An efficient and cost-effective method for primer-induced nucleotide labeling for massive sequencing on next-generation sequencing platforms

DNA Sequencing Technologies and DNA Barcoding

DNA barcodes are short, standardized DNA segments that geneticists can use to identify all living taxa. On the other hand, DNA barcoding identifies species by analyzing these specific regions against a DNA barcode reference library. In its initial years, DNA barcodes sequenced by Sanger's method were extensively used by taxonomists for the characterization and identification of species. But in recent years, DNA barcoding by next-generation sequencing (NGS) has found broader applications, such as quality control, biomonitoring of protected species, and biodiversity assessment. Technological advancements have also paved the way to metabarcoding, which has enabled massive parallel sequ.encing of complex bulk samples using high-throughput sequencing techniques. In future, DNA barcoding along with high-throughput techniques will show stupendous progress in taxonomic classification with reference to available sequence data.

DNA barcoding, an effective tool for species identification: a review

DNA barcoding is a powerful taxonomic tool to identify and discover species. DNA barcoding utilizes one or more standardized short DNA regions for taxon identification. With the emergence of new sequencing techniques, such as Next-generation sequencing (NGS), ONT MinION nanopore sequencing, and Pac Bio sequencing, DNA barcoding has become more accurate, fast, and reliable. Rapid species identification by DNA barcodes has been used in a variety of fields, including forensic science, control of the food supply chain, and disease understanding. The Consortium for Barcode of Life (CBOL) presents various working groups to identify the universal barcode gene, such as COI in metazoans; rbcL, matK, and ITS in plants; ITS in fungi; 16S rRNA gene in bacteria and archaea, and creating a reference DNA barcode library. In this article, an attempt has been made to analyze the various proposed DNA barcode for different organisms, strengths & limitations, recent advancements in DNA barcoding, and methods to speed up the DNA barcode reference library construction. This study concludes that constructing a reference library with high species coverage would be a major step toward identifying species by DNA barcodes. This can be achieved in a short period of time by using advanced sequencing and data analysis methods.

Method for quick DNA barcode reference library construction

DNA barcoding has become one of the most important techniques in plant species identification. Successful application of this technology is dependent on the availability of reference database of high species coverage. Unfortunately, there are experimental and data processing challenges to construct such a library within a short time. Here, we present our solutions to these challenges. We sequenced six conventional DNA barcode fragments (ITS1, ITS2, matK1, matK2, rbcL1, and rbcL2) of 380 flowering plants on next-generation sequencing (NGS) platforms (Illumina Hiseq 2500 and Ion Torrent S5) and the Sanger sequencing platform. After comparing the sequencing depths, read lengths, base qualities, and base accuracies, we conclude that Illumina Hiseq2500 PE250 run is suitable for conventional DNA barcoding. We developed a new "Cotu" method to create consensus sequences from NGS reads for longer output sequences and more reliable bases than the other three methods. Step-by-step instructions to our method are provided. By using high-throughput machines (PCR and NGS), labeling PCR, and the Cotu method, it is possible to significantly reduce the cost and labor investments for DNA barcoding. A regional or even global DNA barcoding reference library with high species coverage is likely to be constructed in a few years.

Biopiracy: Abolish Corporate Hijacking of Indigenous Medicinal Entities

Biopiracy as "a silent disease" is hardly detectable because it does not leave traces frequently. The corporate hijacking of food is the most important health hazard in this era; giant commercial enterprises are using intellectual property rights to patent indigenous medicinal plants, seeds, genetic resources, and traditional medicines. The new era of biotechnology relies on the genes of living organisms as raw materials. The "Gene Rush" has thus become similar to that of the old "Gold Rush." Sri Lanka has been spotted in the top 34 biodiversity hotspots globally. Moreover, localized in the tropics, human generations in Sri Lanka have utilized the array of plant species for herbal treatments and treatment of diseases. Sri Lanka after its 30-year civil war is moving towards a solid growth and conservation of the environment which is a major component in a sustainable development where the conservation of biodiversity plays a significant role. In this paper, we present an overview of typical cases of global biopiracy, bioprospecting via introduction of cost-effective deoxyribonucleic acid (DNA) fingerprinting and international protocol with Private-Public-People Partnership concept as excellent forms of utilization of natural resources. We propose certain perspectives as scientists towards abolishing biopiracy and also to foster the fair utilization of natural resources; since the economy of most developing countries is agriculture based, the gross domestic product of the developing countries could be increased by enhanced bioprospecting via introduction of cost-effective DNA fingerprinting technologies and thus not being a pray of corporate hijacking."Biopiracy is biological theft; illegal collection of indigenous plants by corporations who patent them for their own use" (Vandana Shiva).

Exon sequencing mutation detection algorithm based on PCR matching

BACKGROUND

With the development of second-generation sequencing technology, more and more DNA sequence variations have been detected. Exon sequencing is the first choice for sequencing many cancer genes, and it can be better used to identify disease status by detecting gene variants. PCR sequence is an effective method to capture that sequence of an exon in the process of sequencing. Exon sequencing sequence contains PCR primer sequence, the correct position of the sequence can be determined by PCR primer sequence, which can be found in SNP, Indel mutation point by comparing the sequence of PCR primer sequence.

RESULTS

In this paper, a matching algorithm based on the PCR primer sequence is proposed, which can effectively sequence the position of PCR primer sequence and find out the key position sequence. Then the sequencing sequence is sorted and the number of the same sequence is counted to reduce the matching times. Then, the sequenced sequence was matched with PCR primer sequence, so that the DNA position could be accurately matched and the variation in the sequenced sequence could be found more quickly.

CONCLUSIONS

Compared with the traditional sequence matching method, PCR primer sequence matching method can match many sequences and find more variation. It also showed a high recall rate in the recall rate.