alliaria petiolata
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2022 ◽  
Vol 12 ◽  
Author(s):  
Rachel A. Reeb ◽  
Naeem Aziz ◽  
Samuel M. Lapp ◽  
Justin Kitzes ◽  
J. Mason Heberling ◽  
...  

Community science image libraries offer a massive, but largely untapped, source of observational data for phenological research. The iNaturalist platform offers a particularly rich archive, containing more than 49 million verifiable, georeferenced, open access images, encompassing seven continents and over 278,000 species. A critical limitation preventing scientists from taking full advantage of this rich data source is labor. Each image must be manually inspected and categorized by phenophase, which is both time-intensive and costly. Consequently, researchers may only be able to use a subset of the total number of images available in the database. While iNaturalist has the potential to yield enough data for high-resolution and spatially extensive studies, it requires more efficient tools for phenological data extraction. A promising solution is automation of the image annotation process using deep learning. Recent innovations in deep learning have made these open-source tools accessible to a general research audience. However, it is unknown whether deep learning tools can accurately and efficiently annotate phenophases in community science images. Here, we train a convolutional neural network (CNN) to annotate images of Alliaria petiolata into distinct phenophases from iNaturalist and compare the performance of the model with non-expert human annotators. We demonstrate that researchers can successfully employ deep learning techniques to extract phenological information from community science images. A CNN classified two-stage phenology (flowering and non-flowering) with 95.9% accuracy and classified four-stage phenology (vegetative, budding, flowering, and fruiting) with 86.4% accuracy. The overall accuracy of the CNN did not differ from humans (p = 0.383), although performance varied across phenophases. We found that a primary challenge of using deep learning for image annotation was not related to the model itself, but instead in the quality of the community science images. Up to 4% of A. petiolata images in iNaturalist were taken from an improper distance, were physically manipulated, or were digitally altered, which limited both human and machine annotators in accurately classifying phenology. Thus, we provide a list of photography guidelines that could be included in community science platforms to inform community scientists in the best practices for creating images that facilitate phenological analysis.


Plant Disease ◽  
2021 ◽  
Author(s):  
Michael Robert Fulcher ◽  
Paul C Owen-Smith

Alliaria petiolata (Bieb.) Cavara & Grande (garlic mustard) is a biennial crucifer native to Europe and invasive in North America, where it outcompetes native plants in deciduous forests. In July 2021, powdery mildew was observed on A. petiolata in Frederick County, Maryland. Signs of the disease included white, tomentose mycelium producing abundant conidia (Fig S1). A majority of plants were affected, and severity ranged from the presence of small, discrete infections to complete colonization of leaves, stems, and ripening seed pods. Conidia from field collected leaves were transferred to disease-free A. petiolata for maintenance in a growth chamber at 20°C and 80% RH with a 12 hr photoperiod. Fungal morphology was recorded 30 days after this transfer. Appressoria were irregularly lobed, and conidiophores were straight and composed of 2-3 cells. Cylindrical to oblong conidia were produced singly in pseudochains of 2-6 (x̄ = 3), measured 39-64 by 18-29 (x̄ = 52 by 24) μm, had a length to width ratio greater than two, and germinated at the ends. Fibrosin bodies were absent from conidia, and chasmothecia were not observed in the field or on inoculated plant material. Based on anamorphic characteristics, the pathogen was placed in the genus Erysiphe (Boesewinkel 1980). Species level identity was determined using DNA sequences. Conidia and mycelia were scraped from leaves and used for genomic DNA extraction with the Quick-DNA Fungal/Bacterial Miniprep Kit (Zymo Research, Irvine, CA). A portion of the internal transcribed spacer region of rDNA was amplified using the primers ITS5/ITS4 (White et al. 1990). Purified amplicons (PCR & DNA Cleanup Kit, New England BioLabs Inc., Ipswich, MA) were sequenced at Eurofins Genomics (Louisville, KY). The resulting sequence was compared to those in NCBI GenBank using the blastn algorithm (Altschul et al. 1990). The newly generated sequence (GenBank: OK157430) was identical (599/599 bp) to samples of E. cruciferarum from the United Kingdom (GenBank: KY660931.1, KY660879.1, KY660752.1). Because E. cruciferarum sensu lato is heterogeneous (Pastirčáková et al. 2016), additional sequence comparisons were made to the E. cruciferarum sensu stricto holotype (589/599 bp, GenBank: KU672364) and a vouchered E. cruciferarum s. lat. (596/599 bp, GenBank: LC009943). This supports identification of the pathogen as E. cruciferarum s. lat. and suggests the taxonomy of isolates from A. petiolata should be reassessed following any revision to E. cruciferarum. A modified Koch’s postulates procedure was followed to confirm pathogenicity. Leaves colonized by E. cruciferarum were briefly pressed against the leaves of three disease-free plants grown from seed in a greenhouse. After 14 days, inoculated plants showed signs of powdery mildew similar to those observed in the field, and a control treatment using pathogen-free leaves resulted in no disease. This inoculation experiment was performed twice, and the identity of the pathogen was reconfirmed based on morphology. This is the first report of powdery mildew on A. petiolata in Maryland. Erysiphe cruciferarum s. lat. is widely distributed on other hosts and has been found on A. petiolata throughout Europe and in Ohio and Indiana (Farr and Rossman 2021; Blossey et al. 2001; Enright and Cipollini 2007; Ciola and Cipollini 2011). This pathogen has been proposed as a biological control agent (Cipollini and Enright 2009; Cipollini et al. 2020), and the presence of disease in Maryland suggests the local population of A. petiolata is susceptible to E. cruciferarum and the environment there is favorable to disease development. References: Altschul, S. F., et al. 1990. J. Mol. Biol. 215:403. Blossey, B., et al. 2001. Nat. Areas J. 21:357. Boesewinkel, H. J. 1980. Bot. Rev. 46:167. Ciola, V., and Cipollini, D. 2011. Am. Midl. Nat. 166:40-52. Cipollini, D., and Enright, S. M. 2009. Invasive Plant Sci. Manag. 2:253. Cipollini, D., et al. 2020. Biol. Invasions. 22:1657-1668. Enright, S. M., and Cipollini, D. 2007. Am. J. Bot. 94:1813. Farr, D. F., and Rossman, A. Y. 2021. Fungal Databases, Syst. Mycol. Microbial. Lab., ARS, USDA. https://nt.ars-grin.gov/fungaldatabases/ Pastirčáková, K., et al. 2016. Mycol. Prog. 15:36 White, T. J., et al. 1990. Page 315 in: PCR Protocols. A Guide to Methods and Applications, Academic Press, San Diego. Keywords: Alliaria petiolata, Erysiphe cruciferarum, garlic mustard, powdery mildew, invasive plant, biocontrol Funding and Disclaimer: The author(s) declare no conflict of interest. This work was supported by USDA-ARS Appropriated Project Number 8044-22000-047-000-D. Mention of trade names or commercial products in this report is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity lender, provider, and employer.


2021 ◽  
Author(s):  
Mercedes Harris ◽  
Elsa Cousins ◽  
Kristina Stinson

Abstract The production of secondary defense chemicals in plants represents a trade-off between defense and the primary functions of growth and reproduction, but the relative allocation to growth versus defense varies across species, types of defenses, ontogeny, and environment. Alliaria petiolata (garlic mustard) is a brassica that produces glucosinolates, a class of constituent secondary metabolites that defend against herbivores and pathogens. Sinigrin, a hydrolyzed product of glucosinolate present in garlic mustard, may aid in its success as an invasive species by disrupting native plant–mycorrhizae mutualisms and decreasing forest species diversity in North America. Here, we measured sinigrin concentration in garlic mustard populations of different field densities and in greenhouse experiments to evaluate the relationship between sinigrin concentration and growth in response to density and varying environmental conditions. We found clear evidence for growth vs. defense tradeoffs in both experimental and field settings, as well as higher levels of defense in more densely growing, smaller individual plants. However, sinigrin levels and tradeoffs were not explained by soil fertility or light, allowing us to conclude that sinigrin expression is not controlled by limitations in the measured abiotic factors. Our findings suggest sinigrin leaf concentration increases at high densities despite the pressures of intraspecific competition that demand allocation to growth.


Author(s):  
Nikolay Alabi ◽  
Yihan Wu ◽  
Oliver Bossdorf ◽  
Loren H Rieseberg ◽  
Robert I Colautti

Abstract The emerging field of invasion genetics examines the genetic causes and consequences of biological invasions, but few study systems are available that integrate deep ecological knowledge with genomic tools. Here we report on the de novo assembly and annotation of a genome for the biennial herb Alliaria petiolata (M. Bieb.) Cavara & Grande (Brassicaceae), which is widespread in Eurasia and invasive across much of temperate North America. Our goal was to sequence and annotate a genome to complement resources available from hundreds of published ecological studies, a global field survey, and hundreds of genetic lines maintained in Germany and Canada. We sequenced a genotype (EFCC3-3-20) collected from the native range near Venice, Italy and sequenced paired-end and mate pair libraries at ∼70 × coverage. A de novo assembly resulted in a highly continuous draft genome (N50 = 121 Mb; L50 = 2) with 99.7% of the 1.1 Gb genome mapping to scaffolds of at least 50 Kb in length. A total of 64,770 predicted genes in the annotated genome include 99% of plant BUSCO genes and 98% of transcriptome reads. Consistent with previous reports of (auto)hexaploidy in western Europe, we found that almost one third of BUSCO genes (390/1440) mapped to two or more scaffolds despite < 2% genome-wide average heterozygosity. The continuity and gene space quality of our draft assembly will enable molecular and functional genomic studies of A. petiolata to address questions relevant to invasion genetics and conservation strategies.


Ecosphere ◽  
2021 ◽  
Vol 12 (5) ◽  
Author(s):  
Roger C. Anderson ◽  
M. Rebecca Anderson ◽  
Jonathan T. Bauer ◽  
Christopher Loebach ◽  
Alicia Mullarkey ◽  
...  

2021 ◽  
pp. 1-17
Author(s):  
Leo Roth ◽  
José Luiz C. S. Dias ◽  
Christopher Evans ◽  
Kevin Rohling ◽  
Mark Renz

Garlic mustard [Alliaria petiolata (M. Bieb.) Cavara & Grande] is a biennial invasive plant commonly found in the northeastern and midwestern United States. Although it is not recommended to apply herbicides after flowering, land managers frequently desire to conduct management during this timing. We applied glyphosate and triclopyr (3% v/v and 1% v/v using 31.8% and 39.8% acid equivalent formulations, respectively) postemergence to established, second-year A. petiolata populations at three locations when petals were dehiscing, and evaluated control, seed production and seed viability. Postemergence glyphosate applications at this timing provided 100% control of A. petiolata by 4 weeks after treatment at all locations whereas triclopyr efficacy was variable, providing 38-62% control. Seed production was only reduced at one location, with similar results regardless of treatment. Percent seed viability was also reduced, and when combined with reductions in seed production, we found a 71-99% reduction in number of viable seed produced plant-1 regardless of treatment. While applications did not eliminate viable seed production, our findings indicate that glyphosate and triclopyr applied while petals were dehiscing is a viable alternative to cutting or hand-pulling at this timing as it substantially decreased viable A. petiolata seed production. Management Implications Postemergence glyphosate and triclopyr applications in the early spring to rosettes are standard treatments used to manage A. petiolata. However, weather and other priorities limit the window for management, forcing field practitioners to utilize more labor-intensive methods such as hand-pulling. It is not known how late in the development of A. petiolata these herbicides can be applied to prevent viable seed production. Since prevention of soil seedbank replenishment is a key management factor for effective long-term control of biennial invasive species, we hypothesized late spring foliar herbicide applications to second year A. petiolata plants when flower petals were dehiscing could be an effective management tool if seed production or viability is eliminated. Our study indicated that glyphosate applications at this timing provided 100% control of A. petiolata plants by 4 weeks after treatment at all locations, whereas triclopyr efficacy was inconsistent. Although both glyphosate and triclopyr decreased viable seed production to nearly zero at one of our three study locations, the same treatments produced significant amounts of viable seed at the other two locations. Our findings suggest late spring glyphosate and triclopyr applications should not be recommended over early spring applications to rosettes for A. petiolata management, as our late spring application timing did not prevent viable seed production, and may require multiple years of implementation to eradicate populations. Nonetheless, this application timing holds value in areas devoid of desirable understory vegetation compared to no management practices or mechanical management options including hand-pulling when fruit are present, as overall viable seed production was reduced to similar levels as these treatments.


2021 ◽  
Author(s):  
Nikolay Alabi ◽  
Yihan Wu ◽  
Oliver Bossdorf ◽  
Loren H. Rieseberg ◽  
Robert I. Colautti

AbstractThe emerging field of invasion genetics examines the genetic causes and consequences of biological invasions, but few study systems are available that integrate deep ecological knowledge with genomic tools. Here we report on the de novo assembly and annotation of a genome for the biennial herb Alliaria petiolata (M. Bieb.) Cavara & Grande (Brassicaceae), which is widespread in Eurasia and invasive across much of temperate North America. Our goal was to sequence and annotate a genome to complement resources available from hundreds of published ecological studies, a global field survey, and hundreds of genetic lines maintained in Germany and Canada. We sequenced a genotype (EFCC-3-20) collected from the native range near Venice, Italy and sequenced paired-end and mate pair libraries at ~70× coverage. A de novo assembly resulted in a highly continuous draft genome (N50 = 121Mb; L50 = 2) with 99.7% of the 1.1Gb genome mapping to contigs of at least 50Kb in length. A total of 64,770 predicted genes in the annotated genome include 99% of plant BUSCO genes and 98% of transcriptome reads. Consistent with previous reports of (auto)hexaploidy in western Europe Almost, we found that almost one third of BUSCO genes (390/1440) mapped to two or more scaffolds despite a genome-wide average of < 2% heterozygosity. The continuity and gene space quality of our draft genome assembly will enable genomic studies of A. petiolata to address questions relevant to invasion genetics and conservation efforts.


Author(s):  
Roger C. Anderson ◽  
Rebecca Anderson ◽  
Jonathan T. Bauer ◽  
Christopher Loebach ◽  
Alicia Mullarkey ◽  
...  

Pedobiologia ◽  
2021 ◽  
Vol 84 ◽  
pp. 150700
Author(s):  
Katherine Duchesneau ◽  
Anneke Golemiec ◽  
Robert I. Colautti ◽  
Pedro M. Antunes

Author(s):  
Ю. В. Бенгус ◽  
Р. Є. Волкова

Наведено результати дослідження багаточисельної популяції червонокнижного виду Ornithothogalum boucheanum, виявленої вперше на території міста Харків у 2016 році. Для території міста Харків – це єдине відоме авторам природнє місцезростання виду, хоча він культивується в окремих ботанічних закладах Харкова. Дана популяція знаходиться на північній межі ареалу зростання O. boucheanum в Україні. На единій площі близько 7 га поблизу р. Немишля O. boucheanum масово зростає переважно на трьох основних ділянках загальною чисельністю у кілька тисяч квітучих особин, займаючи від 5 до 15% у загальному проективному покритті. Рястка Буше зростає у складі напівприродних рослинних угруповань з елементами антропогенної трансформації і домінуванням лучних (Ranunculus pedatus, Carex praecox, Poa angustifolia, P. pratensis, P. bulbosa , Elymus repens), лісових (Ficaria verna, Alliaria petiolata, Poa nemoralis) та рудеральних (Urtica dioica, Taraxacum campylodes, Cirsium arvense тощо) видів. Одна досліджена ділянка наразі зайнята лучною рослинністю, дві інші розташовані серед дерев з середньою (0,7) або невеликою (0,3) зімкненістю крон. Територія зростання дослідженої популяції знаходиться під впливом антропогенної діяльності (сінокосіння, косіння трави електричними засобами, випас тварин), але швидкий розвиток рослин O. boucheanum навесні і відмирання листків вже під час цвітіння призводять до того, що косіння і незначний випас не впливають на чисельність рослин дослідженого виду. Присутня велика кількість молодих рослин від вегетативного та насінного розмноження. Велика площа, на якій знайдені квітучі рослини O. boucheanum, практична відсутність на обстежених ділянках штучного озеленення та велика кількість знайдених рослин свідчать про те, що досліджена популяція є автохтонною. Авторські фотографії O. boucheanum з дослідженої території занесені до міжнародних баз даних iNaturalist та UkrBIN. Територія дослідження має важливе значення як місце зростання рослини занесеної до Червоної книги України, тому має отримати природоохоронний статус.


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