scholarly journals The low-copy nuclear gene Agt1 as a novel DNA barcoding marker for Bromeliaceae

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Fabian Bratzel ◽  
Sascha Heller ◽  
Nadine Cyrannek ◽  
Juraj Paule ◽  
Elton M. C. Leme ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Dna Barcoding ◽  
Nuclear Gene ◽  
Research Community ◽  
Ecological Diversity ◽  
Species Determination ◽  
Identification Rate ◽  
Plant Group ◽  
Exon Sequence

Abstract Background The angiosperm family Bromeliaceae comprises over 3.500 species characterized by exceptionally high morphological and ecological diversity, but a very low genetic variation. In many genera, plants are vegetatively very similar which makes determination of non flowering bromeliads difficult. This is particularly problematic with living collections where plants are often cultivated over decades without flowering. DNA barcoding is therefore a very promising approach to provide reliable and convenient assistance in species determination. However, the observed low genetic variation of canonical barcoding markers in bromeliads causes problems. Result In this study the low-copy nuclear gene Agt1 is identified as a novel DNA barcoding marker suitable for molecular identification of closely related bromeliad species. Combining a comparatively slowly evolving exon sequence with an adjacent, genetically highly variable intron, correctly matching MegaBLAST based species identification rate was found to be approximately double the highest rate yet reported for bromeliads using other barcode markers. Conclusion In the present work, we characterize Agt1 as a novel plant DNA barcoding marker to be used for barcoding of bromeliads, a plant group with low genetic variation. Moreover, we provide a comprehensive marker sequence dataset for further use in the bromeliad research community.

Duplex DNA barcoding allows accurate species determination of morphologically similar limpets (Patella spp.) from non-destructive sampling

2016 ◽  
Vol 97 (7) ◽  
pp. 1479-1482 ◽  
Author(s):  
Thomas J. Ashton ◽  
Meriem Kayoueche-Reeve ◽  
Andrew J. Blight ◽  
Jon Moore ◽  
David M. Paterson
Keyword(s):  
Dna Barcoding ◽  
Species Abundance ◽  
Microscopic Analysis ◽  
Cost Effective ◽  
Field Studies ◽  
Similar Species ◽  
Species Determination ◽  
Destructive Sampling ◽  
Species Specific ◽  
Non Destructive

Accurate discrimination of two morphologically similar species of Patella limpets has been facilitated by using qPCR amplification of species-specific mitochondrial genomic regions. Cost-effective and non-destructive sampling is achieved using a mucus swab and simple sample lysis and dilution to create a PCR template. Results show 100% concurrence with dissection and microscopic analysis, and the technique has been employed successfully in field studies. The use of highly sensitive DNA barcoding techniques such as this hold great potential for improving previously challenging field assessments of species abundance.

Parentage determination of black sea bream (Acanthopagrus schlegelii) for stock enhancement: effectiveness and loss of genetic variation

2021 ◽  
Vol 40 (6) ◽  
pp. 41-49
Author(s):  
Binbin Shan ◽  
Yan Liu ◽  
Na Song ◽  
Changping Yang ◽  
Shengnan Liu ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Black Sea ◽  
Stock Enhancement ◽  
Sea Bream ◽  
Acanthopagrus Schlegelii

scholarly journals Species determination of Brazilian mammals implicated in the epidemiology of rabies based on the control region of mitochondrial DNA

2008 ◽  
Vol 12 (6) ◽  
pp. 462-465 ◽  
Author(s):  
Pedro Carnieli Junior ◽  
Willian de Oliveira Fahl ◽  
Juliana Galera Castilho ◽  
Paulo Eduardo Brandão ◽  
Maria Luiza Carrieri ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Control Region ◽  
Species Determination

scholarly journals Determination of morphometric, biochemical and genetic variation in Sclerotium delphinii isolates

2014 ◽  
Vol 8 (16) ◽  
pp. 1696-1703
Author(s):  
P. Gawande S. ◽  
G. Borkar S. ◽  
T. Nagrale D. ◽  
K. Sharma A.
Keyword(s):  
Genetic Variation ◽  
Sclerotium Delphinii

scholarly journals Climatic Refugia and Geographical Isolation Contribute to the Speciation and Genetic Divergence in Himalayan-Hengduan Tree Peonies (Paeonia delavayi and Paeonia ludlowii)

2021 ◽  
Vol 11 ◽  
Author(s):  
Yu-Juan Zhao ◽  
Gen-Shen Yin ◽  
Yue-Zhi Pan ◽  
Bo Tian ◽  
Xun Gong
Keyword(s):  
Genetic Variation ◽  
Late Quaternary ◽  
Demographic History ◽  
Nuclear Gene ◽  
Genetic Distances ◽  
Population Divergence ◽  
Widespread Species ◽  
Isolation With Migration ◽  
Isolation By Environment ◽  
Paeonia Delavayi

Himalaya and Hengduan Mountains (HHM) is a biodiversity hotspot, and very rich in endemic species. Previous phylogeographical studies proposed different hypotheses (vicariance and climate-driven speciation) in explaining diversification and the observed pattern of extant biodiversity, but it is likely that taxa are forming in this area in species-specific ways. Here, we reexplored the phylogenetic relationship and tested the corresponding hypotheses within Paeonia subsect. Delavayanae composed of one widespread species (Paeonia delavayi) and the other geographically confined species (Paeonia ludlowii). We gathered genetic variation data at three chloroplast DNA fragments and one nuclear gene from 335 individuals of 34 populations sampled from HHM. We performed a combination of population genetic summary statistics, isolation-with-migration divergence models, isolation by environment, and demographic history analyses. We found evidence for the current taxonomic treatment that P. ludlowii and P. delavayi are two different species with significant genetic differentiation. The significant isolation by environment was revealed within all sampled populations but genetic distances only explained by geographical distances within P. delavayi populations. The results of population divergence models and demographic history analyses indicated a progenitor–derivative relationship and the Late Quaternary divergence without gene flow between them. The coalescence of all sampled cpDNA haplotypes could date to the Late Miocene, and P. delavayi populations probably underwent a severe bottleneck in population size during the last glacial period. Genetic variation in Paeonia subsect. Delavayanae is associated with geographical and environmental distances. These findings point to the importance of geological and climatic changes as causes of the speciation event and lineage diversification within Paeonia subsect. Delavayanae.

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