These data represent the first reference genome for the invasive Phragmites australis ssp. australis (1.14 giga base pairs (Gbp)), as well as output from comparative genomic and transcriptomic analyses for invasive and native genotypes coexisting in the Great Lakes region of North America. Genome sequencing data used tillers and associated rhizome tissues collected from a single P. australis patch at the Ottawa National Wildlife Refuge near Toledo, Ohio, USA. Transcriptome analyses were produced from samples collected from three invasive and three native genotype P. australis patches from four sites around the Great Lakes in Michigan and Ohio, USA.

To determine how native and non-native lineages of Phragmites australis affect and respond to soil bacteria, fungi and oomycetes, we collected live rhizomes, seeds and soil from native and non-native lineages of Phragmites from 10 sites within Michigan and Ohio, USA. We propagated these field-collected samples to carry out a reciprocal-transplant plant-soil feedback experiment with multiple microbial inhibition treatments. Specifically, we investigated how each Phragmites lineage grew in soils pre-conditioned by each lineage and soils that had been pre-sterilized. Plant biomass was the main response variable collected to determine responses to microbial soil conditioning. We also used DNA meta-barcoding to identify the effects of each plant lineage on soil microbes and link plant responses to microbial communities. Specifically, DNA was extracted from soils and fungal and bacterial DNA was amplified to identify the microbial constituents. Amplicons were sequenced using Illumina MiSeq. This dataset includes outputs of bioinformatic analysis of sequences including operational taxonomic unit (OTU) generation, OTU abundance, resolved taxonomy, and environmental metadata collected in our survey. Raw sequences were uploaded to the NCBI Sequence Read Archive under SRA accession number PRJNA719385.

To determine how native and non-native lineages of Phragmites australis affect and respond to soil bacteria, fungi and oomycetes, we collected live rhizomes, seeds and soil from native and non-native lineages of Phragmites from 10 sites within Michigan and Ohio, USA. We propagated these field-collected samples to carry out a reciprocal-transplant plant-soil feedback experiment with multiple microbial inhibition treatments. Specifically, we investigated how each Phragmites lineage grew in soils pre-conditioned by each lineage and soils that had been pre-sterilized. Plant biomass was the main response variable collected to determine responses to microbial soil conditioning. We also used DNA meta-barcoding to identify the effects of each plant lineage on soil microbes and link plant responses to microbial communities. Specifically, DNA was extracted from soils and fungal and bacterial DNA was amplified to identify the microbial constituents. Amplicons were sequenced using Illumina MiSeq. This dataset includes outputs of bioinformatic analysis of sequences including operational taxonomic unit (OTU) generation, OTU abundance, resolved taxonomy, and environmental metadata collected in our survey. Raw sequences were uploaded to the NCBI Sequence Read Archive under SRA accession number PRJNA719385.

Nonnative Phragmites australis (common reed) is widely distributed across North America and insufficient knowledge of P. australis has impeded the efficiency of management. To aid in Phragmites management and future studies, we used RNA-seq data from multiple types of plant tissue to construct forty-nine P. australis transcriptomes via different assembly tools and multiple parameter settings, resulting in seven assembled transcriptomes for further comprehensive assessments. The optimal transcriptome ("cd-hit") was selected for functional annotation and downstream analyses. This data release contains the seven assembled transcriptomes, and data derived from the optimal transcriptome (functional annotations, tissue-specific expression patterns, putative transcription factors, and simple sequence repeats markers).

Nonnative Phragmites australis (common reed) is widely distributed across North America and insufficient knowledge of P. australis has impeded the efficiency of management. To aid in Phragmites management and future studies, we used RNA-seq data from multiple types of plant tissue to construct forty-nine P. australis transcriptomes via different assembly tools and multiple parameter settings, resulting in seven assembled transcriptomes for further comprehensive assessments. The optimal transcriptome (“cd-hit”) was selected for functional annotation and downstream analyses. This data release contains the seven assembled transcriptomes, and data derived from the optimal transcriptome (functional annotations, tissue-specific expression patterns, putative transcription factors, and simple sequence repeats markers).

These data were compiled to provide land-management relevant information on the native and nonnative subspecies (subsp.) of Phragmites australis (subsp. americanus and subsp. australis, respectively) in Glen Canyon National Recreation Area (NRA), Grand Canyon National Park (NP), Arches National Park, and Bill Williams National Wildlife Refuge. Specifically, the goals of this work were to determine the extent and distribution of Phragmites australis subspecies in the Glen and Grand Canyon regions, evaluate if P.a. subsp. americanus can be reliably distinguished from P.a. subsp. australis using morphological characters in this region, and determine if P.a. subsp. americanus exhibits genetic structure in the study area. The objectives of our study were to determine how prevalent the nonnative Phragmites is in the study area and support native plant material development for restoration activities in Glen Canyon NRA and Grand Canyon NP. These data represent real-time PCR cycle threshold values (Ct scores) for two target regions, nuclear microsatellite data for seven loci, and morphological data. These data were collected for 84 sites including five nonnative Phragmites locations and 79 native Phragmites locations. Tissue samples were mostly collected along the Colorado River between Glen Canyon Dam and Lake Mead, around Lake Powell, and in tributaries to the Colorado River from 2021 through 2024. Tissue samples and herbarium collections were collected from one to fifteen ramets across each stand, where multiple samples from one stand were spread across its full area. Reference samples for both the native and nonnative Phragmites, Phragmites australis subsp. berlandieri, and a hybrid of P.a. australis and P.a. americanus were acquired and included in analyses. Samples were dried and total genomic DNA was extracted using Qiagen DNeasy Plant MiniKits. Real-time polymerase chain reactions (PCR) with two target regions, AMER and AMAU, were used to identify nonnative Phragmites individuals (Lindsay et al, 2023). We then amplified 7 microsatellite loci (Saltonstall, 2003; Meyerson and others, 2010) using PCR and analyzed the fragments on an ABI 3730XL Genetic Analyzer with GeneScan LIZ500 internal size standard. Although P. australis is polyploid, these loci all had no more than two alleles, so were treated as diploid data. We then collected field and lab data on morphological characters for the stands we genetically tested, following previously described diagnostic characters (Swearington and Saltonstall, 2012; McTavish et al, 2023) These data can be used to evaluate if a stand of Phragmites is nonnative, native, or a hybrid of the two. It can also be used to determine genetic diversity and structure across the sampled stands. Finally, they can be used to assess morphological variability in native Phragmites stands across the region.

These data tables contain data collections from field experiments of Phragmites australis (ssp. australis) treated with known fungal endophytes. Tiller counts, tiller diameter, and tiller height measurements were taken every two weeks over an eight-week study period. Clones of Phragmites plants were collected from three different locations: Sandusky, Michigan; Bloomington, Indiana; and the Ottawa National Wildlife Refuge near Oak Harbor, Ohio. Additionally, data collections from a similar experiment of Phragmites australis (ssp. australis) treated with known fungal endophytes performed in a growth chamber are included. Tiller numbers and tiller heights were measured every three weeks over 15 total weeks for the growth chamber experiment. Plants from both experiments were collected and processed to determine dry weights and fungal communities were sequenced. All sequence data were submitted to GenBank (NCBI Accession Numbers: OM26200-OM262384).

The data document the results of several microbe bioassays performed by the USGS on Phragmites australis plants, including those performed on mature leaves, seedlings, and dead leaf tissues exploration of the literature to find accounts of microbes associated with Phragmites worldwide. For the bioassays, we prepared 162 pure cultures isolated from Phragmites plants in North America along the east coast, Florida, the Gulf of Mexico, and the Great Lakes area, 125 of which were from a previous study, and 38 represent new collections. The DNA sequences used to identify the 37 new collections are included. Microbes were isolated from plants collected from 2015-2018. We performed assays using both North American plant lineages (Phragmites australis subsp. australis and Phragmites australis subsp. americanus) on mature leaves and seedlings. Data included here report each plant's reaction to microbial inoculation. Finally, to put our findings in context, we surveyed Phragmites-associated microbes assembled from multiple extensive literature sources representing a worldwide extent These data will be valuable to researchers interested in effects of leaf microbes on Phragmites health and invasiveness of the non-native lineage. Additionally, the data have implications for potential biocontrol of Phragmites.

The data document the results of several microbe bioassays performed by the USGS on Phragmites australis plants, including those performed on mature leaves, seedlings, and dead leaf tissues exploration of the literature to find accounts of microbes associated with Phragmites worldwide. For the bioassays, we prepared 162 pure cultures isolated from Phragmites plants in North America along the east coast, Florida, the Gulf of Mexico, and the Great Lakes area, 125 of which were from a previous study, and 38 represent new collections. The DNA sequences used to identify the 37 new collections are included. Microbes were isolated from plants collected from 2015-2018. We performed assays using both North American plant lineages (Phragmites australis subsp. australis and Phragmites australis subsp. americanus) on mature leaves and seedlings. Data included here report each plant's reaction to microbial inoculation. Finally, to put our findings in context, we surveyed Phragmites-associated microbes assembled from multiple extensive literature sources representing a worldwide extent These data will be valuable to researchers interested in effects of leaf microbes on Phragmites health and invasiveness of the non-native lineage. Additionally, the data have implications for potential biocontrol of Phragmites.

Briefly, sample collection will entail collecting soil samples at 5 sites within 1 suggested area, with each site being more than a quarter mile apart. Sample sites would be between 150 feet from roads, and 75 feet from trails. At each site, 3 subsamples of topsoil (0-8 inches) using scoop will be collected, yielding 1 pooled sample (about 1.2 lbs).