Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s.

Raiyemo, Damilola A.; Tranel, Patrick J.

doi:10.1186/s12862-023-02121-1

Cited by 3 publications

References 112 publications

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Innovative multi‐scale approach to study the phenotypic variation of seedling leaves in four weedy Amaranthus species

Scarpin,

Este,

D'Este

et al. 2024

Plant Biol J

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Plant phenotyping on morpho‐anatomical traits through image analysis, from microscope images to large‐scale acquisitions through remote sensing, represents a low‐invasive tool providing insight into physiological and structural trait variation, as well as plant–environment interactions. High phenotype diversity in the genus Amaranthus includes annual weed species with high invasiveness and impact on important summer crops, and nutritive grain or vegetable crops. Identification of morpho‐anatomical leaf characters at very young stages across weedy amaranths could be useful for better understanding their performance in agroecosystems. We used an innovative multi‐scale approach with phenotype analyses of about 20 single‐leaf morphometric traits of four Amaranthus species through processing confocal microscopy and camera acquisitions. The results highlight that determination of leaf traits at different investigation levels highlight species‐specific traits at a juvenile stage, which are crucial for plant development, competition and establishment. Specifically, leaf circularity and hairiness Aspect Ratio better discriminated A. tuberculatus from other species. Also, leaf DW, hairiness area and perimeter variables allowed identification of dioecious amaranth species as distinct from monoecious species. The methodology used here provides a promising, reliable and low‐impact approach for the functional characterization of phylogenetically related species and for statistical quantification of traits involved in taxonomy and biodiversity studies.

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Innovative multi‐scale approach to study the phenotypic variation of seedling leaves in four weedy Amaranthus species

Scarpin,

Este,

D'Este

et al. 2024

Plant Biol J

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Seed protein biotyping in Amaranthus species: a tool for rapid identification of weedy amaranths of concern

Murphy,

Hubert,

Wang

et al. 2023

Plant Methods

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Background The Amaranthus genus contains at least 20 weedy and invasive species, including Amaranthus palmeri (palmer’s amaranth) and Amaranthus tuberculatus (tall waterhemp), two species of regulatory concern in North America, impacting production and yield in crops like corn, soybean and cotton. Amaranthus tuberculatus is regulated in Canada with limited establishment, while current climate models predict a range expansion of A. palmeri impacting crop growing areas in Ontario, Quebec and Manitoba. Since many Amaranthus species are similar in their morphology, especially at the seed stage, this demands the development of additional methods that can efficiently aid in the detection and identification of these species. Protein biotyping using Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF-MS) has been traditionally used to identify microorganism species, races and pathotypes. Major protein fractions extracted from an organism, ionized and run through a biotyper using mass spectrometry, result in protein spectra that represent a fingerprint at the species or lower taxonomic rank, providing an efficient molecular diagnostics method. Here we use a modified protein biotyping protocol to extract major protein fractions from seeds of the family Brassicaceae to test our protocol, and then implemented the standardized approach in seeds from Amaranthus species. We then created a database of Amaranthus protein spectra that can be used to test blind samples for a quick identification of species of concern. Results We generated a protein spectra database with 16 Amaranthus species and several accessions per species, spanning target species of regulatory concern and species which are phylogenetically related or easily confused at the seed stage due to phenotypic plasticity. Testing of two Amaranthus blind sample seed sets against this database showed accuracies of 100% and 87%, respectively. Conclusions Our method is highly efficient in identifying Amaranthus species of regulatory concern. The mismatches between our protein biotyping approach and phenotypic identification of seeds are due to absence of the species in the database or close phylogenetic relationship between the species. While A. palmeri cannot be distinguished from A. watsonii, there is evidence these two species have the same native range and are closely related.

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Seed protein biotyping in Amaranthus species: A tool for rapid identification of weedy amaranths of concern

Murphy,

Hubert,

Wang

et al. 2023

Preprint

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Background: The Amaranthus genus contains at least 20 weedy and invasive species, including Amaranthus palmeri (palmer’s amaranth) and Amaranthus tuberculatus (tall waterhemp), two species of regulatory concern in North America, impacting production and yield in crops like corn, soybean and cotton. Amaranthus tuberculatus is regulated in Canada with limited establishment, while current climate models predict a range expansion of A. palmeri impacting crop growing areas in Ontario, Quebec and Manitoba. Since many Amaranthus species are similar in their morphology, especially at the seed stage, this demands the development of additional methods that can efficiently aid in the detection and identification of these species. Protein biotyping using Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF-MS) has been traditionally used to identify microorganism species, races and pathotypes. Major protein fractions extracted from an organism, ionized and run through a biotyper using mass spectrometry, result in protein spectra that represent a fingerprint at the species or lower taxonomic rank, providing an efficient molecular diagnostics method. Here we use a modified protein biotyping protocol to extract major protein fractions from seeds of the family Brassicaceae to test our protocol, and then implemented the standardized approach in seeds from Amaranthusspecies. We then created a database of Amaranthus protein spectra that can be used to test blind samples for a quick identification of species of concern. Results: We generated a protein spectra database with 16 Amaranthus species and several accessions per species, spanning target species of regulatory concern and species which are phylogenetically related or easily confused at the seed stage due to phenotypic plasticity. Testing of two Amaranthus blind sample seed sets against this database showed accuracies of 100% and 87%, respectively. Conclusions: Our method is highly efficient in identifying Amaranthus species of regulatory concern. The mismatches between our protein biotyping approach and phenotypic identification of seeds are due to absence of the species in the database or close phylogenetic relationship between the species. While A. palmeri cannot be distinguished from A. watsonii, there is evidence these two species have the same native range and are closely related.

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Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s.

Cited by 3 publications

References 112 publications

Innovative multi‐scale approach to study the phenotypic variation of seedling leaves in four weedy Amaranthus species

Innovative multi‐scale approach to study the phenotypic variation of seedling leaves in four weedy Amaranthus species

Seed protein biotyping in Amaranthus species: a tool for rapid identification of weedy amaranths of concern

Seed protein biotyping in Amaranthus species: A tool for rapid identification of weedy amaranths of concern

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