Analysis Of Barcode Sequences Research Articles

Development of specific barcodes for identification of Aloe species based on chloroplast DNA barcoding

DNA barcoding is a widely used taxonomic tool for correctly identifying plant species. The chloroplast matK and rbcL are some of the most extensively studied variable coding genes of angiosperms and have been recommended as a universal barcode for terrestrial plants. Genus Aloe contains around 500 species, and most Aloe species have extensive traditional medicinal usage worldwide, viz., A. arborescens, A. ferox, A. maculate, and A. vera. This study evaluated the two chloroplast DNA barcodes (matK and rbcL) to develop a theoretical base for species identification and germplasm conservation of Aloe species. The Maximum Parsimony analysis was conducted to study the evolutionary relatedness of Aloe sequences using matK and rbcL sequences obtained from the NCBI nucleotide database. The results revealed that 49 Aloe accessions were segregated into four major clades using matK phylogenetic analysis. Likewise, the 29 Aloe accessions were allocated into two clades based on the rbcL phylogeny. Additionally, specific barcodes have been developed for the following species: A. vera, A. boylei, A. ciliaris, A. karasbergensis, and A. sinkatana based on SNP (Single Nucleotide Polymorphism) site analysis of barcode sequences and the corresponding DNA QR (quick response) code of each sequence was generated. This study provides a unique method for species identification of the genus Aloe and indicates the possibility of correctly identifying, discriminating, and documenting the Aloe species.

When barcoding fails: Genome chimerization (admixing) and reticulation obscure phylogenetic and taxonomic relationships

DNA barcoding is based on the premise that the barcode sequences can distinguish individuals (strains) of different species because their sequence variation between species exceeds that within species. The primary barcodes used in fungal and yeast taxonomy are the ITS segments and the LSU (large subunit) D1/D2 domain of the homogenized multicopy rDNA repeats. The secondary barcodes are conserved segments of protein‐encoding genes, which usually have single copies in haploid genomes. This study shows that the analysis of barcode sequences fails to reconstruct accurate species trees and differentiate species when the organisms have chimeric genomes composed of admixed mosaics of different origins. It is shown that the type strains of 10 species of the pulcherrima clade of the ascomycetous yeast genus Metschnikowia cannot be differentiated with standard barcodes because their intragenomic diversity is comparable to or even higher than the interstrain diversity. The analysis of a large group of genes of the sequenced genomes of the clade and the viability and segregation of the hybrids of ex‐type strains indicate that the high intragenomic barcode differences can be attributed to admixed genome structures. Because of the mosaic structures of the genomes, the rDNA repeats do not form continuous arrays and thus cannot be homogenized. Since the highly diverse ITS and D1/D2 sequences of the type strains form a continuous pool including pseudogenes, the evolution of their rDNA appears to involve reticulation. The secondary barcode sequences and the nonbarcode genes included in the analysis show incongruent phylogenetic relationships among the type strains, which can also be attributed to differences in the phylogenetic histories of the genes.

Identification of Marker Nucleotides for the Molecular Authentication of Arisaematis Rhizoma Based on the DNA Barcode Sequences

ABSTRACT Objectives : Official Arisaematis Rhizoma is described only three species, Arisaema amurnse , Arisaema erubescens , and Arisaema heterophyllum, in national Pharmacopoeia. However, other Arisaema species, Arisaema ringens, Arisaema takesimense and Arisaema serratum, also have been distributed as an inauthentic Arisaematis Rhizoma in the herbal market. To develop a reliable molecular a uthentication method for Arisaematis Rhizoma in species level, we analyzed DNA barcode regions using six Arisaema species.Methods : Thirty-eight samples of six Arisaema plants species (A. amurense, A. amurense f. serratum, A. heterophyllum, A. takesimense, and A. serratum) were collected from different habitate and nucleotide sequences of DNA barcode regions (rDNA-ITS, matK, and rbcL gene) were analyzed after PCR amplification. The species-spec ific sequences and phylogenetic relations were estimated using entire sequence s of three DNA barcodes based on the analysis of ClastalW and UPGMA, respectively.Results : The comparative analysis of DNA barcode sequences were revealed inter-species specific nucleotides to distinguish the medicinal plant of Arisaema Rhizoma in species levels excluding between A. amurense and its subspecies (A. amurense f. serratum) and A. takesimense and A. serratum, respectively. However, we obtained sequence differences enough to discriminate authentic and inaut hentic Arisaematis Rhizoma. Therefore, we suggest that these SNP type molecular genetic markers were an r eliable method avaliable to identify official herbal medicines.Conclusions : These marker nucleotides could be useful to identify the official herbal medicines by providing definitive information that can identify original medicinal pla nt and distinguish from inauthentic adulterants and substitutes.Key words : Arisaema species, Arisaematis Rhizoma, DNA barcode, Marker Nucleotide, Molecular Authentication

Alignment-free analysis of barcode sequences by means of compression-based methods

BackgroundThe key idea of DNA barcode initiative is to identify, for each group of species belonging to different kingdoms of life, a short DNA sequence that can act as a true taxon barcode. DNA barcode represents a valuable type of information that can be integrated with ecological, genetic, and morphological data in order to obtain a more consistent taxonomy. Recent studies have shown that, for the animal kingdom, the mitochondrial gene cytochrome c oxidase I (COI), about 650 bp long, can be used as a barcode sequence for identification and taxonomic purposes of animals. In the present work we aims at introducing the use of an alignment-free approach in order to make taxonomic analysis of barcode sequences. Our approach is based on the use of two compression-based versions of non-computable Universal Similarity Metric (USM) class of distances. Our purpose is to justify the employ of USM also for the analysis of short DNA barcode sequences, showing how USM is able to correctly extract taxonomic information among those kind of sequences.ResultsWe downloaded from Barcode of Life Data System (BOLD) database 30 datasets of barcode sequences belonging to different animal species. We built phylogenetic trees of every dataset, according to compression-based and classic evolutionary methods, and compared them in terms of topology preservation. In the experimental tests, we obtained scores with a percentage of similarity between evolutionary and compression-based trees between 80% and 100% for the most of datasets (94%). Moreover we carried out experimental tests using simulated barcode datasets composed of 100, 150, 200 and 500 sequences, each simulation replicated 25-fold. In this case, mean similarity scores between evolutionary and compression-based trees span between 83% and 99% for all simulated datasets.ConclusionsIn the present work we aims at introducing the use of an alignment-free approach in order to make taxonomic analysis of barcode sequences. Our approach is based on the use of two compression-based versions of non-computable Universal Similarity Metric (USM) class of distances. This way we demonstrate the reliability of compression-based methods even for the analysis of short barcode sequences. Compression-based methods, with their strong theoretical assumptions, may then represent a valid alignment-free and parameter-free approach for barcode studies.

Analysis of barcode sequences by means of compression-based methods

Motivations. The key idea of DNA barcode initiative is to identify, for each group of species belonging to different kingdoms of life, a short DNA sequence that can act as a true taxon barcode. DNA barcode represents a valuable type of information that can be integrated with ecological, genetic, and morphological data in order to obtain a more consistent taxonomy. Recent studies have shown that, for the animal kingdom, the mitochondrial gene cytochrome c oxidase I (COI), about 650 bp long, can be used as a barcode sequence for identification and taxonomic purposes of animals. The analysis of DNA barcode sequences is carried out with well known bioinformatics techniques: for example the most common approach to create a phylogenetic tree for a group of species uses the multi-alignment of genetic sequences, the computation of a dissimilarity matrix, using one of the current available evolutionary distance model, and finally the building of a tree by means of hierarchical algorithms such as Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and Neighbor Joining (NJ). In the present work we aims at introducing the use of an alignment-free approach in order to make taxonomic analysis of barcode sequences. Our approach is based on the use of two compression-based versions of non-computable Universal Similarity Metric (USM) class of distances. This way we try to overcome some flaws of classic techniques, such as the time-consuming and parameter-dependent alignment procedure and the use of stochastic evolutionary distance models, that do not represent a distance metric. Methods. Universal Similarity Metric represents a class of distance measures based on the non-computable Kolmogorov complexity. That means it needs some approximation in order to be used. USM is said to be "universal" because it can be applied for computing a distance matrix among input data belonging to very different application domains. In fact it has been used for the analysis of text, images, music. In bioinformatics, it has been applied for obtaining phylogenetic trees from complete mythocondrial genome of mammalian species. Our purpose is to justify the employ of USM also for the analysis of short DNA barcode sequences, showing USM is able to correctly extract taxonomic information among those kind of sequences. We, then, downloaded from Barcode of Life data System database (BOLD) 20 datasets of barcode sequences belonging to different animal species. For each dataset we computed dissimilarity matrices by means of two compression-based approximation of USM, namely Normalized Compression Distance (NCD) and its conditional compression version. In both cases we used GenCompres compressor, that is a dictionary-based compressor suited to work with DNA sequences. From those matrices we built, using UPGMA and NJ algorithms, phylogenetic trees of every dataset and compared them, in terms of topology preservation, with the trees obtained through Kimura 2-parameter evolutionary distance model. Results. Experimental tests aim to evaluate the quality of phylogenetic reconstruction in terms of both topological similarity and differences in the relative branch length. As regard the tree similarity, we obtain good results with a percentage of similarity between evolutionary and compression-based tree greater than 82% and, for the most of datasets, between 90% and 100%. Lower results are for datasets having an high percentage of sequences with ambiguous bases. We detect the same trend for differences in the relative branch of trees, except that poorer results are reached by those datasets containing some COI-5P gene sequences longer than the other ones.

An integrated approach to fast and informative morphological vouchering of nematodes for applications in molecular barcoding

Molecular surveys of meiofaunal diversity face some interesting methodological challenges when it comes to interstitial nematodes from soils and sediments. Morphology-based surveys are greatly limited in processing speed, while barcoding approaches for nematodes are hampered by difficulties of matching sequence data with traditional taxonomy. Intermediate technology is needed to bridge the gap between both approaches. An example of such technology is video capture and editing microscopy, which consists of the recording of taxonomically informative multifocal series of microscopy images as digital video clips. The integration of multifocal imaging with sequence analysis of the D2D3 region of large subunit (LSU) rDNA is illustrated here in the context of a combined morphological and barcode sequencing survey of marine nematodes from Baja California and California. The resulting video clips and sequence data are made available online in the database NemATOL (http://nematol.unh.edu/). Analyses of 37 barcoded nematodes suggest that these represent at least 32 species, none of which matches available D2D3 sequences in public databases. The recorded multifocal vouchers allowed us to identify most specimens to genus, and will be used to match specimens with subsequent species identifications and descriptions of preserved specimens. Like molecular barcodes, multifocal voucher archives are part of a wider effort at structuring and changing the process of biodiversity discovery. We argue that data-rich surveys and phylogenetic tools for analysis of barcode sequences are an essential component of the exploration of phyla with a high fraction of undiscovered species. Our methods are also directly applicable to other meiofauna such as for example gastrotrichs and tardigrades.