Genetic analysis of North American Phragmites australis guides management approaches

Lindsay, Denise L.; Freeland, Joanna R.; Gong, Peng; Guan, Xin Yuan; Harms, Nathan E.; Kowalski, Kurt P.; Lance, Richard F.; Oh, Dong-Ha; Sartain, Bradley; Wendell, Douglas L.

doi:10.1016/j.aquabot.2022.103589

Cited by 5 publications

(6 citation statements)

References 108 publications

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“…These three P. australis assays are accurate (zero non‐target amplification and consistent target amplification) and offer faster identification of unknown samples than existing methods of Phragmites genetic discrimination (e.g., sequencing, Saltonstall, 2002 ; genotyping, Saltonstall 2003 ; RNase H–dependent PCR, Zuzak et al, 2018 ) to the subspecies level among all three P. australis subspecies present in the United States (e.g., PCR‐RFLP, Wendell et al, 2021 ). The specific advantages and disadvantages of each available genetic discrimination method are summarized in Table 1 of Lindsay et al ( 2022 ). We expect these qPCR assays to be valid for the discrimination of P. australis subspecies across the United States, including regions of southern California and southern Arizona where all three subspecies co‐occur, because our sample set included specimens from these regions (Appendix 1 ).…”

Section: Discussionmentioning

confidence: 99%

DNA assays for genetic discrimination of threePhragmites australissubspecies in the United States

et al. 2023

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To genetically discriminate subspecies of the common reed (Phragmites australis), we developed real-time quantitative (qPCR) assays for identifying P. australis subsp. americanus, P. australis subsp. australis, and P. australis subsp. berlandieri. Methods and Results: Utilizing study-generated chloroplast DNA sequences, we developed three novel qPCR assays. Assays were verified on individuals of each subspecies and against two non-target species, Arundo donax and Phalaris arundinacea. One assay amplifies only P. australis subsp. americanus, one amplifies P. australis subsp. australis and/or P. australis subsp. berlandieri, and one amplifies P. australis subsp. americanus and/or P. australis subsp. australis. This protocol enhances currently available rapid identification methods by providing genetic discrimination of all three subspecies. Conclusions: The newly developed assays were validated using P. australis samples from across the United States. Application of these assays outside of this geographic range should be preceded by additional testing.

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Section: Discussionmentioning

confidence: 99%

DNA assays for genetic discrimination of threePhragmites australissubspecies in the United States

et al. 2023

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“…australis as a model species for studying plant invasions. As such, further research on this species is required, including transcriptomic studies on multiple types of tissues [ 10 ].…”

Section: Introductionmentioning

confidence: 99%

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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“…& Hauber ("Gulf Coast P. australis") is an endemic lineage distributed along the Gulf Coast (Colin and Eguiarte 2016;Saltonstall and Hauber 2007). In the Great Lakes Region of northern North America, only the native and introduced P. australis subspecies occur (Lindsay et al 2023). Pollination studies indicate that the introduced and native P. australis subspecies can hybridize (Meyerson et al 2010), but hybrids have rarely been found in the field (Paul et al 2010;Saltonstall et al 2014Saltonstall et al , 2016Wu et al 2015).…”

Section: Introductionmentioning

confidence: 99%

“…Genetic tools are useful for discriminating between different P. australis lineages and are reviewed by Lindsay et al (2023), including a method to screen for native-introduced P. australis hybrids (Wendell et al 2021). However, for land managers, availability of genetic tools can be limited by a lack of access to laboratory resources and technical expertise, financial costs, and the challenges of proper collection and preservation of tissue samples to extract high-quality genetic material (Lambert et al 2016).…”

Section: Introductionmentioning

confidence: 99%

“…Despite the existence of these guides, reports have emerged from land managers around the Great Lakes region of unknown P. australis populations with “unusual” traits that they worry may be hybrids (Lindsay et al 2023; MJM, personal observation). However, genetic surveys have not detected hybrids within any of these “unusual” populations (Tippery et al 2020; Warren 2020), suggesting that land managers are encountering normal native and introduced P. australis populations beyond their expected range of variation for the subspecies and signaling a need to improve current morphological identification tools.…”

Section: Introductionmentioning

confidence: 99%

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Morphological traits for rapid and simple separation of native and introduced common reed (Phragmites australis)

McTavish

Smith

Mechanda

et al. 2023

Invasive plant sci. manag.

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Effective management of the introduced invasive grass Phragmites australis (Cav.) Trin. ex Steud requires the ability to differentiate between the introduced and native subspecies found in North America. While genetic tools are useful for discriminating between the subspecies, morphological identification is a useful complementary approach that is low to zero-cost and does not require specialized equipment nor technical expertise. The objective of our study was to identify the best morphological traits for rapid and simple identification of native and introduced P. australis. A suite of 22 morphological traits were measured in 21 introduced and 27 native P. australis populations identified by genetic barcoding across southern Ontario, Canada. Traits were compared between the subspecies to identify measurements that offered reliable, diagnostic separation. Overall, 21 of the 22 traits differed between the subspecies, with four offering complete separation: the retention of leaf sheaths on dead stems, a categorical assessment of stem colour, the base height of the ligule excluding the hairy fringe, and a combined measurement of leaf length and lower glume length. Additionally, round fungal spots on the stem occurred only on the native subspecies and never on the sampled introduced populations. The high degree of variation observed in traits within and between the subspecies cautions against a “common wisdom” approach to identification or automatic interpretation of intermediate traits as indicative of aberrant populations or hybridization. As an alternative, we have compiled the five best traits into a checklist of simple and reliable measurements to identify native and introduced P. australis. This guide will be most applicable for samples collected in the late summer and fall in the Great Lakes region but can also inform best practices for morphological identification in other regions as well.

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Genetic analysis of North American Phragmites australis guides management approaches

Cited by 5 publications

References 108 publications

DNA assays for genetic discrimination of threePhragmites australissubspecies in the United States

DNA assays for genetic discrimination of threePhragmites australissubspecies in the United States

Optimization and application of non-native Phragmites australis transcriptome assemblies

Morphological traits for rapid and simple separation of native and introduced common reed (Phragmites australis)

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