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Resource: Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize
- Laura E. Tibbs-Cortes,
- Tingting Guo,
- Carson M. Andorf,
- Xianran Li,
- and Jianming Yu
Genome Res. August 2024 34: 1253-1263; Published in Advance September 13, 2024, doi:10.1101/gr.279027.124
...authors: xianran.li@usda.gov, jmyu@iastate.eduAbstractMaize phenotypes are plastic, determined by the complex interplay of genetics and environmental variables. Uncovering the genes responsible and understanding how their effects change across a large geographic region are challenging. In this study, we...
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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
...in a pan context. We then generated a unified TE annotation for a maize pan derived from 26 reference-quality s, which reveals an excess of 35.1 Mb of TE sequences per in tropical maize relative to temperate maize. A small number (n = 216) of TE families, mainly LTR retrotransposons, drive...
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Method: Partitioned multi-MUM finding for scalable pangenomics with MumemtoM
- Vikram S. Shivakumar and
- Ben Langmead
Genome Res. February 2026 36: 397-404; Published in Advance November 7, 2025, doi:10.1101/gr.280940.125
...:10.1093/bioinformatics/btaf104 ↵Shivakumar VS, Langmead B. 2025. Mumemto: Efficient maximal matching across pans. Genome Biol 26: 169. doi:10.1186/s13059-025-03644-0 ↵Taylor DJ, Eizenga JM, Li Q, Das A, Jenike KM, Kenny EE, Miga KH, Monlong J, McCoy RC, Paten B, et al. 2024. Beyond the human project...
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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
...and the production of viable reproducing offspring, the architecture of both parental haplotypes must be highly similar. Changes to the genetic architecture can result in reproductive isolation/incompatibility or nonviable gametes (Hardigan et al. 2020; Simakov et al. 2020). Therefore, a common architecture within...
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