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Comparative Genomics/Transcriptomics

Ramachandran, Dhanushya [1], Corbett, Cameron [2], Huebner, Cynthia [3], Daly, Mark [4], Haimovitz, Jasmine [4], McKain, Michael [5], Swale, Thomas [4], Barrett, Craig [6].

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

Invasive species cause billions of dollars in damage annually, and represent major threats to biodiversity and economies globally. Yet, invasive species are underrepresented among sequenced genomes, translating to a lack of tools for managers and researchers. Japanese stiltgrass (Microstegium vimineum) is an invasive, annual grass that poses a major threat to biodiversity across the eastern USA. As a shade-tolerant, C4 grass, it invades high and low light environments, and affects a wide range of ecosystems from forests to agricultural areas. Nevertheless, the genomic underpinnings of rapid adaptation, plasticity, and epigenetics in the invasive range are largely unknown. Here, 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 contig and scaffold N50 length of 597 Kb and 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 from OrthoDB were present in the assembly. Combined with Illumina RNA-seq data from four tissues collected at three localities in West Virginia, 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, the most abundant LTR-retrotransposon family present in M. vimineum genome is Gypsy (41.07%), followed by Copia (32%). And, 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. The recent LTR-retrotransposon activity could be the consequence of polyploidization events, as observed in other plants. We also identified 5,429,741 low-copy repeats in the genome that span 1-82 Kb distributed within and between chromosomes, sharing >90% identity. We are performing a comparative study on the M. vimineum genome and related grasses to detect evidence for polyploidy and to infer synteny between duplicated regions. We find corroborating evidence from self-Ks plots for a stiltgrass-specific duplication event, distinct from the more ancient grass-specific duplication event. The assembly and annotation of M. vimineum we report will serve as a genomic resource for facilitating studies of rapid adaptation in invasive plants, the history and consequences of polyploidy in grasses, and a crucial tool for natural resource managers.

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1 - West Virginia University, Biology, 53, Campus Drive, Morgantown, WV, 26501, USA
2 - 53 Campus Drive, Morgantown, WV, 26505, United States
3 - Northern Research Station, USDA Forest Service, Morgantown, WV, 26505, United States
4 - Dovetail Genomics
5 - University of Alabama
6 - West Virginia University, Biology, 53 Campus Drive, Morgantown, WV, 26506, USA

Japanese stiltgrass
Genome Assembly
transposable elements
invasive species
rapid adaptation
Comparative genomics.

Presentation Type: Oral Paper
Session: CGT3, Comparative Genomics/Transcriptomics III
Location: /
Date: Tuesday, July 20th, 2021
Time: 3:30 PM(EDT)
Number: CGT3003
Abstract ID:780
Candidate for Awards:Margaret Menzel Award

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