Abstract Detail

Comparative Genomics/Transcriptomics

Hubert, Julia [1], Kyte, Sarah [1], Charron, Andréanne [1], Colville, Adam [1], Klein, Daniel [1], Brière, Stephan C. [1], Gagnon, Marie-Claude [1], Galindo Gonzalez, Leonardo Miguel [2].

Omic strategies for identification of Amaranth species.

Plant and seed identification are key components in the regulatory context of trade as well as to control the entry of invasive and noxious species which may affect crop production, human health or the ecological balance. Some amaranths have had an increasing impact as invasive species bearing multiple herbicide resistance mechanisms. For example Amaranthus palmeri is an aggressive and prolific weed that has evolved herbicide resistance in multiple populations in the United States, and has impacted the production of crops like corn and soybean. A. palmeri has been reported as being present in Ontario and Manitoba, and therefore its detection has become a priority to prevent its spread.
Omic technologies provide a toolbox for efficient and sensitive identification of plants and seeds, to complement classical phenotypic taxonomic approaches. While DNA barcoding is now commonplace as one of the main methodologies in plant identification, a universal DNA plant barcode is absent and some taxa are not sufficiently resolved by typical plant barcoding genes like ITS, psbA, matK or rbcL. Additionally, novel methodologies including protein biotyping are seldom tested as alternatives for distinguishing plant species/populations.
We used Illumina sequencing on 18 amaranth plant and seed samples including six different A. palmeri populations, three A. tuberculatus and nine other amaranth species. Reads from each sample were used in a pipeline of Genome skimming, which relies on the empiric low coverage sequencing of a full plant genome, to obtain high coverage of the high copy genomic fractions such as chloroplasts and rDNA. Our results showed that genome skimming was an effective technique for high coverage assembly of amaranth chloroplasts. We obtained an average of 47 million reads for each one of the amaranth nuclear genomes, which range in size between 400-700Mb approximately. These reads provided an average theoretical coverage of 10-15X for each nuclear genome, but resulted in an average chloroplast genome coverage in the range of 500-8000X due to multiple chloroplast genome copies per cell. Alignment of the chloroplast genomes shows high variability in the single copy regions and especially on intergenic sections. Preliminary analyses also show variation among different populations of the same species, demonstrating the importance of studying both inter and intraspecific diversity to design reliable and accurate DNA barcodes that can be used in species identification.
We also tested and improved a simple protein extraction procedure along with Matrix Assisted Laser Desorption/Ionization (MALDI) protein biotyping to see if amaranth seeds would give consistent and distinctive protein spectra that could be used to separate species. After preliminary analysis with seeds from the Brassicaceae family showing clustering success between 80 and 100% for samples from the same species, the methodology was applied to 17 amaranth species. Our results showed that A. tuberculatus (a regulated noxious weed seed species in Canada) protein spectra can be clearly distinguished from other species, while A. palmeri spectra seemed closer to spectra from A. watsonii and A. spinosus, two species that have shown a close evolutionary relationship to A. palmeri in previous studies.

1 - Canadian Food Inspection Agency, Ottawa Plant Laboratory, 3851 Fallowfield Rd. , Ottawa, ON, K2J 4S1, Canada
2 - Canadian Food Inspection Agency, Ottawa Plant Laboratory, 3851 Fallowfield Rd. , Ottawa, Ontario, K2J 4S1, Canada

Amaranthus palmeri
genome skimming
chloroplast sequencing
Comparative -omics
protein biotyping
DNA barcoding.

Presentation Type: Oral Paper
Number: CGT3005
Abstract ID:200
Candidate for Awards:Margaret Menzel Award

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