DNA Barcoding Approach Research Articles

Evaluating the effectiveness of DNA-based methods to detect mislabelling and adulteration of chestnut honey

Honey is a naturally sweet and viscous substance that is consumed worldwide for its specific flavour, taste and biological properties, which in turn depend on the type of plant from which bees collect nectar. The quality of honey and, in particular, the information on the product label determines consumer choice and market price. In this study, the true botanical composition of chestnut monofloral honeys produced in Calabria (South Italy) was determined by DNA barcoding, PCR-RFLP and LAMP approaches, all based on the chloroplast trnL-trnF intergenic spacer region. All three DNA-based techniques were reliable in unambiguously identifying the floral composition of the different honeys tested at species level. However, the LAMP assay has the advantage over DNA barcoding and PCR-RFLP of greatly simplifying and speeding up the identification of Castanea sativa as the dominant plant species of the Calabrian chestnut honeys. This may encourage the adoption of this method by the food industry for the rapid detection of intentionally or accidentally mislabelled ingredients in this valuable natural product, thus ensuring consumer safety and protection.

Assembly-free reads accurate identification (AFRAID) approach outperforms other methods of DNA barcoding in the walnut family (Juglandaceae)

DNA barcoding has been extensively used for species identification. However, species identification of mixed samples or degraded DNA is limited by current DNA barcoding methods. In this study, we use plant species in Juglandaceae to evaluate an assembly-free accurate reads identification (AFRAID) method of species identification, a novel approach for precise species identification in plants. Specifically, we determined (1) the accuracy of DNA barcoding approaches in delimiting species in Juglandaceae, (2) the minimum size of chloroplast dataset for species discrimination, and (3) minimum amount of next generation sequencing (NGS) data required for species identification. We found that species identification rates were highest when whole chloroplast genomes were used, followed by taxon-specific DNA barcodes, and then universal DNA barcodes. Species identification of 100% was achieved when chloroplast genome sequence coverage reached 20% and the original sequencing data reached 500,000 reads. AFRAID accurately identified species for all samples tested after 500,000 clean reads, with far less computing time than common approaches. These results provide a new approach to accurately identify species, overcoming limitations of traditional DNA barcodes. Our method, which uses next generation sequencing to generate partial chloroplast genomes, reveals that DNA barcode regions are not necessarily fixed, accelerating the process of species identification.

DNA barcoding: An effective molecular tool for species identification, molecular authentication and phylogeny studies in plant science research

DNA barcoding is a technique for identifying specimens using brief, standardised DNA segments. In a variety of fields, including phylogeny, ecology, population genetics and biodiversity, DNA barcoding has become a successful method for precisely distinguishing species. The method is straightforward, efficient in both time and money and accurate. The key to successful DNA barcoding is choosing the right DNA marker. Since the idea of a quick approach for species identification was first put up in 2003, the scientific community has been keen to realise the potential of DNA barcodes. Cytochrome c oxidase, I (COI) region of the mitochondrial genome is mostly recognised as a standard barcoding region in animals. Later, rbcL + matK pairing, with a 70 % discriminating efficiency, was suggested by the Plant Working Group (PWG) of the Consortium for the Barcoding of Life (CBOL) as the standard barcode in plants. Three conditions must be met for a gene region to be an efficient DNA barcode: it must have sufficient species-level genetic divergence and variability, it must have conserved flanking regions for the widest taxonomic use and for generating universal PCR primers and it should be long enough to facilitate current capability for sequencing and extracting DNA. Different combinations of plastid coding, non-coding and nuclear markers are utilised as supplemental markers to boost the degree of plant species differentiation. The reliability of different barcodes in distinguishing species varies among different groups of plants. As DNA barcoding approaches its twentieth anniversary, technologies are still being developed that make use of this resource, which is constantly expanding in a variety of biological disciplines. Plant DNA barcoding, which became a scientific advance during the last ten years, is frequently employed as a taxonomical aid in identifying species. It is a way of choosing genetic loci that identifies and distinguishes an organism's membership from specific species, variations or even intervarieties. It varies from molecular phylogeny, which identifies an unknown sample from an existing classification rather than identifying patterns of association.

Exploring Taxonomic and Genetic Relationships in the Pinus mugo Complex Using Genome Skimming Data.

Genome skimming is a novel approach that enables obtaining large-scale genomic information based on high-copy DNA fractions from shallow whole-genome sequencing. The simplicity of this method, low analysis costs, and large amounts of generated data have made it widely used in plant research, including species identification, especially in the case of protected or endangered taxa. This task is particularly difficult in the case of closely related taxa. The Pinus mugo complex includes several dozen closely related taxa occurring in the most important mountain ranges in Europe. The taxonomic rank, origin, or distribution of many of these taxa have been debated for years. In this study, we used genome skimming and multilocus DNA barcoding approaches to obtain different sequence data sets and also to determine their genetic diversity and suitability for distinguishing closely related taxa in the Pinus mugo complex. We generated seven different data sets, which were then analyzed using three discrimination methods, i.e., tree based, distance based, and assembling species by automatic partitioning. Genetic diversity among populations and taxa was also investigated using haplotype network analysis and principal coordinate analysis. The proposed data set based on divergence hotspots is even twenty-times more variable than the other analyzed sets and improves the phylogenetic resolution of the Pinus mugo complex. In light of the obtained results, Pinus × rhaetica does not belong to the Pinus mugo complex and should not be identified with either Pinus uliginosa or Pinus rotundata. It seems to represent a fixed hybrid or introgressant between Pinus sylvestris and Pinus mugo. In turn, Pinus mugo and Pinus uncinata apparently played an important role in the origins of Pinus uliginosa and Pinus rotundata.

Species diversity and phylogeny of the green macroalga Ulva (Ulvophyceae, Chlorophyta) in Singapore

The green macroalgal genus Ulva (Ulvaceae, Ulvophyceae, Chlorophyta) is commonly found in coastal ecosystems and confers many important marine ecological services. Despite prior research interest and recent advancements in Ulva taxonomy, in many parts of the world, its species diversity remains unresolved due to a high degree of morphological variation and phenotypic plasticity. DNA barcoding and phylogenetic approaches can potentially assist in identifying Ulva species precisely. Here, we analysed chloroplast tufA, rbcL and nuclear ITS from 49 Ulva specimens from Singapore. Gross and microscopic morphological examinations were also performed to characterise the morphological range of each species. Our results confirm the presence of three Ulva species in Singapore, all of which are new local records: U. meridionalis, U. ohnoi, and U. tepida. Although 10 Ulva species have been historically recorded in Singapore, none of them were found in the present study, likely due to prior misidentification, limited seasonal sampling, or local extirpations. Ulva ohnoi shows high morphological variation with five morphotypes. This study demonstrates that molecular analyses combined with morphological examinations are useful for characterising Ulva diversity.

Molecular characterization of Armigeres Subalbatus from Hyderabad region of Telangana state, India.

The mosquito Armigeres subalbatus (Coquillett, 1898) is a significant vector for Japanese encephalitis infection, and breeds in high organic polluted water. Understanding mosquito diversity and there abundance in relation to mosquito-borne diseases is an important component for public health managers. Though the conventional methods for systematic position of mosquito species by using morphological characteristics is a classical method, but it requires perfect expertise and well preserved specimen. Conversely, the molecular analysis of mitochondrial cytochrome C oxidase subunit I (COI) serves as a gene-centric DNA barcoding approach and offers a promising alternative method for mosquito species identification. The study at hand delves into the morphological characteristics of Armigeres subalbatus were compared with COI- gene to ensure a more dependable verification for identification of mosquito species found in Hyderabad region of Telangana. The 489 base pair amplicons were acquired and deposited into the NCBI Gene Bank nucleotide database under the accession number MG686500. The maximum likelihood tree infers that, the Hyderabad species was diverged from USA and Japan species but had ancestral relationship with Tamil Nadu, Karnataka, Maharastra, Kerala and Goa species. Mitochondrial gene (COI) based DNA barcoding is the most reliable and potential alternative technique to identify the mosquito species.

Morphological and genetic identification of the gill monogenean parasite (Diclidophora merlangi) that infects Twobar Seabream Fish (Acanthopagrus bifasciatus) in the Arabian Gulf, Saudi Arabia.

Ectoparasites, particularly monogeneans, negatively affect fish health and growth. This study identified monogenean parasites in the twobar seabream, Acanthopagrus bifasciatus (Sparidae), inhabited the Arabian Gulf (Saudi Arabia). Following that, forty A. bifasciatus fish samples were visually examined for monogeneans. Parasite species were collected from the gills and then analyzed morphometrically, morphologically, and molecularly using the partial regions of the large subunit of ribosomal RNA (28S rRNA) and mitochondrial cytochrome C oxidase subunit I (COI) genes. Fish species were also identified using a DNA barcoding approach based on the COI gene. The monogenean species of Diclidophora merlangi (Diclidophoridae) were found in 45% of the fish species studied. The generic features of the Diclidophora genus distinguish this species. This species discriminated itself from congeners by having a muscular bulb with 17 grooved and recurved hooks, 218±10 (184-267) post-ovarian testes, and four pairs of pedunculated clamps of relative sizes. Partial 28S rRNA sequencing from monogeneans revealed that they grouped with members of the genus Diclidophora, forming a monophyletic group that supported the morphological descriptions. Molecular identification revealed that D. merlangi has a unique barcode made up of a COI sequence. The host identity was established as A. bifasciatus based on the COI gene sequences. Furthermore, a molecular phylogenetic study was performed to determine the phylogenetic affinity of parasite species and fish hosts. This study on Diclidophora species is considered the first record of this genus in the examined area.

A first species-wide phylogenetic analysis of small mammals from Costa Rica using mitochondrial cytochrome b

Costa Rica is within the Mesoamerican biodiversity hotspot and has about 53 native species of small mammals. This high diversity, along with recent records of new species and indications of cryptic genetic diversity, suggest that application of the DNA barcoding approach would be worthwhile. Here we used 131 tissue samples of small mammals from multiple localities in Costa Rica and sequenced the complete mitochondrial cytochrome b (1140 bp). These samples represented 17 recognized species and two taxa of uncertain status. The new sequence data were supplemented with previously published data from INSDC. Our phylogenetic analyses are consistent with and extend upon recent revisions in Heteromys, Peromyscus and Reithrodontomys and suggest possible new cryptic forms within what are currently named Melanomys chrysomelas, Nyctomys sumichrasti and Proechimys semispinosus. The previously named “Heteromys sp” is indeed likely a new species requiring a full taxonomic description. Moreover, we found new localities for previously described species substantiating recent taxonomic surveys and field guides for the small mammals of Costa Rica. To confirm the presence of cryptic species and major genetic forms in Heteromys, Peromyscus, Reithrodontomys, Melanomys, Nyctomys and Proechimys there needs to be greater sampling, additional genetic markers, morphometrics and other studies. Scotinomys also shows interesting phylogenetic subdivision, requiring further investigation.

An empirical DNA-based identification of morphologically similar snappers (Lutjanus campechanus, Lutjanus purpureus) using a versatile bioinformatics workflow for the discovery and analysis of informative single-nucleotide polymorphisms

The commercially important species Lutjanus campechanus (Northern/Gulf red snapper) and Lutjanus purpureus (Southern/Caribbean red snapper) are the protagonists of a decade’s long taxonomic debate over their species delimitation, due in part to partial habitat overlap, extensive morphological similarity, and the lack of resolution when applying canonically reliable DNA barcoding approaches. In this study, we leveraged publicly available RAD-Seq data for L. campechanus and L. purpureus to identify species-informative single‐nucleotide polymorphisms (SNPs) at the genome scale that were successful in distinguishing the Northern and Southern red snappers, while also detecting individuals exhibiting introgression. This 4-step empirical approach demonstrates the value of applying novel bioinformatics pipelines to existing genome-scale data to maximize the distillation of informative subsets. Our results facilitate economically relevant species identification in addition to confirming or challenging species identifications for specimens with data in public databases. These findings and their applications will benefit future sustainability strategies and broader research questions surrounding these overfished and evolutionarily entangled snapper species.

Multiomic profiling of human clonal hematopoiesis reveals genotype and cell-specific inflammatory pathway activation

AbstractClonal hematopoiesis (CH) is an age-associated phenomenon that increases the risk of hematologic malignancy and cardiovascular disease. CH is thought to enhance disease risk through inflammation in the peripheral blood.1 Here, we profile peripheral blood gene expression in 66 968 single cells from a cohort of 17 patients with CH and 7 controls. Using a novel mitochondrial DNA barcoding approach, we were able to identify and separately compare mutant Tet methylcytosine dioxygenase 2 (TET2) and DNA methyltransferase 3A (DNMT3A) cells with nonmutant counterparts. We discovered the vast majority of mutated cells were in the myeloid compartment. Additionally, patients harboring DNMT3A and TET2 CH mutations possessed a proinflammatory profile in CD14+ monocytes through previously unrecognized pathways such as galectin and macrophage inhibitory factor. We also found that T cells from patients with CH, although mostly unmutated, had decreased expression of GTPase of the immunity associated protein genes, which are critical to T-cell development, suggesting that CH impairs T-cell function.

Molecular characterization and demographic insights into soybean bud borer (Lepidoptera: Tortricidae) in Brazil.

The soybean bud borer, a soybean pest in Brazil, was initially identified as Crocidosema aporema (Walsingham 1914) (Lepidoptera: Tortricidae). Outbreaks of this species have recently increased, but identification of this pest remains uncertain, and the historical factors associated with its geographic distribution in Brazil are little known. Here, we conducted a species characterization and phylogeographic analysis based on molecular and morphological evidence. Ninety individuals of bud-borers Lepidoptera were collected in different regions of Brazil. We sequenced COI and COII mitochondrial genes and examined wing patterns and male genital morphology. DNA barcoding approach revealed that 10 individuals were Argyrotaenia sphaleropa (Meyrick 1909) (Lepidoptera: Tortricidae) and 80 were a species of the genus Crocidosema Zeller. The morphology of the adult genitalia and wings proved to be insufficient to confirm the identification of Brazilian individuals as C. aporema, a species originally described from a high-elevation site in Costa Rica. Furthermore, the genetic distance between putative C. aporema specimens from Brazil and Costa Rica (ranging from 5.2% to 6.4%) supports the hypothesis that the Brazilian specimens are not referable to C. aporema. Our analysis revealed a single genetic strain (i.e., species) with low genetic diversity on soybean crops. We found no indication that the genetic structure was related to geographic distance among populations or edaphoclimatic regions. The population expansion of the soybean bud borer coincides with the increase in the area of soybean production in Brazil, suggesting that expanded soybean farming has allowed a significant increase in the effective population size of this pest.

Molecular characterization and phylogenetic position of the giant deep-sea oyster Neopycnodonte zibrowii Gofas, Salas & Taviani, 2009

The giant deep-sea oyster Neopycnodonte zibrowii Gofas, C. Salas & Taviani, 2009 is a keystone deep-sea habitat builder species. Discovered about fifteen years ago in the Azores, it has been described and assigned to the genus Neopycnodonte Fischer von Waldheim, 1835 based on morphological features. In this study, we generated DNA sequence data for both mitochondrial (COI and 16S) and nuclear (ITS2 and 28S) markers based on the holotype specimen of N. zibrowii to establish a molecular phylogenetic framework for the systematic assessment of this species and to provide a reliable (i.e., holotype-based) reference sequence set for multilocus DNA barcoding approaches. Molecular data provide compelling evidence that the giant deep-sea oyster is a distinct species, rather than a deep-water ecophenotype of Neopycnodonte cochlear (Poli, 1795), with extremely high genetic divergence from any other gryphaeid. Multilocus phylogenetic analyses place the giant deep-sea oyster within the clade “Neopycnodonte/Pycnodonte” with closer affinity to N. cochlear rather than to P. taniguchii Hayami & Kase, 1992, thus supporting its assignment to the genus Neopycnodonte. Relationships within this clade are not well supported because mitochondrial variation is inflated by saturation that eroded phylogenetic signal, implying an old split between taxa within this clade. Finally, the set of reference barcode sequences of N. zibrowii generated in this study will be useful for a wide plethora of barcoding applications in deep-sea biodiversity surveys. Molecular validation of recent records of deep-sea oysters from the Atlantic Ocean and the Mediterranean Sea will be crucial to clarify the distribution of N. zibrowii and assess the phenotypic variation and ecology of this enigmatic species.

Scratching the tip of the iceberg: integrative taxonomy reveals 30 new species records of Microgastrinae (Braconidae) parasitoid wasps for Germany, including new Holarctic distributions.

Substantial parts of the European and German insect fauna still remain largely unexplored, the so-called "dark taxa". In particular, midges (Diptera) and parasitoid wasps (Hymenoptera) are abundant and species-rich throughout Europe, yet are often neglected in biodiversity research. One such dark taxon is Microgastrinae wasps (Hymenoptera: Braconidae), a group of parasitoids of lepidopteran caterpillars with 252 species reported in Germany so far. As part of the German Barcode of Life Project GBOL III: Dark Taxa, reverse DNA barcoding and integrative taxonomic approaches were used to shed some light on the German Fauna of Microgastrinae wasps. In our workflow, DNA barcoding was used for molecular clustering of our specimens in a first step, morphological examination of the voucher specimens in a second step, and host data compared in a third step. Here, 30 species are reported for the first time in Germany, adding more than 10% to the known German fauna. Information for four species is provided in a new Holarctic context, reporting them for the Nearctic or, respectively, Palaearctic region, and 26 additional country records are added from sequenced material available in the collections accessible to us. Molecular clusters that show signs of discrepancies are discussed. Results show that we are just scratching the tip of the iceberg of the unexplored Microgastrinae diversity in Germany.

DNA Barcoding of Catfishes (Order: Siluriformes) with New Records of Two Species from Eastern Nepal

The freshwater bodies of Nepal host a great deal of fish diversity; however, the molecular study of Nepalese fish is still in its early stages. Conservation management tactics require knowledge of the real species composition, often impeded by descriptions of intermittent species based on traditional taxonomy. Catfish, one of the most overfished taxa on the planet, are abundant and heavily exploited in the eastern region of Nepal. Hence, actual catfish diversity in this region needs to be examined using a combined morphological and molecular DNA barcoding approach. In this study, we sequenced the cytochrome oxidase subunit I (COI) gene in Nepalese fish species for the first time and used it for molecular identification. Altogether, 99 specimens representing 29 species belonging to 21 genera and 8 families were successfully barcoded. They were found to be 98.5–100% identical to the known sequences deposited in the GenBank and BOLD databases. Of these, two species, Amblyceps arunachalense and Erethistoides sicula, were recorded for the first time in Nepal. Out of 29 species, one species was found to be Endangered, one species under Vulnerable, two species under Near Threatened, one species under Data Deficient, and 24 species under Least Concern. The intraspecific genetic distances within species ranged from 0 to 5%. The highest intraspecific genetic distances (Kimura 2‐parameter) were found among the individuals of two species, namely, E. sicula (4%) and Glyptothorax telchitta (5%), indicating the presence of putative (sub)species. The interspecific genetic distances among the catfishes in eastern Nepal ranged between 8.47% (between Glyptothorax trilineatus and G. cavia) and 26.38% (between Amblyceps arunachalense and Chaca chaca). The GC content at the 1st, 2nd, and 3rd positions of the codons was found to be 42.4%, 49.3%, and 43.8%, respectively. These findings will support future initiatives for fish resource inventory, monitoring, and management. It is also an important input to the DNA barcode library of catfish in the eastern region of Nepal.

DNA barcoding indicates the presence of unrecognized species and phylogenetic diversity within the Biatora vernalis- and B. meiocarpa- groups

The Biatora vernalis- and meiocarpa-groups comprise species with pale beige to reddish brown apothecia and 0-, rarely also 1(–3)-septate ascospores. A DNA barcoding approach based on ITS sequences shows that these two groups comprise more species and phylogenetic diversity than previously known. Specimens identified as B. vernalis, the type species of the genus, appear to be paraphyletic with regard to B. chrysantha. In addition, there is a morphologically similar species belonging to the B. meiocarpa-group and tentatively named “B. orientalis” in previous publications. Biatora subduplex has for some time been known to comprise specimens from the B. vernalis-, as well as the B. meiocarpa-group. Similar to the situation in B. vernalis, samples from the meiocarpa-clade form several subclades close to B. meiocarpa. Anatomical studies reveal subtle, but recognizable morphological differences between B. subduplex s.str. and the species in the meiocarpa-clade, but not between the subclades. Here, we describe Biatora orientalis as new to science, raise B. meiocarpa var. tacomensis to species rank and provide revised identification keys for the B. vernalis- and B. meiocarpa-groups.

Gastrointestinal parasite community structure in horses after the introduction of selective anthelmintic treatment strategies

A relatively new method to study the species richness and diversity of nematode parasites in grazing animals is to perform deep sequencing on composite samples containing a mixture of parasites. In this work, we compared species composition of strongyles in two groups of horses as a function of egg count and age, based on a DNA barcoding approach. Faecal egg counts and larval cultures were obtained from nearly 300 horses, i.e., domestic horses (n = 167) and trotters (n = 130) sampled nationwide. The second internal transcribed spacer region (ITS2) of strongyle nematodes in the larval cultures was first amplified using barcoded universal primers and then sequenced on the PacBio platform. Subsequently, bioinformatic sequence analysis was performed using SCATA to assign operational taxonomic units (OTU). Finally, species occurrence and composition were assessed using R. ITS2 sequences were found in the majority (89%) of larval samples. Sequencing yielded an average of 140 (26 to 503) reads per sample. The OTUs were assigned to 28 different taxa, of which all but three could be identified as species. The average relative abundance of the seven most abundant species (all Cyathostominae) accounted for 87% of the combined data set. The three species with the highest prevalence in both horse groups were Cyathostomum catinatum, Cylicocyclus nassatus and Cylicostephanus calicatus, and they were frequently found in different combinations with other species regardless of horse group. Interestingly, this result is largely consistent with a previous Swedish study based on morphological analysis of adult worms. In addition, two migratory strongylids (Strongylus vulgaris and S. edentatus) occurred in few domestic horses and trotters. Except for C. minutus and C. nassatus, which decreased with age, and C. catinatum and S. vulgaris, which increased, no specific trends were observed with respect to horse age. Taken together, these results are broadly consistent with data obtained before the introduction of selective targeted treatment in Sweden in 2007. All in all, our results suggest that this treatment strategy has not led to a significant change in strongyle nematode community structure in Swedish horses. The study also confirms that nemabiome analysis in combination with diversity index analysis is an objective method to study strongyle communities in horses.

Investigating the impacts of agricultural land use on soil earthworm communities: A case study of northern Zagros Mountains of Iran

Earthworms play a crucial role in the invertebrate community of soil by contributing to the belowground biomass and biogeochemical cycle. Environmental stresses, such as human activities and land use changes, have been found to negatively affect their abundance and diversity. To investigate the impact of agricultural land use and pastures on earthworms' genetic diversity in the Northern Zagros Mountains, we used COI molecular marker and DNA barcoding approaches. We collected earthworm specimens from four farmland sites and six pastures and assessed the abundance and species composition of earthworm communities across the two land uses using quadrat sampling. Using the barcoding method, we identified 13 molecular operational taxonomic units (MOTUs) among the captured earthworms. Our results showed that the number of total MOTUs, density, and earthworm communities differed significantly between the two land uses. We also found that pastures had more abundant earthworms, while farmlands had greater diversity. The diversity of OTUs in the Lumbricidae family was dominant in the agricultural system. Overall, the population of invasive earthworm species in cultivation systems is influenced by chemical inputs and organic materials from plant residues, cover crops, manure, or organic fertilizers. Given the rapid rate of land use change worldwide, especially in Iran, it is crucial to understand the impact of disturbances on earthworms.

DNA barcoding application for potential medicinal plants on Ziziphus species from Aketajawe-Lolobata National Park, North Moluccas

Aketajawe-Lolobata National Park is a protected national park located in the province of North Moluccas, Indonesia. The national park has been known to be rich in biodiversity with the existence of many potential medicinal plants such as Ziziphus. DNA barcoding can be a useful tool for identifying and characterizing these plants for potential medical applications. Research and exploration have been conducted in Aketajawe-Lolobata National Park in November and December 2022. This study aimed to analyze how the DNA barcoding regions aid identification for potential medicinal plants. The genomic DNA were amplified by matK primers, and the sequences showed high similarity rate with their homologs, then the phylogenetic tree was constructed using the Neighbor-Joining method to assess their cross-species relationship. The phylogenetic study showed that the species that have been identified based on morphological characters, i.e., Ziziphus angustifolia and Z. mauritiana were clustered with Z. angustifolia and Z. mauritiana retrieved from GenBank. However, the unidentified species are closely related with Z. calophylla obtained from GenBank but with low bootstrap support. All the results indicate that DNA barcoding approach could be successfully used for reliable identification of medicinal plants and matK gene is a good candidate for this approach.

Unveiling the close relationship between Betta burdigala and Betta uberis through DNA barcoding based on COI Gene

A Wild Betta burdigala is only known from Bangka Island, while a Wild Betta uberis resides in Kalimantan Tengah and Kalimantan Barat in Indonesia. Both species share numerous physical characteristics, particularly in the meristic count, body color, and specific habitat. In this study, we estimate the degree of similarity between Betta burdigala and Betta uberis using DNA barcoding based on the Cytochrome Oxidase Sub Unit I (COI) gene. The COI gene is a unique and small gene which found in mitochondrial DNA and is used in the DNA barcoding approach to identify species. This approach allows for the analysis of species similarities and the learning of the evolutionary histories of those species. Based on the COI gene, Betta burdigala and Betta uberis have a close genetic distance and a DNA similarity of 96.66%, much higher than other bettas. They differ by eight nucleotide bases, and their genetic distance is 0.04, while a genetic distance between 0.010 and 0.099 is considered to be low and indicative of high similarity. According to the phylogenetic tree, these species are descended from a single, closely related ancestor on the same branch. Based on the COI gene, we assume that they are identical. Additionally, we advise conducting additional research using the mitochondrial DNA complex and in-depth morphological examination to confirm the accuracy of the study’s findings.

DNA barcoding of marine fish species in the waters surrounding Hainan Island, northern South China Sea

IntroductionHainan Island is encompassed within the shallow waters of the tropical continental shelf in China, which is recognized as a significant hotspot for fish biodiversity. Despite extensive research conducted on marine fish taxonomy surrounding Hainan Island, there remains a substantial gap between our current understanding and the actual fish diversity within this oceanic area.MethodsIn this study, we employed DNA barcoding and molecular identification approaches to explore the species diversity and distribution pattern of marine fish in both the northern and southern sea areas of Hainan Island in the northern South China Sea.ResultsA total of 186 sequences were obtained from the collected marine fish samples in the two sea areas surrounding Hainan Island. Through DNA identification, it was confirmed that all 186 sequences corresponded to typical fish species found in the northern South China Sea, all sequences represented a total of 56 species, 47 genera, 34 families, and 17 orders. The average Kimura 2-parameter (K2P) distances within species, genus, family, order and class were 0.15%, 6.53%, 13.17%, 16.95% and 24.81%, respectively.DiscussionOur investigation in the northern sea areas of Hainan Islands identified a total of 33 distinct species, while the southern sea areas exhibited 29 distinct species, with only 5 species found to be shared between both regions. These findings clearly indicate a significant disparity in the species composition of fish communities between the northern and southern sea regions.