Novel genome characteristics contribute to the invasiveness of <i>Phragmites australis</i> (common reed)

Oh, Dong Ha; Kowalski, Kurt P.; Quach, Quynh N.; Wijesinghege, Chathura; Tanford, Philippa; Dassanayake, Maheshi; Clay, Keith

doi:10.1111/mec.16293

Cited by 15 publications

(8 citation statements)

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“…P. australis belongs to Arundinoideae subfamily, which is the sister subfamily of Panicoideae where S. italica is grouped. A recent work confirmed the closed relationship between P. australis and S. italica based on multiple amino acid alignments [66]. Since S. italica is well annotated [24], we could delve into the putative function of interesting transcripts more deeply.…”

Section: Plos Onesupporting

confidence: 56%

Optimization and application of non-native Phragmites australis transcriptome assemblies

et al. 2023

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Phragmites australis (common reed) has a cosmopolitan distribution and has been suggested as a model organism for the study of invasive plant species. In North America, the non-native subspecies (ssp. australis) is widely distributed across the contiguous 48 states in the United States and large parts of Canada. Even though millions of dollars are spent annually on Phragmites management, insufficient knowledge of P. australis impeded the efficiency of management. To solve this problem, transcriptomic information generated from multiple types of tissue could be a valuable resource for future studies. Here, we constructed forty-nine P. australis transcriptomes assemblies via different assembly tools and multiple parameter settings. The optimal transcriptome assembly for functional annotation and downstream analyses was selected among these transcriptome assemblies by comprehensive assessments. For a total of 422,589 transcripts assembled in this transcriptome assembly, 319,046 transcripts (75.5%) have at least one functional annotation. Within the transcriptome assembly, we further identified 1,495 transcripts showing tissue-specific expression pattern, 10,828 putative transcription factors, and 72,165 candidates for simple sequence repeats markers. The identification and analyses of predicted transcripts related to herbicide- and salinity-resistant genes were shown as two applications of the transcriptomic information to facilitate further research on P. australis. Transcriptome assembly and selection would be important for the transcriptome annotation. With this optimal transcriptome assembly and all relative information from downstream analyses, we have helped to establish foundations for future studies on the mechanisms underlying the invasiveness of non-native P. australis subspecies.

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Section: Plos Onesupporting

confidence: 56%

Optimization and application of non-native Phragmites australis transcriptome assemblies

et al. 2023

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“… 23 , 24 To date, only a few weedy/invasive plant species genomes have been sequenced (e.g. Conyza canadensis ; 25 Mikania micrantha ; 26 Microstegium vimineum ; 27 and Phragmites australis 28 ) no genome has been reported for the family Menyanthaceae (Asterales). Our understanding of the adaptations of the weeds or widely distributed plant species is still limited, especially for aquatic plants that include a large number of globally notorious invasive species.…”

Section: Introductionmentioning

confidence: 99%

Chromosome-level genome assembly of the aquatic plant Nymphoides indica reveals transposable element bursts and NBS-LRR gene family expansion shedding light on its invasiveness

et al. 2022

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Nymphoides indica, an aquatic plant, is an invasive species that causes both ecological and economic damage in North America and elsewhere. However, the lack of genomic data of N. indica limits the in-depth analysis of this invasive species. Here, we report a chromosome-level genome assembly of nine pseudochromosomes of N. indica with a total size of approximately 520 Mb. More than half of the N. indica genome consists of transposable elements (TEs), and a higher density of TEs around genes may play a significant role in response to an ever-changing environment by regulating the nearby gene. Additionally, our analysis revealed that N. indica only experienced a gamma (γ) whole-genome triplication event. Functional enrichment of the N. indica-specific and expanded gene families highlighted genes involved in the responses to hypoxia and plant-pathogen interactions, which may strengthen the ability to adapt to external challenges and improve ecological fitness. Furthermore, we identified 160 members of the nucleotide-binding site and leucine-rich repeat (NBS-LRR) gene family, which may be linked to the defense response. Collectively, the high-quality N. indica genome reported here opens a novel avenue to understand the evolution and rapid invasion of Nymphoides spp.

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“…We then manipulated the endophytic community by inoculating seedlings with endophytes collected from one of the 30 field sites that varied in salinity, from fresh (no salt) to high salt (40 ppt). To do this, we gently abraded all seedling leaves with sterilized (three times at 121°C) quartz sand (Red Devil 580 Silica Sand, Meeco Mfg Co. Inc., Seattle, WA, USA) and treated with either I+ or I− inoculum applied with sterile cotton gauze to all leaves on the adaxial and abaxial leaf surfaces (the number of leaves ranged from 8 to 12) (Oh et al, 2021; Xu et al, 1997). In total, there were 90 different endophyte communities applied—3 endophyte communities from each of the 30 sites (i.e., 1 community came from each of the 3 trees sampled).…”

Section: Methodsmentioning

confidence: 99%

Salinity legacy: Foliar microbiome's history affects mutualist‐conferred salinity tolerance

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et al. 2022

Ecology

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The rapid human‐driven changes in the environment during the Anthropocene have placed extreme stress on many plants and animals. Beneficial interactions with microorganisms may be crucial for ameliorating these stressors and facilitating the ecosystem services host organisms provide. Foliar endophytes, microorganisms that reside within leaves, are found in essentially all plants and can provide important benefits (e.g., enhanced drought tolerance or resistance to herbivory). However, it remains unclear how important the legacy effects of the abiotic stressors that select on these microbiomes are for affecting the degree of stress amelioration provided to their hosts. To elucidate foliar endophytes' role in host‐plant salt tolerance, especially if salinity experienced in the field selects for endophytes that are better suited to improve the salt tolerance of their hosts, we combined field collections of 90 endophyte communities from 30 sites across the coastal Everglades with a manipulative growth experiment assessing endophyte inoculation effects on host‐plant performance. Specifically, we grew >350 red mangrove (Rhizophora mangle) seedlings in a factorial design that manipulated the salinity environment the seedlings experienced (freshwater vs. saltwater), the introduction of field‐collected endophytes (live vs. sterilized inoculum), and the legacy of salinity stress experienced by these introduced endophytes, ranging from no salt stress (0 parts per thousand [ppt] salinity) to high salt stress (40 ppt) environments. We found that inoculation with field‐collected endophytes significantly increased mangrove performance across almost all metrics examined (15%–20% increase on average), and these beneficial effects typically occurred when the endophytes were grown in saltwater. Importantly, our study revealed the novel result that endophyte‐conferred salinity tolerance depended on microbiome salinity legacy in a key coastal foundation species. Salt‐stressed mangroves inoculated with endophyte microbiomes from high‐salinity environments performed, on average, as well as plants grown in low‐stress freshwater, while endophytes from freshwater environments did not relieve host salinity stress. Given the increasing salinity stress imposed by sea level rise and the importance of foundation species like mangroves for ecosystem services, our results indicate that consideration of endophytic associations and their salinity legacy may be critical for the successful restoration and management of coastal habitats.

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Novel genome characteristics contribute to the invasiveness of Phragmites australis (common reed)

Cited by 15 publications

References 151 publications

Optimization and application of non-native Phragmites australis transcriptome assemblies

Optimization and application of non-native Phragmites australis transcriptome assemblies

Chromosome-level genome assembly of the aquatic plant Nymphoides indica reveals transposable element bursts and NBS-LRR gene family expansion shedding light on its invasiveness

Salinity legacy: Foliar microbiome's history affects mutualist‐conferred salinity tolerance

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