Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants

Reynolds, Gillian; Mumey, Brendan; Strnadova‐Neeley, Veronika; Lachowiec, Jennifer

doi:10.1002/aps3.11581

Title: Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants

Journal Article · 29 April 2024 · Applications in Plant Science

DOI: https://doi.org/10.1002/aps3.11581 · OSTI ID:2471978

Reynolds, Gillian ^[1]; Mumey, Brendan ^[2]; Strnadova‐Neeley, Veronika ^[2];

^[2]

Montana State Univ., Bozeman, MT (United States); Montana State University, Bozeman, MT (United States)
Montana State Univ., Bozeman, MT (United States)

Premise: The genomes of polyploid plants archive the evolutionary events leading to their present forms. However, plant polyploid genomes present numerous hurdles to the genome comparison algorithms for classification of polyploid types and exploring genome dynamics. Methods: Here, the problem of intra- and inter-genome comparison for examining polyploid genomes is reframed as a metagenomic problem, enabling the use of the rapid and scalable MinHashing approach. To determine how types of polyploidy are described by this metagenomic approach, plant genomes were examined from across the polyploid spectrum for both k-mer composition and frequency with a range of k-mer sizes. In this approach, no subgenome-specific k-mers are identified; rather, whole-chromosome k-mer subspaces were utilized. Results: Given chromosome-scale genome assemblies with sufficient subgenome-specific repetitive element content, literature-verified subgenomic and genomic evolutionary relationships were revealed, including distinguishing auto- from allopolyploidy and putative progenitor genome assignment. The sequences responsible were the rapidly evolving landscape of transposable elements. An investigation into the MinHashing parameters revealed that the downsampled k-mer space (genomic signatures) produced excellent approximations of sequence similarity. Furthermore, the clustering approach used for comparison of the genomic signatures is scrutinized to ensure applicability of the metagenomics-based method. Discussion: The easily implementable and highly computationally efficient MinHashing-based sequence comparison strategy enables comparative subgenomics and genomics for large and complex polyploid plant genomes. Such comparisons provide evidence for polyploidy-type subgenomic assignments. In cases where subgenome-specific repeat signal may not be adequate given a chromosomes' global k-mer profile, alternative methods that are more specific but more computationally complex outperform this approach.

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Research Organization:: Montana State Univ., Bozeman, MT (United States)

Sponsoring Organization:: National Institutes of Health (NIH), National Institute of General Medical Sciences (NIGMS); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0021369

OSTI ID:: 2471978

Journal Information:: Applications in Plant Science, Journal Name: Applications in Plant Science Journal Issue: 4 Vol. 12; ISSN 2168-0450

Publisher:: Botanical Society of AmericaCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
MinHash sketching
genome
k-mers
polyploidy
transposable elements

Title: Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants

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