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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #417838
Research Project: Enabling Mechanistic Allele Mining to Accelerate Genomic Selection for New Agro-Ecosystems

Location: Plant, Soil and Nutrition Research

Title: New whole-genome alignment tools are needed for tapping into plant diversity

Author
item SONG, BAOXING - Northwest A&f University
item Buckler, Edward - Ed
item STITZER, MICHELLE - Cornell University

Submitted to: Trends in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/23/2023
Publication Date: 9/23/2023
Citation: Song, B., Buckler Iv, E.S., Stitzer, M.C. 2023. New whole-genome alignment tools are needed for tapping into plant diversity. Trends in Plant Science. 29(3):355. https://doi.org/10.1016/j.tplants.2023.08.013.
DOI: https://doi.org/10.1016/j.tplants.2023.08.013

Interpretive Summary: The review article highlights the need for new genome alignment tools to tap into the diversity of plant genomes. Recent advances in genome sequencing have allowed for high-quality, whole-genome assemblies of plants at the population scale. However, existing alignment methods developed for animal genomes are not suitable for plants due to their structural and sequence diversity, frequent whole-genome duplications, and high transposable element activity. The review summarizes classical and emerging genome alignment techniques, emphasizing the challenges and importance of developing optimized methods for plant genomes. Improved alignment tools are essential for understanding plant genome evolution, structural variations, and functional genomics, which are crucial for advancing plant science and breeding programs.

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.