An Efficient DNA Extraction Method for Desert Calligonum Species

Abdellaoui, Raoudha; Gouja, Hassen; Salhi-Hannachi, Amel; Neffati, Mohamed

doi:10.1007/s10528-011-9443-7

Cited by 11 publications

(7 citation statements)

References 12 publications

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“…Herbarium samples from A. javanica, C. imbricatum, T. aucherana and Z. simplex were not amplified with any of the three primers. Isolating high quality DNA from Calligonum species can be difficult as it contains large amounts of polyphenolic compounds and polysaccharides, among others (Abdellaoui et al 2011). The primers rbcL and matK were highly conservative and failed in Calligonum species discrimination (Li et al 2014).…”

Section: Resultsmentioning

confidence: 99%

DNA barcoding of selected UAE medicinal plant species: a comparative assessment of herbarium and fresh samples

Enan

Palakkott

Ksiksi

2017

Physiol Mol Biol Plants

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It is commonly difficult to extract and amplify DNA from herbarium samples as they are old and preserved using different compounds. In addition, such samples are subjected to the accumulation of intrinsically produced plant substances over long periods (up to hundreds of years). DNA extraction from desert flora may pause added difficulties as many contain high levels of secondary metabolites. Herbarium samples from the Biology Department (UAE University) plant collection and fresh plant samples, collected from around Al-Ain (UAE), were used in this study. The three barcode loci for the coding genes matK, rbcL and rpoC1-were amplified. Our results showed that T. terresteris, H. robustum,T. pentandrus and Z. qatarense were amplified using all three primers for both fresh and herbaium samples. Both fresh and herbarium samples of C. comosum, however, were not amplified at all, using the three primers. Herbarium samples from A. javanica, C. imbricatum, T. aucherana and Z. simplex were not amplified with any of the three primers. For fresh samples 90, 90 and 80% of the samples were amplified using matK, rbcL and rpoC1, respectively. In short, fresh samples were significantly better amplified than those from herbarium sources, using the three primers. Both fresh and herbarium samples from one species (C. comosum), however, were not successfully amplified. It is also concluded that the rbcL regions showed real potentials to distinguish the UAE species under investigation into the appropriate family and genus.

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Section: Resultsmentioning

confidence: 99%

DNA barcoding of selected UAE medicinal plant species: a comparative assessment of herbarium and fresh samples

Enan

Palakkott

Ksiksi

2017

Physiol Mol Biol Plants

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“…Pure cultures of isolates were grown on PDA plates for 5 days at 28 °C prior to DNA extraction. DNA was extracted from cultures using the CTAB method 42 . Fungal 28S rRNA genes were amplified using the primers LR0R/LR7 43 .…”

Section: Methodsmentioning

confidence: 99%

Microbial community analysis and biodeterioration of waterlogged archaeological wood from the Nanhai No. 1 shipwreck during storage

Liu

et al. 2018

Sci Rep

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Wooden shipwrecks are a significant part of the underwater cultural heritage. In 2007, the Nanhai No. 1 shipwreck was salvaged from the seabed and moved into the Marine Silk Road Museum, where it is still stored in a water tank. We analysed the microbial communities colonizing the hull surface of the Nanhai No. 1 shipwreck during storage. Six samples exposed to air were collected from different spots of the ship that exhibited obvious microbial plaques. High-throughput sequencing revealed the bacterial community includes both aquatic and terrestrial species, while in the fungal community, Fusarium was the most abundant genus across all samples and accounted for 84.91% to 98.40% of the total community composition. Two Fusarium species were isolated from the samples and were identified as F. solani and F. oxysporum. Both of the isolates were able to degrade cellulose, but only F. solani had the ability to degrade lignin. Antimicrobial efficacy in inhibiting the growth of Fusarium was assessed with five kinds of biocides, and isothiazolinones exhibited specific inhibition of Fusarium growth. These results provide critical background information to protect and reduce the biodegradation and destruction of this important historical shipwreck, and inform efforts to protect other similar artifacts.

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“…The evolutionary relationships of C. bakuense to other members of Calligonum are currently unknown, as is the population structure within the species. Calligonum L. is a lineage of xerophytic shrubs with an estimated 30–40 species; it is distributed from northern Africa, the Arab Peninsula, South West Asia, the Caucasus, the Irano-Turanian region, and Central Asia to China (Brandbyge, 1993; Abdellaoui et al, 2011). Several species of the genus are globally red-listed and exhibit declining population sizes (Baillie et al, 2004).…”

Section: Methodsmentioning

confidence: 99%

Software choice and depth of sequence coverage can impact plastid genome assembly – A case study in the narrow endemic Calligonum bakuense

Giorgashvili

Reichel

Caswara

et al. 2021

Preprint

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Most plastid genome sequences are assembled from short-read whole-genome sequencing data, yet the impact that sequence coverage and the choice of assembly software can have on the accuracy of the resulting assemblies is poorly understood. In this study, we test the impact of both factors on plastid genome assembly in the threatened and rare endemic shrub Calligonum bakuense, which forms a distinct lineage in the genus Calligonum. We aim to characterize the differences across plastid genome assemblies generated by different assembly software tools and levels of sequence coverage and to determine if these differences are large enough to affect the phylogenetic position inferred for C. bakuense. Four assembly software tools (FastPlast, GetOrganelle, IOGA, and NOVOPlasty) and three levels of sequence coverage (original depth, 2,000x, and 500x) are compared in our analyses. The resulting assemblies are evaluated with regard to reproducibility, contig number, gene complement, inverted repeat length, and computation time; the impact of sequence differences on phylogenetic tree inference is also assessed. Our results show that software choice can have a considerable impact on the accuracy and reproducibility of plastid genome assembly and that GetOrganelle produced the most consistent assemblies for C. bakuense. Moreover, we found that a cap in sequence coverage can reduce both the sequence variability across assembly contigs and computation time. While no evidence was found that the sequence variability across assemblies was large enough to affect the phylogenetic position inferred for C. bakuense, differences among the assemblies may influence genotype recognition at the population level.

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An Efficient DNA Extraction Method for Desert Calligonum Species

Cited by 11 publications

References 12 publications

DNA barcoding of selected UAE medicinal plant species: a comparative assessment of herbarium and fresh samples

DNA barcoding of selected UAE medicinal plant species: a comparative assessment of herbarium and fresh samples

Microbial community analysis and biodeterioration of waterlogged archaeological wood from the Nanhai No. 1 shipwreck during storage

Software choice and depth of sequence coverage can impact plastid genome assembly – A case study in the narrow endemic Calligonum bakuense

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