Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward

GENETIC VARIATION OF LEPTOTROMBIDIUM (ACARI: TROMBICULIDAE) MITES CARRYING ORIENTIA TSUTSUGAMUSHI, THE BACTERIAL PATHOGEN CAUSING SCRUB TYPHUS

Leptotrombidium (Acari: Trombiculidae) mites are carriers of Orientia tsutsugamushi, the bacterial pathogen causing scrub typhus in humans. Classification of Leptotrombidium is vital because limited mite species carry O. tsutsugamushi. Generally, Leptotrombidium at the larval stage (approximately 0.2 mm in size) are used for morphological identification. However, morphological identification is often challenging because it requires considerable skills and taxonomic expertise. In this study, we found that the full-length sequences of the mitochondrial cytochrome c oxidase subunit 1 gene varied among the significant Leptotrombidium. On the basis of these, we modified the canonical deoxyribonucleic acid (DNA) barcoding method for animals by redesigning the primer set to be suitable for Leptotrombidium. Polymerase chain reaction with the redesigned primer set drastically increased the detection sensitivity, especially against Leptotrombidium scutellare (approximately 17% increase), one of the significant mites carrying O. tsutsugamushi. Phylogenetic analysis showed that the samples morphologically classified as L. scutellare and Leptotrombidium pallidum were further split into 3 and 2 distinct subclusters respectively. The mean genetic distance (p-distance) between L. scutellare and L. pallidum was 0.2147, whereas the mean distances within each species were 0.052 and 0.044, respectively. Within L. scutellare, the mean genetic distances between the 3 subclusters were 0.1626-0.1732, whereas the distances within each subcluster were 0.003-0.017. Within L. pallidum, the mean genetic distance between the 2 subclusters was 0.1029, whereas the distances within each subcluster were 0.010-0.013. The DNA barcoding uncovered a broad genetic diversity of Leptotrombidium, especially of L. scutellare and L. pallidum, the notable species carrying O. tsutsugamushi. We conclude that the DNA barcoding using our primers enables precise and detailed classification of Leptotrombidium and implies the existence of a subgenotype in Leptotrombidium that had not been found by morphological identification.

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.

Sık Kullanılan Bazı Hücre Hatları için Kalite Kontrol: Mikoplazma Kontaminasyon Tespiti, Sitokrom B ve Sitokrom Oksidaz Alt Birim I Genlerinin DNA Dizi Analizlerinin Gerçekleştirilmesi

Amaç: Laboratuvarlarda sık kullanılan serviks epitelyal karsinom (HeLa), insan periferal kan promiyelösitik lösemi (HL-60), fare C3/bağ dokusu (L929), Madin Darby köpek böbrek (MDCK), fare nöroblastom (Neuro-2a) gibi bazı hücre hatlarının mikoplazma kontaminasyon kontrollerinin yapılması, kimlik doğrulamalarının gerçekleştirilmesi ve klonalitelerinin belirlenmesidir.Yöntem: Bu çalışmada üç farklı türe ait beş hücre hattı kullanılmıştır. Çalışılan tüm hatların Bisbenzimid (Hoechst 33258) ile deoksiribonükleik asit (DNA) floresan işaretlemesi yapılarak mikoplazma kontaminasyonu kontrolleri gerçekleştirilmiştir. Hücre hatlarından DNA izolasyonları yapılmış, elde edilen DNA örneklerinden sitokrom B (CYTB) geninin bölgesel amplifikasyonu için L14816 ve H15173 primerleri; sitokrom oksidaz alt birim I (COI) geni için ise LCO 1490 and HCO 2198 primerleri kullanılmıştır. İlgili amplifikasyonların DNA dizi analiz sonuçları, biyoinformatik araçlar kullanılarak referans dizilerle karşılaştırmalı olarak değerlendirilmiştir.Bulgular: Çalışmada ilgili hücrelerin, Bisbenzimid (Hoechst 33258) ile üretici firmanın protokollerine göre belirlenen konsantrasyon ve sürede yapılan boyama sonucunda mikoplazma kontaminasyonuna rastlanılmamıştır. Ayrıca CYTB gen bölgesi için veritabanında yer alan referans dizi ile yapılan karşılaştırma sonucu HL-60 için %97; "HeLa, L929, MDCK, Neuro-2a” hücre hatları için ise %98 oranında benzerlik bulunmuştur. COI gen bölgesi için ise bu benzerlik oranları “HeLa, HL-60, L929, MDCK ve Neuro-2a” hücre hatları için sırasıyla %95, %99, %96, %96 ve %98 olarak bulunmuştur.Sonuç: Bu bağlamda, çalışmadan elde edilen Bisbenzimid (Hoechst 33258) işaretleme ve DNA dizi analiz sonuçları, pek çok araştırmada kullanılan bu hücre hatlarının kalitesi konusunda kabul edilebilir bir belirteç ve güven sağlamıştır.   

The continuing evolution of barcode applications: Functional toxicology to cell lineage

DNA barcoding is a method to identify biological entities, including individual cells, tissues, organs, or species, by unique DNA sequences. With the advent of next generation sequencing (NGS), there has been an exponential increase in data acquisition pertaining to medical diagnosis, genetics, toxicology, ecology, cancer, and developmental biology. While barcoding first gained wide access in identifying species, signature tagged mutagenesis has been useful in elucidating gene function, particularly in microbes. With the advent of CRISPR/CAS9, methodology to profile eukaryotic genes has made a broad impact in toxicology and cancer biology. Designed homing guide RNAs (hgRNAs) that self-target DNA sequences facilitate cell lineage barcoding by introducing stochastic mutations within cell identifiers. While each of these applications has their limitations, the potential of sequence barcoding has yet to be realized. This review will focus on signature-tagged mutagenesis and briefly discuss the history of barcoding, experimental problems, novel detection methods, and future directions.