Reliability of <i>in silico</i> Modeling Based on Restriction Patterns for the Study of the Carotenogenic Gene <i>pds</i> of <i>Haematococcus</i> sp

Rapid Molecular Identification of <i></i>Tetraselmis Using Enzymatic Digestion of the <i></i>18S rDNA Gene

“…The PCR product has been generally sequenced and evaluated using bioinformatic programs that ensure the functional or phylogenetic relationship [13,16,14]. However, the benefit of using restriction enzymes could be an alternative technique based on the PCR product and is faster and reliable [21,28,19]. For example, Olmos, et al (2000) implemented this technique in the molecular identification of Dunaliella sp [8]; while Chin, et al (2018) and Pillacela, et al (2020) performed an in silico analysis to obtain the restriction pattern before being experimentally evaluated Pyrodinium bahamense [34] and Haematococcus sp [19], respectively.…”

“…However, the benefit of using restriction enzymes could be an alternative technique based on the PCR product and is faster and reliable [21,28,19]. For example, Olmos, et al (2000) implemented this technique in the molecular identification of Dunaliella sp [8]; while Chin, et al (2018) and Pillacela, et al (2020) performed an in silico analysis to obtain the restriction pattern before being experimentally evaluated Pyrodinium bahamense [34] and Haematococcus sp [19], respectively. In our study, we predicted the in silico restriction patterns for two PCR products, and then we digested experimentally using the enzymes BbvCI and Eco53kI; BstUI, RsaI, and MspI.…”

“…The PCR product was digested with the enzymes BbvCI and Eco53kI for the first reaction; BstUI, MspI and Rsal for the second. All enzymes were from Invitrogen TM and the performance was according to a previous protocol [19]. 10 µl of the PCR product was used for the enzyme reaction (1U/enzyme) in a final volume of 50 µl.…”

“…Commonly, the identification of genes is realized with DNA extraction, the amplification of a specific product and its sequencing [17,18,14]. However, mapping genes, using restriction enzymes, generates fast and reliable results instead of sequencing [19]. Bioinformatics programs can predict restriction patterns through in silico modeling, which is based on the sequence of the molecular marker and the relative location of the restriction sites for different enzymes [20][21].…”

“…Bioinformatics programs can predict restriction patterns through in silico modeling, which is based on the sequence of the molecular marker and the relative location of the restriction sites for different enzymes [20][21]. In silico modeling provides the size of the DNA fragments and can subsequently be validated experimentally [22,19].…”