Molecular Distinction of Algae Using Molecular Marker (original) (raw)
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International Journal of Pharmacy and Pharmaceutical Sciences, 2021
Objective: Identification of Chlorella species from the environment through 18s ribosomal RNA sequencing. This study was aimed to design primer targeting Chlorella and other closely related algal species targeting 18s ribosomal RNA, ITS1 region. Methods: Sanger sequencing was carried out for the identification of algae up to the genus and species level using an in-house designed primer and optimized PCR conditions. Results: Out of 2 algae samples identified phenotypically, one isolate identified as Chlorella vulgaris and other one identified as Chlorella sorokiniana based on the results of Basic Alignment Search Tool (BLAST). Conclusion: To conclude, this study provided primers with PCR conditions to characterize algal samples through molecular identification with 100% accuracy than the phenotypic method.
IOP Conference Series: Materials Science and Engineering
Identification of microalgae has relied on microscopic observation which is timeconsuming and high accuracy requiring. Molecular identification provides a solution to identify microalgae accurately and quickly. This study aims to identify locally isolated of Chlorella vulgaris by using rbcL gene. The study used exploration methods. The sample was C. vulgaris obtained from the local region in Situbondo, Indonesia. C. vulgaris DNA was isolated using the kit Zymo Research Plant. The C. vulgaris DNA was amplificated by PCR using rbcL gene primer then the sequencing of the PCR product was conducted. Phylogenetic analysis was conducted using the MEGA6 software. Research shows that DNA sequences were located at 593bp. After compared with the Chlorella sequences data in the GenBank using BLAST methods, it shows similarities of 88-99% and E-value of 0.0. The phylogenetic reconstruction shows that the local C. vulgaris with code STB01 was clade with another C. vulgaris, the population originates from a common ancestor. Although all population groups are separated by ecogeography. Each population was still genetically similar to short distance among populations. Molecular identification of local C. vulgaris was successfully carried out using primers rbcl and local isolate C. vulgaris have a genetic similarity of 99% with C. vulgaris in others region in the world.
2021
Identifying the newly isolated species is crucial to establishing a reliable algal database with successful commercial applications for different biotechnological applications. Morphological identification does not give sufficient description, especially for tiny unicellular microalgae. The rbcL gene encodes the large unit of ribulose-1, 5-bisphosphate carboxylase /oxygenase (Rubisco) has been widely known for barcoding in plants and developed for microalgae molecular identification. In this study, we examined the local strains of green microalgae from Indonesia using the rbcL partial gene sequence to identify the strains. Green microalgae isolates originated from Yogyakarta, Serayu, Gondol, Ancol, Cilegon, and Teluk Jakarta were cultured in f/2 media and harvested for DNA extraction. The DNA extracted was proceeded to PCR using 1AB_rbcL primer pair to amplify the sequences of rbcL gene with target band located at 582 bp, followed by the sequencing of the PCR product was conducted. ...
Genomic DNA Extraction and Genotyping of Dictyochloropsis Green Algae Strains
BIO-PROTOCOL, 2015
Dictyochloropsis is an ecologically important genus of free-living and symbiotic green algae. Representatives of this genus are horizontally transmitted among several fungi of the family Lobariaceae, thus forming photobiont-mediated guilds. This protocol is suitable for extracting DNA from algal cultures and lichen samples and for genotyping seven unlinked Dictyochloropsis reticulata microsatellite markers in a single PCR multiplex.
Journal of Phycology, 1988
Plastid DNA band patterns generated by electrophoresis of endonuclease digests demonstrate remarkable conservation of DNA sequences at the species and subspecies level in flowering plants. Generally, patterns are identical or near-identical from different populations belonging to the same species. This methodology has now been applied to red algae to ascertain its value in systematic studies.Plastid DNA from nine bangiophycean and florideophycean red algae was isolated and cut with restriction endonucleases that recognize different 6-base pair sequences. The patterns generated upon the electrophoretic separation of digestion fragments show that within a species patterns are identical, but not within higher taxa. The proper identification of one Gracilaria population of uncertain taxonomic affinity was clearly established by this method of plastid DNA analysis.Differences between species in plastid DNA sequences were confirmed by probing blots of restriction fragments with known gene sequences. A number of heterologous plastid DNA probes were found to be sufficiently homologous to be useful in studying red algal DNA.Unexpectedly, supercoiled circular plasmids ranging in size from ca. 1.5–8 kb were found in some red algal species but not in others. The position of these plasmids in agarose gels following electrophoresis is uniform within a species but differs between different species of the same genus, contributing further patterns for taxonomic analysis.
Molecules, 2011
Haematococcus pluvialis (Flotow) is a unicellular green alga, which is considered to be the best astaxanthin-producing organism. Molecular markers are suitable tools for the purpose of finding out genetic variations in organisms; however there have been no studies conducted on ISSR or RAPD molecular markers for this organism. The DNA of 10 different strains of H. pluvialis (four strains from Iran, two strains from Finland, one strain from Switzerland and three strains from the USA) was extracted. A genetic similarity study was carried out using 14 ISSR and 12 RAPD primers. Moreover, the molecular weights of the bands produced ranged from 0.14 to 3.4 Kb. The PCA and dendrogram clustered the H. pluvialis strains into various groups according to their geographical origin. The lowest genetic similarity was between the Iran2 and USA2 strains (0.08) and the highest genetic similarity was between Finland1 and Finland2 (0.64). The maximum numbers of bands produced by the ISSR and RAPD primers were 35 and 6 bands, respectively. The results showed that ISSR and RAPD markers are useful for genetic diversity studies of Haematococcus as they showed geographical discrimination.
BMC research notes, 2014
DNA comparison is becoming the leading approach to the analysis of microbial diversity. For eukaryotes, the internal transcribed spacer 2 (ITS2) has emerged as a conspicuous molecule that is useful for distinguishing between species. Because of the small number of usable ITS data in GenBank, ITS2 sequence comparisons have only been used for limited taxa. However, major institutions with planktonic algal culture collections have now released small subunit (SSU) to ITS rDNA sequence data for their collections. This development has uplifted the level of molecular systematics for these algae. Forty-three strains of green algae isolated from German inland waters were investigated by using SSU-ITS rDNA sequencing. The strains were isolated through the direct plating method. Many of the strains went extinct during the years of culture. Thus, it could be expected that the surviving strains would be common, vigorous species. Nevertheless, 12 strains did not match any known species for which ...
Aquaculture, 2004
Dunaliella salina (Chlorophyta) is a halophilic microalga cultivated as a natural source of hcarotene in several countries, including Chile. Previous studies of some Chilean strains of this microalga have shown a great variability in their physiological and genetic attributes. Random amplified polymorphic DNA (RAPD) band patterns and nuclear ribosomal DNA internal transcribed spacer (ITS-1 and ITS-2) sequences were used to genotypically characterize three Chilean and four foreign (from Mexico, China, Australia and Israel) strains of D. salina with industrial potential. Unweighted pair group mean average (UPGMA) cluster analysis of RAPD data distinguished, at 70% similarity, two clusters. One cluster included all of the foreign strains, except the one from Australia, and the other grouped two of the Chilean strains (CONC-001 and CONC-007). The other Chilean strain (CONC-006) and the Australian strain appeared as single entities. Neighbor-joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) analyses of the ITS sequence data yielded four clades, most of them well supported: there were two clades containing exclusively one strain, CONC-006 from Chile (86 -94% support) and the one from Australia (98 -100% support); the third clade grouped the strains from Mexico, China and Israel (99 -100% support), and, the fourth clade, the strains CONC-001 and CONC-007 from Chile (100% support). Both RAPD banding pattern and ITS sequence data were consistent in resolving the same genetic relatedness among the strains analyzed. For both approaches, the strain CONC-006 from Chile and the strain from Australia were the most divergent entities within the group. Furthermore, the strain CONC-006 appeared genetically more related to the foreign strains than to the other Chilean ones. The physiological attributes exhibited by these 0044-8486/$ -see front matter D (P.I. Gómez).