Chromosome Level Genome Assembly and Annotation of Highly Invasive Japanese Stiltgrass (Microstegium vimineum)

Area of Science:

• Genomics
• Evolutionary Biology
• Invasive Species Ecology

Background:

• Japanese stiltgrass (Microstegium vimineum) is an invasive plant threatening biodiversity in the eastern USA.
• Mechanisms of its rapid adaptation, phenotypic plasticity, and epigenetic changes in invasive ranges remain poorly understood.

Purpose of the Study:

• To generate a chromosome-level genome assembly for Microstegium vimineum.
• To investigate genome dynamics, evolution, adaptation, and the genomics of phenotypic plasticity in this invasive grass.

Main Methods:

• Utilized a de novo assembly approach combining PacBio and Dovetail Genomics Omni-C sequencing.
• Generated a 1.12 Gb genome assembly with 23 pseudochromosomes (99.96% of the genome).
• Analyzed genome content, including protein-coding genes and repetitive elements like LTR retrotransposons.

Main Results:

• The assembly contains 39,604 predicted protein-coding genes, with 80.3% of Poales gene groups present.
• 66.68% of the genome is repetitive, dominated by unclassified elements and LTR retrotransposons (Gypsy and Copia families).
• Evidence suggests a stiltgrass-specific duplication event and expansion of young LTR retrotransposon lineages in the past 1-2 Myr.

Conclusions:

• The chromosome-level genome assembly of Microstegium vimineum is a vital resource for studying invasion biology.
• Facilitates research into grass polyploidy history, evolutionary adaptation, and provides tools for natural resource managers.
• Enables deeper understanding of the genetic basis for phenotypic plasticity and adaptation in invasive species.