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Research: Differences in activity and stability drive transposable element variation in tropical and temperate maize
- Shujun Ou,
- Armin Scheben,
- Tyler Collins,
- Yinjie Qiu,
- Arun S. Seetharam,
- Claire C. Menard,
- Nancy Manchanda,
- Jonathan I. Gent,
- Michael C. Schatz,
- Sarah N. Anderson,
- Matthew B. Hufford,
- and Candice N. Hirsch
Genome Res. August 2024 34: 1140-1153; Published in Advance September 9, 2024, doi:10.1101/gr.278131.123
..., not only into the genomic dynamics in maize but also into the general contribution of LTR-RTs to biodiversity in plants. The selective determinants of TE content are likely diverse, occurring at the TE family level based on insertional preference (e.g., genic vs. nongenic regions) (Stitzer et al. 2021...
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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
...variations,” such as gene presence/absence variations (PAVs) and PAVs of transposable elements (TEs) that contain open reading frames (ORFs) (Joly-Lopez and Bureau 2018), have been shown to be important determinants of evolution and phenotypic variability in a range of species (Gao et al. 2019; Niu et al...
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Research: A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits
- Steffen Knauer,
- Marie Javelle,
- Lin Li,
- Xianran Li,
- Xiaoli Ma,
- Kokulapalan Wimalanathan,
- Sunita Kumari,
- Robyn Johnston,
- Samuel Leiboff,
- Robert Meeley,
- Patrick S. Schnable,
- Doreen Ware,
- Carolyn Lawrence-Dill,
- Jianming Yu,
- Gary J. Muehlbauer,
- Michael J. Scanlon,
- and Marja C.P. Timmermans
Genome Res. December 2019 29: 1962-1973; Published in Advance November 19, 2019, doi:10.1101/gr.250878.119
...from light signaling (Harris et al. 2011; Siddiqui et al. 2016), pointing to mechanisms allowing for plasticity in the specification of functional SAM domains in response to environmental cues. Conversely, the promoters of CZ-specific genes contain cis-regulatory motifs for, on average, five distinct...
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Research: Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements
- Yuyun Zhang,
- Zijuan Li,
- Yu'e Zhang,
- Kande Lin,
- Yuan Peng,
- Luhuan Ye,
- Yili Zhuang,
- Meiyue Wang,
- Yilin Xie,
- Jingyu Guo,
- Wan Teng,
- Yiping Tong,
- Wenli Zhang,
- Yongbiao Xue,
- Zhaobo Lang,
- and Yijing Zhang
Genome Res. December 2021 31: 2276-2289; Published in Advance September 9, 2021, doi:10.1101/gr.275658.121
...: In this window In a new window Figure 1. Genome-wide binding of wheat transcription factors underlying responses to environmental stimuli. (A) Schematic of the experimental design and filtering steps. The detailed filtering steps were listed in Supplemental Table S2. (B) Genomic tracks illustrating the targeting...
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Research: Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis
- Alexandra Dallaire,
- Bethan F. Manley,
- Maya Wilkens,
- Iliana Bista,
- Clement Quan,
- Edouard Evangelisti,
- Charles R. Bradshaw,
- Navin B. Ramakrishna,
- Sebastian Schornack,
- Falk Butter,
- Uta Paszkowski,
- and Eric A. Miska
Genome Res. December 2021 31: 2290-2302; Published in Advance November 12, 2021, doi:10.1101/gr.275752.121
...of environments and can even engage in symbioses with multiple plant species simultaneously. The complex life cycles of AMF suggest a requirement for strong developmental and phenotypic plasticity. However, although AMF carry meiosis-related genes (Halary et al. 2011) and heterokaryotic strains originating from...
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Research: Genetic analysis in the Collaborative Cross breeding population
- Vivek M. Philip,
- Greta Sokoloff,
- Cheryl L. Ackert-Bicknell,
- Martin Striz,
- Lisa Branstetter,
- Melissa A. Beckmann,
- Jason S. Spence,
- Barbara L. Jackson,
- Leslie D. Galloway,
- Paul Barker,
- Ann M. Wymore,
- Patricia R. Hunsicker,
- David C. Durtschi,
- Ginger S. Shaw,
- Sarah Shinpock,
- Kenneth F. Manly,
- Darla R. Miller,
- Kevin D. Donohue,
- Cymbeline T. Culiat,
- Gary A. Churchill,
- William R. Lariviere,
- Abraham A. Palmer,
- Bruce F. O'Hara,
- Brynn H. Voy,
- and Elissa J. Chesler
Genome Res. August 2011 21: 1223-1238; Published in Advance July 6, 2011, doi:10.1101/gr.113886.110
...scores >1 in the CC lines, fewer extreme high scores were observed, suggesting a restoration of continuous variation of this phenotype. Breeding effects in the Collaborative Cross Genome Research 1227 www..org increase in frequency while other alleles decrease in frequency through the process...
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Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
.... S18), we named the Spirodela SUVH5/6 ortholog as spSUVH6(5) until its sequence binding preference is determined. In addition, with regards to mCHH maintenance, CMT2, required to maintain mCHH together with SUVH4 (Stroud et al. 2014), is missing like in maize (Bewick et al. 2017), as previously...
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Research: Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence
- Scott Ferguson,
- Ashley Jones,
- Kevin Murray,
- Rose Andrew,
- Benjamin Schwessinger,
- and Justin Borevitz
Genome Res. April 2024 34: 606-619; Published in Advance April 8, 2024, doi:10.1101/gr.277999.123
...of inversions, which may be underreported, and translocations, which may contribute less to ongoing divergence than reported (Supplemental Results).Genome-specific and group-wide sequencesUnaligned sequences occupied on average 30.65% of each Eucalyptus within each pairwise alignment. To determine...
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Research: Historical RNA expression profiles from the extinct Tasmanian tiger
- Emilio Mármol-Sánchez,
- Bastian Fromm,
- Nikolay Oskolkov,
- Zoé Pochon,
- Panagiotis Kalogeropoulos,
- Eli Eriksson,
- Inna Biryukova,
- Vaishnovi Sekar,
- Erik Ersmark,
- Björn Andersson,
- Love Dalén,
- and Marc R. Friedländer
Genome Res. August 2023 33: 1299-1316; Published in Advance July 18, 2023, doi:10.1101/gr.277663.123
...of convergent evolution (Newton et al. 2021; Rovinsky et al. 2021).Despite diverging from placental carnivorous mammals ∼160 million years ago (Bininda-Emonds et al. 2007), thylacines showed striking phenotypic similarities with extant species like those belonging to the Canidae family. This illustrates how...
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Resource: Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii
- Carlos Vargas-Chavez,
- Neil Michel Longo Pendy,
- Sandrine E. Nsango,
- Laura Aguilera,
- Diego Ayala,
- and Josefa González
Genome Res. January 2022 32: 189-202; Published in Advance December 29, 2021, doi:10.1101/gr.275761.121
....3%) and the false negative rate (0.87%) of our annotations were low (for further details, see Supplemental Methods).Identification of newly described families in other speciesTo determine the presence of the newly described TE families in other species, RepeatMasker version open-4.0.9 (Smit et al. 2013...

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