Assessment, validation and deployment strategy of a two-barcode protocol for facile genotyping of duckweed species

DC FieldValueLanguage
dc.contributor.authorBorisjuk, N.
dc.contributor.authorChu, P.
dc.contributor.authorGutierrez, R.
dc.contributor.authorZhang, H.
dc.contributor.authorAcosta, K.
dc.contributor.authorFriesen, N.
dc.contributor.authorSree, K. S.
dc.contributor.authorGarcia, C.
dc.contributor.authorAppenroth, K. J.
dc.contributor.authorLam, E.
dc.date.accessioned2021-12-23T16:18:59Z-
dc.date.available2021-12-23T16:18:59Z-
dc.date.issued2015
dc.identifier.issn14358603
dc.identifier.urihttps://osnascholar.ub.uni-osnabrueck.de/handle/unios/12935-
dc.description.abstractLemnaceae, commonly called duckweeds, comprise a diverse group of floating aquatic plants that have previously been classified into 37 species based on morphological and physiological criteria. In addition to their unique evolutionary position among angiosperms and their applications in biomonitoring, the potential of duckweeds as a novel sustainable crop for fuel and feed has recently increased interest in the study of their biodiversity and systematics. However, due to their small size and abbreviated structure, accurate typing of duckweeds based on morphology can be challenging. In the past decade, attempts to employ molecular barcoding techniques for species assignment have produced promising results; however, they have yet to be codified into a simple and quantitative protocol. A study that compiles and compares the barcode sequences within all known species of this family would help to establish the fidelity and limits of this DNA-based approach. In this work, we compared the level of conservation between over 100 strains of duckweed for two intergenic barcode sequences derived from the plastid genome. By using over 300 sequences publicly available in the NCBI database, we determined the utility of each of these two barcodes for duckweed species identification. Through sequencing of these barcodes from additional accessions, 30 of the 37 known species of duckweed could be identified with varying levels of confidence using this approach. From our analyses using this reference dataset, we also confirmed two instances where mis-assignment of species has likely occurred. Potential strategies for further improving the scope of this technology are discussed.
dc.description.sponsorshipHatch grant from NIFA-USDA through the New Jersey Agricultural Experiment Station [12116]; School of Environmental and Biology Sciences at Rutgers University; NSF-IGERTNational Science Foundation (NSF) [DGE-0903675]; This paper is dedicated to Elias Landolt (1926-2013), whose work on curating and sharing the first comprehensive duckweed collection has laid the cornerstone for this model system to understand natural diversity and adaptation. Duckweed research in the Lam laboratory is supported in part by a Hatch grant from NIFA-USDA through the New Jersey Agricultural Experiment Station (project #12116), support from the School of Environmental and Biology Sciences at Rutgers University, as well as funding through an NSF-IGERT project on Renewable and Sustainable Fuel Solutions (DGE-0903675).
dc.language.isoen
dc.publisherWILEY
dc.relation.ispartofPLANT BIOLOGY
dc.subjectBarcoding
dc.subjectbioinformatics
dc.subjectBLAST
dc.subjectDNA BARCODES
dc.subjectEVOLUTION
dc.subjectgenotyping
dc.subjectLEMNACEAE
dc.subjectPlant Sciences
dc.titleAssessment, validation and deployment strategy of a two-barcode protocol for facile genotyping of duckweed species
dc.typejournal article
dc.identifier.doi10.1111/plb.12229
dc.identifier.isiISI:000347799100007
dc.description.volume17
dc.description.issue1, SI
dc.description.startpage42
dc.description.endpage49
dc.contributor.orcid0000-0001-5250-9771
dc.contributor.orcid0000-0003-3547-3257
dc.contributor.orcid0000-0001-5309-2760
dc.contributor.researcheridAAI-3809-2020
dc.contributor.researcheridABC-9413-2021
dc.contributor.researcheridQ-6030-2017
dc.identifier.eissn14388677
dc.publisher.place111 RIVER ST, HOBOKEN 07030-5774, NJ USA
dcterms.isPartOf.abbreviationPlant Biol.
crisitem.author.deptFB 05 - Biologie/Chemie-
crisitem.author.deptidfb05-
crisitem.author.orcid0000-0003-3547-3257-
crisitem.author.parentorgUniversität Osnabrück-
crisitem.author.netidFrNi535-
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