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Huebner, C. D.

Publications and source records attributed to Huebner, C. D..

2 recordsLinked to original sources

Harnessing historical collections to reconstruct the invasion history of Microstegium vimineum (Poaceae)

The evolutionary processes underlying successful invasions are often difficult to disentangle. Historical collections provide a temporal perspective, offering great potential to reconstruct invasion histories and identify the processes driving invasions. Japanese stiltgrass (Microstegium vimineum) is an invasive C4 grass introduced to eastern North America over a century ago and now established in 31 USA states. To reconstruct its invasion history, we leveraged low-coverage whole-genome sequencing of 142 herbarium and 330 contemporary samples spanning the temporal and spatial extent of the North American invasion and the native range in Asia. We identified three independent introductions in the USA: an awnless form in the South and two independent introductions of awned forms in the North, with limited admixture among introductions across space and time. In both regions, we observed high genetic diversity in the earliest available collections despite demographic bottlenecks and identified several putative selective sweeps in or near flowering-time genes, suggesting rapid evolution in the introduced range. Our analyses support separate invasions in the USA, likely facilitated by standing genetic variation and selection, but provide little support for admixture playing a major role. Our study highlights the power of historical collections to uncover the processes and mechanisms underlying successful biological invasions.

evolutionary biology↗

Chromosome level genome assembly and annotation of highly invasive Japanese stiltgrass (Microstegium vimineum)

The invasive Japanese stiltgrass (Microstegium vimineum) affects a wide range of ecosystems and threatens biodiversity across the eastern USA. However, the mechanisms underlying rapid adaptation, plasticity, and epigenetics in the invasive range are largely unknown. We present a chromosome-level assembly for M. vimineum to investigate genome dynamics, evolution, adaptation, and the genomics of phenotypic plasticity. We generated a 1.12 Gb genome with scaffold N50 length of 53.44 Mb respectively, taking a de novo assembly approach that combined PacBio and Dovetail Genomics Omni-C sequencing. The assembly contains 23 pseudochromosomes, representing 99.96% of the genome. BUSCO assessment indicated that 80.3% of Poales gene groups are present in the assembly. The genome is predicted to contain 39,604 protein-coding genes, of which 26,288 are functionally annotated. Furthermore, 66.68% of the genome is repetitive, of which unclassified (35.63%) and long terminal repeat (LTR) retrotransposons (26.90%) are predominant. Similar to other grasses, Gypsy (41.07%) and Copia (32%) are the most abundant LTR-retrotransposon families. The majority of LTR-retrotransposons are derived from a significant expansion in the past 1-2 million years, suggesting the presence of relatively young LTR-retrotransposon lineages. We find corroborating evidence from Ks plots for a stiltgrass-specific duplication event, distinct from the more ancient grass-specific duplication event. The assembly and annotation of M. vimineum will serve as an essential genomic resource facilitating studies of the invasion process, the history and consequences of polyploidy in grasses, and provides a crucial tool for natural resource managers. SignificanceThe current lack of genomic resources for the invasive Japanese stiltgrass--and thousands of other invasive species globally--severely limits our understanding of the invasion process and hinders decision-making for effective management and control. In this study, we present a chromosome-level genome assembly and annotation of Japanese stiltgrass, a problematic weed in eastern North America, identifying a clear history of polyploidy and recent activity of transposable elements. The ultimate goal is to advance genomic studies to better understand the dynamics of non-native species during the various invasion phases, thereby providing insights into effective control strategies to manage current and future invasions.

genomics↗