborah E. Stage and
    • Thomas H. Eickbush
    Genome Res. December 2007 17: 1888-1897; Published in Advance November 7, 2007, doi:10.1101/gr.6376807
    ..., and the “expansion regions,” which vary in sequence and account for most of the length differences among eukaryotic and prokaryotic rRNA genes ( Clark et al. 1984 ; Hassouna et al. 1984 ). Figure 2 plots the sequence differences among the 12 species (vertical lines). The expansion regions (white boxes) contained...
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  8. Research: Evolutionary assembly patterns of prokaryotic genomes
    • Maximilian O. Press,
    • Christine Queitsch,
    • and Elhanan Borenstein
    Genome Res. June 2016 26: 826-833; Published in Advance April 14, 2016, doi:10.1101/gr.200097.115
    ...by epistasis between residues. In prokaryotes, evolutionary innovation frequently happens by macrogenomic events such as horizontal gene transfer (HGT). Previous work has suggested that HGT can be influenced by ancestral genomic content, yet the extent of such gene-level constraints has not yet been...
  9. PERSPECTIVE: Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity
    • Michael Freeling and
    • Brian C. Thomas
    Genome Res. July 2006 16: 805-814; doi:10.1101/gr.3681406
    ...) by ( Lynch and Conery 2000 ), were overestimated by ∼100-fold because of the prevalence of gene conversion. In general, gene family loss and concomitant loss of coregulated genes characterizes eukaryotes ( Koonin et al. 2004 , and citations therein). The tetraploidies that decorate the eukaryotic...
  10. Research: Evolutionary rate covariation reveals shared functionality and coexpression of genes
    • Nathan L. Clark,
    • Eric Alani,
    • and Charles F. Aquadro
    Genome Res. April 2012 22: 714-720; Published in Advance January 27, 2012, doi:10.1101/gr.132647.111
    ...of bias. However, we found the same patterns of ERC presented above when we restricted analysis to only genes whose orthologs were found in all 18 species (data not shown). Evolutionary rate covariation is uniformly distributed over the protein primary sequence If intermolecular coevolution contributes...
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