Location: Plant, Soil and Nutrition Research
Title: Transposable element abundance subtly contributes to lower fitness in maizeAuthor
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STITZER, MICHELLE - Cornell University |
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KHAIPHO-BURCH, MERRITT - Cornell University |
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HUDSON, ASHER - North Carolina State University |
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SONG, BAOXING - Peking University |
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VALDEZ-FRANCO, JOSE ARCADIO - Cornell University |
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RAMSTEIN, GUILLAUME - Aarhuis University |
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FESCHOTTE, CEDRIC - Cornell University |
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Buckler, Edward - Ed |
Submitted to: bioRxiv
Publication Type: Pre-print Publication Publication Acceptance Date: 9/18/2023 Publication Date: 9/18/2023 Citation: Stitzer, M.C., Khaipho-Burch, M.B., Hudson, A.L., Song, B., Valdez-Franco, J., Ramstein, G., Feschotte, C., Buckler Iv, E.S. 2023. Transposable element abundance subtly contributes to lower fitness in maize. bioRxiv. https://doi.org/10.1101/2023.09.18.557618. DOI: https://doi.org/10.1101/2023.09.18.557618 Interpretive Summary: This study explores the impact of transposable elements (TEs) on maize fitness. TEs are DNA sequences that can move around the genome, potentially causing harmful mutations. Researchers used data from nearly 5,000 maize inbred lines to measure TE content and its effect on grain yield, an important indicator of reproductive success. They found that higher TE content is associated with slightly lower yield, suggesting that while TEs contribute to genetic diversity, they also impose a small fitness cost. This research provides valuable insights into the balance between genetic variation and fitness in crop plants. Technical Abstract: Genome alignment is one of the most foundational methods for genome sequence studies. With rapid advances in sequencing and assembly technologies, these newly assembled genomes present challenges for alignment tools to meet the increased complexity and scale. Plant genome alignment is technologically challenging because of frequent whole-genome duplications (WGDs) as well as chromosome rearrangements and fractionation, high nucleotide diversity, widespread structural variation, and high transposable element (TE) activity causing large proportions of repeat elements. We summarize classical pairwise and multiple genome alignment (MGA) methods, and highlight techniques that are widely used or are being developed by the plant research community. We also outline the remaining challenges for precise genome alignment and the interpretation of alignment results in plants. |