Comparison of seven DNA extraction and amplification protocols in historical herbarium specimens of juncaceae

Drábková, Lenka Záveská; Kirschner, Jan; Vlček, Čestmı́r

doi:10.1007/bf02799431

Cited by 147 publications

(121 citation statements)

References 12 publications

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“…As shown here, for 151 Guatteria herbarium specimens there is no relationship between age and the extraction success of DNA and at first sight this corroborates the earlier qualitative findings of Rogers & Bendich (1985), Savolainen et al (1995), Drábková et al (2002) and Jankowiak et al (2005). These small scale studies each reported that DNA was successfully extracted from an old specimen and the authors therefore suggested that an apparent correlation between age and DNA extraction or amplification success did not exist.…”

Section: Discussionsupporting

confidence: 88%

“…they found in their study of 18 samples that the method of drying (as indicated by the colour of the leaves) was more important for isolation of DNA than the age of the sample. These results agree with earlier studies on the effects of different protocols for DNA extraction such as the extraction from 18 herbarium specimens of Juncaceae (Drábková et al 2002). However, the colour of leaves is affected by other factors, such as the above mentioned 'wet' collecting.…”

supporting

confidence: 91%

“…So far, only some small scale studies have shown that the relationship between age and extraction success might be absent (e.g. Drábková et al 2002;Jankowiak et al 2005).…”

Section: Discussionmentioning

confidence: 99%

“…We extracted total genomic DNA using a modified cetyl-trimethyl-ammoniumbromide (CtAB) method , a method that has performed comparatively well for the extraction of DNA from herbarium specimens (Drábková et al 2002). 0.05 g Leaf material was weighed for each sample (large veins were removed) and put into a mortar preheated to 65 °C with some fine sand and ground to rough powder with a pestle; 650 µl CTAB solution was added and ground further; another 650 µl CTAB solution was added, mixed, and the whole content of the pestle poured into a 2 µl eppendorf tube; 12 µl β-mercaptoethanol was pipetted into the eppendorf tube and mixed again; the eppendorf tube was transferred into a 65 °C water-bath and left there for 15-20 minutes, mixing thoroughly at least every 5 minutes; thereafter the eppendorf tube was topped off with a 24 : 1 chloroform:isoamylalcohol mixture almost to the rim and placed in a rocking machine for at least 1.5 hours; finally, the tubes were centrifuged at 14,400 rpm for 10 minutes and the top phase was pipetted into a new eppendorf tube.…”

Section: Guatteriamentioning

confidence: 99%

“…Because of this degradation several studies were conducted to determine which method of DNA extraction is most suitable for herbarium specimens (e.g. Rogers & Bendich 1985;savolainen et al 1995;Drábková et al 2002;Jankowiak et al 2005). These studies generally involved a small number of specimens (< 50) and investigated which of several extraction methods yielded the highest amount of DNA for these specimens.…”

mentioning

confidence: 99%

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Assessment of age and greenness of herbarium specimens as predictors for successful extraction and amplification of DNA

Erkens

Cross²,

Maas³

et al. 2008

blum - j plant tax and plant geog

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sUMMARyAge and the greenness of leaves have been frequently used as indicators for selecting herbarium specimens for molecular studies. Although plant DNA extraction and amplification have been common lab procedures for the past 20 years, no studies specifically investigated the success of these indicators. Here the predictive value of age and the greenness for extraction and amplification success is assessed, using a large number of herbarium specimens from different plant groups. the investigation of these indicators is important because herbarium material is a precious commodity, and is often the only remaining floral record of now extinct ecosystems. In cases where little leaf material is available, most researchers still attempt to extract DNA. This study shows that age and greenness of leaves are unreliable indicators of extraction and amplification success, although together they can have limited usefulness. Furthermore, we found that the amount of extracted DNA from herbarium specimens decreases with c. 1% per year in age of the specimens. Therefore, researchers sometimes should refrain from using old rare specimens because chances of success are unpredictable and precious herbarium material might be wasted. The uncritical use of indicators such as age or leaf colour is therefore not recommendable. Furthermore, botanists should annotate how specimens were collected and dried because this information is essential for successful DNA extraction. Hopefully, similar studies will be reported in order to identify the best approaches to extract DNA from herbarium specimens.

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Section: Discussionsupporting

confidence: 88%

supporting

confidence: 91%

“…So far, only some small scale studies have shown that the relationship between age and extraction success might be absent (e.g. Drábková et al 2002;Jankowiak et al 2005).…”

Section: Discussionmentioning

confidence: 99%

Section: Guatteriamentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations

Assessment of age and greenness of herbarium specimens as predictors for successful extraction and amplification of DNA

Erkens

Cross²,

Maas³

et al. 2008

blum - j plant tax and plant geog

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Microsatellite markers for the biogeographically enigmatic sandmyrtle (Kalmia buxifolia, Phyllodoceae: Ericaceae)

et al. 2019

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Premise Microsatellite markers were developed for sandmyrtle, Kalmia buxifolia (Ericaceae), to facilitate phylogeographic studies in this taxon and possibly many of its close relatives. Methods and Results Forty‐eight primer pairs designed from paired‐end Illumina MiSeq data were screened for robust amplification. Sixteen pairs were amplified again, but with fluorescently labeled primers to facilitate genotyping. Resulting chromatograms were evaluated for variability using three populations from Tennessee, North Carolina, and New Jersey, USA . Eleven primer pairs were reliable and polymorphic (mean 3.92 alleles), one was reliable but monomorphic, and four were not reliable. The markers exhibited lower heterozygosity (mean 0.246) than expected (mean 0.464). Cross‐amplification in the remaining nine Kalmia species exhibited a phylogenetic pattern, suggesting broad applicability of the markers across the genus. Conclusions These microsatellite markers will be useful in population genetics and species boundaries studies of K. buxifolia , K. procumbens , and likely all other Kalmia species.

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Fourteen polymorphic microsatellite markers for the widespread Labrador tea (Rhododendron groenlandicum)

Sheik

LaBounty

Mitchell³

et al. 2019

Appl Plant Sci

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PremiseMicrosatellite markers were developed for Labrador tea (Rhododendron groenlandicum, Ericaceae) to facilitate downstream genetic investigation of this species and the extremely closely related, circumboreal Rhododendron subsect. Ledum.Methods and ResultsForty‐eight primer pairs were designed using Illumina data and screened for excellent amplification. Sixteen successful pairs were developed as microsatellite markers using fluorescently labeled amplification to generate chromatogram data. These data were evaluated for intrapopulation and interpopulation variability in three populations from Alaska and Maine, USA, and the Northwest Territories, Canada. Fourteen polymorphic markers genotyped reliably, each with one to eight alleles. Cluster analysis indicates that across the range, populations can be easily discriminated. Cross‐amplification in other Rhododendron subsect. Ledum species shows broad application of the developed markers within this small, well‐supported clade.ConclusionsThese microsatellite markers exhibit significant variability and will be useful in population genetics within R. groenlandicum and for investigation of species boundaries across Rhododendron subsect. Ledum.

show abstract

Comparison of seven DNA extraction and amplification protocols in historical herbarium specimens of juncaceae

Cited by 147 publications

References 12 publications

Assessment of age and greenness of herbarium specimens as predictors for successful extraction and amplification of DNA

Assessment of age and greenness of herbarium specimens as predictors for successful extraction and amplification of DNA

Microsatellite markers for the biogeographically enigmatic sandmyrtle (Kalmia buxifolia, Phyllodoceae: Ericaceae)

Fourteen polymorphic microsatellite markers for the widespread Labrador tea (Rhododendron groenlandicum)

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