DNA barcoding – A new device in phycologist's toolbox

Kowalska, Zuzanna; Pniewski, Filip; Latała, Adam

doi:10.1016/j.ecohyd.2019.01.002

Cited by 13 publications

(15 citation statements)

References 63 publications

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“…According to previous studies (Kowalska et al, 2019 andFierer 2017), with the advent of molecular biology, rapid identification of large populations of bacteria is now possible. Four bacterial primers were designed for species in urban park soils.…”

Section: Resultsmentioning

confidence: 99%

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Molecular Markers for Detection of Species From the Soil Microbiota of the Brazilian Cerrado/ Marcadores Moleculares Para Detecção De Espécies Da Microbiota Do Solo Do Cerrado Brasileiro

Alves

Camolezi

Bernardes

et al. 2020

BJD

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Section: Resultsmentioning

confidence: 99%

“…The development of molecular approaches to characterize soil bacteria brings a new perspective in the characterization of the vast diversity of microbial communities (Kowalska et al, 2019). Isolating and identifying microorganisms in soil fragments is critical for obtaining genetically stable strains (Adnan and Tan, 2007).…”

Section: Introductionmentioning

confidence: 99%

Molecular Markers for Detection of Species From the Soil Microbiota of the Brazilian Cerrado/ Marcadores Moleculares Para Detecção De Espécies Da Microbiota Do Solo Do Cerrado Brasileiro

Alves

Camolezi

Bernardes

et al. 2020

BJD

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“…DNA barcoding is simple, accurate, and fast, and is therefore the most effective method for species identification 19 , 20 . Sequences with high success rates of amplification and sequencing, high variability among species but low nucleotide variation within species (less than 2%) are considered to be excellent DNA markers 21 . The rpl22 gene is efficient for species identification in the genus as it can identify species with a single gene, as it has high rates of variable sites (8.48%) within genus and only 0.45% nucleotide variation within species.…”

Section: Discussionmentioning

confidence: 99%

Insights into chloroplast genome structure, intraspecific variation, and phylogeny of Cyclamen species (Myrsinoideae)

Mao¹,

Zou²,

Sun

et al. 2023

Sci Rep

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Species from the flowering plant genus Cyclamen are popular amongst consumers. In particular Cyclamen persicum Mill. has been significantly used commercially, and certain small flowering species such as Cyclamen hederifolium and Cyclamen coum are gradually growing in popularity in the potted flower market. Here, the chloroplast genomes of nine Cyclamen samples including four Cyclamen species and five varieties of C. hederifolium were sequenced for genome structure comparison, White green septal striped leaves related gene screening and DNA molecular markers were developed for phylogenetic analysis. In comparing Cyclamen species’ chloroplast genomes, gene content and gene order were found to be highly similar with the length of genomes ranging from 151,626 to 153,058 bp. The chloroplast genome of Cyclamen has 128 genes, including 84 protein-coding genes, 36 transfer RNA genes, and 8 ribosomal RNA genes. Based on intraspecific variation, seven hotspots, including three genes and four intergenic regions, were identified as variable markers for downstream species delimitation and interspecific relationship analyses. Moreover, a phylogenetic tree constructed with complete chloroplast genomes, revealed that Cyclamen are monophyletic with Lysimachia as the closest neighbor. Phylogenetic analyses of the 14 Cyclamen species with the seven variable regions showed five distinct clades within this genus. The highly supported topologies showed these seven regions may be used as candidate DNA barcode sequences to distinguish Cyclamen species. White green septal striped leaves is common in C. hederifolium, however the molecular mechanism of this has not yet been described. Here, we find that the intergenic region rps4-trnT-UGU seems related to white green septal striped leaves.

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“…It has been proposed as a potential barcode for both algae and terrestrial plants, finding widespread use in the phylogenetics of green algae species. The ITS1 and ITS2 markers exhibit sufficient variability to distinguish between different strains of algae (Kowalska et al, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

Applying an internal transcribed spacer as a single molecular marker to differentiate between Tetraselmis and Chlorella species

Fathy,

Techen,

Elsayed

et al. 2023

Front. Microbiol.

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In the realm of applied phycology, algal physiology, and biochemistry publications, the absence of proper identification and documentation of microalgae is a common concern. This poses a significant challenge for non-specialists who struggle to identify numerous eukaryotic microalgae. However, a promising solution lies in employing an appropriate DNA barcoding technique and establishing comprehensive databases of reference sequences. To address this issue, we conducted a study focusing on the molecular characterization and strain identification of Tetraselmis and Chlorella species, utilizing the internal transcribed spacer (ITS) barcode approach. By analyzing the full nuclear ITS region through the Sanger sequencing approach, we obtained ITS barcodes that were subsequently compared with other ITS sequences of various Tetraselmis and Chlorella species. To ensure the reliability of our identification procedure, we conducted a meticulous comparison of the DNA alignment, constructed a phylogenetic tree, and determined the percentage of identical nucleotides. The findings of our study reveal the significant value of the ITS genomic region as a tool for distinguishing and identifying morphologically similar chlorophyta. Moreover, our results demonstrate that both the ITS1 and ITS2 regions are capable of effectively discriminating isolates from one another; however, ITS2 is preferred due to its greater intraspecific variation. These results underscore the indispensability of employing ITS barcoding in microalgae identification, highlighting the limitations of relying solely on morphological characterization.

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DNA barcoding – A new device in phycologist's toolbox

Cited by 13 publications

References 63 publications

Molecular Markers for Detection of Species From the Soil Microbiota of the Brazilian Cerrado/ Marcadores Moleculares Para Detecção De Espécies Da Microbiota Do Solo Do Cerrado Brasileiro

Molecular Markers for Detection of Species From the Soil Microbiota of the Brazilian Cerrado/ Marcadores Moleculares Para Detecção De Espécies Da Microbiota Do Solo Do Cerrado Brasileiro

Insights into chloroplast genome structure, intraspecific variation, and phylogeny of Cyclamen species (Myrsinoideae)

Applying an internal transcribed spacer as a single molecular marker to differentiate between Tetraselmis and Chlorella species

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