A deep learning model for fish classification base on DNA barcode

DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding database of coastal ray-finned fishes in Vietnam. A total of 3,638 specimens were collected from fish landing sites in northern, central and southern Vietnam. Seven hundred and sixty-five COI sequences of ray-finned fishes were generated, belonging to 458 species, 273 genera, 113 families and 43 orders. A total of 59 species were newly recorded in Vietnam and sequences of six species were new to the Genbank and BOLD online databases. Only 32 species cannot be annotated to species level because difficulty in morphological identifications and their Kimura-2-Parameter (K2P) genetic distances to most similar sequences were more than 2%. Moreover, intra-specific genetic distances in some species are also higher than 2%, implying the existence of putative cryptic species. The mean K2P genetic distances within species, genera, families, orders and classes were 0.34%, 12.14%, 17.39%, 21.42%, and 24.80, respectively. Species compositions are quite different with only 16 common species among northern, central and southern Vietnam. This may attribute to multiple habitats and environmental factors across the 3,260 km Vietnamese coastline. Our results confirmed that DNA barcoding is an efficient and reliable tool for coastal fish identification in Vietnam, and also established a reliable DNA barcode reference library for these fishes. DNA barcodes will contribute to future efforts to achieve better monitoring, conservation, and management of fisheries in Vietnam.

Although mammals are a well-studied group of animals, making accurate field identification of small mammals is still complex because of morphological variation across developmental stages, color variation of pelages, and often damaged osteological and dental characteristics. In 2008, small mammals were collected for an epidemiological study of a spotted fever outbreak in Hainan, China. Ten species of small mammals were identified by morphological characters in the field, most using pelage color characters only. The study is extended here, in order to assess whether DNA barcoding would be suitable as an identification tool in these small mammals. Barcode clusters showed some incongruence with morphospecies, especially for some species of Rattus and Niviventer, so molecular delineation was carried out with an expanded dataset of combined cytochrome b (Cyt-b) and cytochrome c oxidase subunit I (COI) sequences. COI sequences were successfully amplified from 83% of collected mammals, but failed in all specimens of Suncus murinus, which were thus excluded in DNA barcoding analysis. Of note, ten molecular taxonomic units were found from samples of nine morphologically identified species. Accordingly, 11 species of small mammals were present in the investigated areas, including four Rattus species, three Niviventer species, Callosciurus erythraeus, Neohylomys hainanensis, Tupaia belangeri, and Suncus murinus. Based on the results of the phylogenetic and molecular delineation analyses, the systematic status of some rodent species should be redefined. R. rattus hainanicus and R. rattus sladeni are synonyms of R. andamanensis. R. losea from China and Southeast Asia comprises two independent species: R. losea and R. sakeratensis. Finally, the taxonomic status of three putative species of Niviventer should be further confirmed according to morphological, molecular and ecological characters.

DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene in the mitochondrial genome is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding reference database of fishes in the Taiwan Strait and evaluate the applicability of using the COI gene for the identification of fish at the species level. A total of 284 mitochondrial COI barcode sequences were obtained from 85 genera, 38 families and 12 orders of fishes. The mean length of the sequences was 655 base pairs. The average Kimura two parameter (K2P) distances within species, genera, families, orders and classes were 0.21%, 6.50%, 23.70% and 25.60%, respectively. The mean interspecific distance was 31-fold higher than the mean intraspecific distance. The K2P neighbor-joining trees based on the sequence generally clustered species in accordance with their taxonomic classifications. High efficiency of species identification was demonstrated in the present study by DNA barcoding, and we conclude that COI sequencing can be used to identify fish species.

DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene from the mitochondrial genome is widely applied in species identification, species discovery and biodiversity studies. The aim of this study was to establish a barcoding reference database of sponges collected from South Africa, and evaluate the applicability of the COI gene for aiding in the identification of sponges in combination with tentative morphological identifications. A total of 317 mitochondrial COI barcode sequences, with an additional 21 extended COI fragments and 24 nuclear ITS sequences, were obtained from 11 orders, 38 families, 58 genera and 124 species of spiculated sponges. A Neighbour Joining (NJ) trees that were reconstructed using these sequences in most cases clustered species in accordance with their current taxonomic identification, and we conclude that COI sequencing can be used to aid in the identification of sponge species. We further demonstrate that DNA barcoding analysis has potential to uncover cryptic sponge species, and to reveal dubious morphological identifications. We recommend that future taxonomic studies of South African sponges incorporate multiple sources of information for species identification or discovery.

DNA barcoding has become a promising tool for species identification and phylogeny in a wide range of animal taxa using mitochondrial cytochrome c oxidase subunit I (COI). The Corvidae (Aves: Passeriformes) is a species rich and morphologically diverse family. In the present study, we analyzed the COI barcodes of 39 species from 12 genera of Corvidae. COI gene was also used to examine phylogenetic relationships of Corvidae. Every species possessed a barcode distinct from that of other species. Kimura two-parameter distances were calculated between species barcodes. The average genetic distance between the species was 22 times higher compared to the average genetic distance within species. Maximum likelihood method was used to construct a phylogenetic tree. All the species could be discriminated by their distinct clades in the phylogenetic tree. COI gene data provided good evidence for the monophyly of the Corvidae. Members of Cyanopica and Pyrrhocorax were the first to split from the Corvidae lineage. Analysis of COI genes supported the others genera fell into two clades. DNA barcoding is an effective molecular tool for Corvidae species identification and phylogenetic inference.

Recently, the study about Marine fish identification is becoming a big challenge for us. Marine biodiversity is always to been underestimated for we can’t know how enormous it is. And because of the boundedness, the existing traditional taxonomic methods have not enough ability to detect the mystery of ocean and we must seek for a new way to research how many kinds of fishes in ocean and what kind of the fish is. What’s more, with the internationalization of market, not only taxonomy, but the seafood market chaos and plenty of issues about food safety also reflect the importance of Marine fish identification. In this context, a new identification tool -- --DNA barcodes has appeared. DNA barcodes is a Molecular identification methods which through sequencing the mitochondrial genes of Cytochrome c Oxidase subunit I(COI) sequence and being compared with DNA barcodes database to rapid identification of the sample. In this study, we will introduce the principle, advantages and limitations of DNA barcodes and summarize the application of DNA barcodes in the aspect of Marine fish and seafood identification. All kinds of application research show that DNA barcodes has high resolution and can easily identify fishes to species level. So we have reason to believe that the DNA barcodes can been made full use of in the field of Marine fish authenticity identification though the research of predecessors. What’s more, it benefits to enhance the effectiveness of food anti-counterfeit and can help to manage the seafood market more effectively.

DNA barcoding has become a promising means for the identification of organisms of all life-history stages. Currently, distance-based and tree-based methods are most widely used to define species boundaries and uncover cryptic species. However, there is no universal threshold of genetic distance values that can be used to distinguish taxonomic groups. Alternatively, DNA barcoding can deploy a “character-based” method, whereby species are identified through the discrete nucleotide substitutions. Our research focuses on the delimitation of moth species using DNA-barcoding methods. We analyzed 393 Lepidopteran specimens belonging to 80 morphologically recognized species with a standard cytochrome c oxidase subunit I (COI) sequencing approach, and deployed tree-based, distance-based, and diagnostic character-based methods to identify the taxa. The tree-based method divided the 393 specimens into 79 taxa (species), and the distance-based method divided them into 84 taxa (species). Although the diagnostic character-based method found only 39 so-identifiable species in the 80 species, with a reduction in sample size the accuracy rate substantially improved. For example, in the Arctiidae subset, all 12 species had diagnostics characteristics. Compared with traditional morphological method, molecular taxonomy performed well. All three methods enable the rapid delimitation of species, although they have different characteristics and different strengths. The tree-based and distance-based methods can be used for accurate species identification and biodiversity studies in large data sets, while the character-based method performs well in small data sets and can also be used as the foundation of species-specific biochips.

Comparative phylogenetic and sequence identity analysis of internal transcribed spacer 2 and cytochrome c oxidase subunit I as DNA barcode markers for the most common equine Strongylidae species.

Beetles (Coleoptera) represent one of the most diverse insect groups and play vital ecological roles, yet their accurate identification is often challenging due to morphological similarities among taxa. DNA barcoding has emerged as a powerful and reliable tool for species-level identification and biodiversity monitoring. In this study, we established a local DNA barcode reference database for beetles in the Liancheng Nature Reserve, Gansu Province, China. From May to August 2024, beetle specimens were collected and identified using both morphological traits and DNA barcoding. Three species delimitation methods—Automatic Barcode Gap Discovery (ABGD), Assemble Species by Automatic Partitioning (ASAP), and Bayesian Poisson Tree Processes (bPTP)—were employed as complementary analytical tools, and phylogenetic relationships were inferred from cytochrome c oxidase subunit I (COI) sequences. A total of 164 COI sequences (650 bp) were obtained, representing 126 beetle species from 95 genera and 20 families. DNA barcoding successfully resolved morphologically ambiguous taxa, with many sequences reported here for the first time. Phylogenetic analysis revealed that species within the same genus formed cohesive clades before clustering at the family level, confirming the species-level discriminative power of the COI gene. Collectively, these findings demonstrate that COI-based DNA barcoding is a powerful complement to traditional taxonomy. The establishment of this preliminary reference database provides a valuable molecular resource for beetle identification and a practical tool to support biodiversity conservation, resource management, and long-term monitoring in the Liancheng Nature Reserve.

Objective To make up the limitations of traditional morphological classification methods, we identified vector fleas by DNA barcoding in Qinghai Province. Methods The mt DNA cytochrome c oxidase subunit Ⅰ(COⅠ) gene was amplified by PCR from 36 muscle tissues of fleas in 3 states, 2 cities and 5 counties of Qinghai Province, and the obtained COⅠ gene fragments were sequenced and aligned. The intra- and inter-species genetic distances were calculated with Mega 6 software using K2-P model and a phylogenetic tree was constructed with neighbor-joining (NJ) method. Results Totally 36 COⅠ gene sequences of 2 superfamilies, 4 genera and 6 kinds of vector fleas were measured, the average genetic distance was 0.119, and the intraspecific distance was 0.002 - 0.027, the interspecific distance was 0.039 - 0.207, and the interspecific genetic distance was significantly greater than the intraspecific genetic distance. NJ tree showed the same species had formed a single line with high support rate and interspecific branch was clear. Conclusion DNA barcoding is suitable for identification of vector fleas in Qinghai Province, may make up the limitations of traditional morphological classification methods. Key words: Siphonaptera; Cytochrome c oxidase subunit Ⅰ; DNA barcoding

Oomycete species occupy many different environments and many ecological niches. The genera Phytophthora and Pythium for example, contain many plant pathogens which cause enormous damage to a wide range of plant species. Proper identification to the species level is a critical first step in any investigation of oomycetes, whether it is research driven or compelled by the need for rapid and accurate diagnostics during a pathogen outbreak. The use of DNA for oomycete species identification is well established, but DNA barcoding with cytochrome c oxidase subunit I (COI) is a relatively new approach that has yet to be assessed over a significant sample of oomycete genera. In this study we have sequenced COI, from 1205 isolates representing 23 genera. A comparison to internal transcribed spacer (ITS) sequences from the same isolates showed that COI identification is a practical option; complementary because it uses the mitochondrial genome instead of nuclear DNA. In some cases COI was more discriminative than ITS at the species level. This is in contrast to the large ribosomal subunit, which showed poor species resolution when sequenced from a subset of the isolates used in this study. The results described in this paper indicate that COI sequencing and the dataset generated are a valuable addition to the currently available oomycete taxonomy resources, and that both COI, the default DNA barcode supported by GenBank, and ITS, the de facto barcode accepted by the oomycete and mycology community, are acceptable and complementary DNA barcodes to be used for identification of oomycetes.

Mitochondrial cytochrome c oxidase subunit I (COI) has been used as a powerful marker in a variety of phylogenetic studies. According to studies of bird species, the 694-bp sequence of the mitochondrial gene encoding COI is extremely useful for species identification and phylogeny. In the present study, we analyzed the COI barcodes of 79 species from 26 genera belonging to the Anatidae family. Sixty-six species (83.54%) of the species were identified correctly from their DNA barcodes. The remaining 13 species shared barcodes sequences with closely related species. Kimura two-parameter (K2P) distances were calculated between barcodes. The average genetic distance between species was 41 times higher compared to the average genetic distance within species. Neighbor-joining method was used to construct a phylogenetic tree, which grouped all of the genera into three divergent clades. Dendrocygna and Nomonyx + Oxyura were identified as early offshoots of the Anatidae. All the remaining taxa fell into two clades that correspond to the two subfamilies Anserinae and Anatiane. Based on our results, DNA barcoding is an effective molecular tool for Anatidae species identification and phylogenetic inference.

The identification of mosquito species is necessary for determining the entomological components of disease transmission. However, identification can be difficult in species that are morphologically similar. The cytochrome c oxidase subunit I (COI) DNA barcode region is considered a valuable and reliable diagnostic tool for mosquito species recognition, including those that belong to species complexes. Mansonia mosquitoes are found in forests near swampy areas. They are nocturnal and are highly attracted to light. Hematophagous adult females exhibit aggressive biting behavior and can become infected with and transmit pathogens during their feeding, including some epizootic viruses and avian malaria. In Brazil, twelve Mansonia species have been reported. In a recent study from the São Paulo Zoo in Brazil, three morphologically distinct species were collected and identified, namely: Mansonia (Mansonia) indubitans, Ma. (Man.) pseudotitillans and Ma. (Man.) titillans. However, confirmation of these species by molecular identification was unsuccessful due to a lack of COI sequences in the GenBank database. Thus, this research aimed to describe the COI DNA barcode sequences of some morphologically characterized Mansonia (Man.) species from Brazil and to determine their utility in delimiting species collected from the Atlantic Forest and Brazilian Savanna. Accordingly, we provide tools for the genetic identification of species that play a significant role in pathogen transmission in wildlife and potentially humans. We show that the delimitation of Mansonia species via five different approaches based on COI DNA sequences (BI, NJ, ASAP, bPTP and GMYC) yield basically the same groups identified by traditional taxonomy, and we provide the identification of specimens that were previously identified only up to the subgenus level. We also provide COI sequences from two Mansonia species that were not previously available in sequence databases, Ma. wilsoni and Ma. pseudotitillans, and thus contribute to the ongoing global effort to standardize DNA barcoding as a molecular means of species identification.

DNA barcoding is a method that examines a specific part of the mitochondrial genome known as the cytochrome c oxidase subunit I (COI) gene, for species identification and biodiversity studies. The current study assessed the effectiveness of using the COI gene for the identification of fish species by constructing a phylogenetic tree with the help of a reference database of fish from the Head Balloki, River Ravi, Pakistan. A total of 15 fish species were analyzed with a 685-base pair (bp) segment of the mitochondrial COI gene sequenced (or "barcoded") for each species. These species represented 15 genera, 10 families, and 6 orders. On average, the sequences were 630 base pairs long. In terms of base composition, the average T content was the highest, while the average G content was the lowest. The AT content (54.1%) was higher than the GC content (45.9%). An analysis of nucleotide pair frequencies across the dataset revealed that out of 685 sites, 385 (56.20%) were conserved within the sequence. Of the 685 sites, 294 sites (42.92%) were variable and 226 (33%) were parsimony informative, while 66 of 685 sites (9.64%) were singletons. In the dataset, transitional pairings (si= 64) were more common than trans-versional pairings (sv = 57), with a si/sv (R) ratio of 1.1. On average, there were 483 pairs where the nucleotides were the same (ii). The average frequencies of nucleotide bases in these sequences were as follows: T (28.8%), C (28.1%), A (25.3%), and G (17.8%). The average Kimura two-parameter (K2P) distances within species, families, and orders were 0.24±0.01%, 0.24±0.02%, and 0.24±0.01%, respectively. Although, each species has a distinct cox1 sequence, various species might occasionally have similar haplotypes. In order to investigate evolutionary links, the maximum likelihood analysis approach was merged with the barcode-based method. In line with the taxonomy categories, the phylogenetic tree generated various groupings that were verified. The current study showed that cox1 sequencing, or DNA barcoding, is a useful method to accurately identify fish species based on both genetic and morphological characteristics.

We aim to characterize the diversity of amphibians and reptiles associated with plantations of avocado cv. Hass (Persea americana) in the department of Risaralda, Colombia from an ecological, molecular, and evolutionary perspective. Two sampling periods were implemented between 2019 and 2020 using visual encounter surveys; rarefaction curves and species richness estimators were used to evaluate the completeness of the sampling. Identification of the material was based on both morphological characters as well as DNA barcoding methods sequencing the mitochondrial cytochrome C oxidase subunit I (COI) marker. We also used the COI sequences to construct phylogenies and evaluate the phylogenetic diversity (PD) of the community. Seven amphibian and 18 reptile species were recorded, for which 49 COI sequences were obtained, 15 of which represent the first sequence barcoding records for Colombia. We also found 12 instances of incongruence between the morphological and DNA barcoding identification methods, and we provide a discussion on the correct identification. Finally, although we commonly observed a positive relationship between species richness and PD, we also found that PD can provide valuable information when species richness values are uninformative at comparing two communities. Our results support the need for a greater sampling effort in the area to recognize its true diversity, as this will allow a better understanding of the complex dynamics present in modified landscapes. Also, we conclude with the great contribution of DNA barcoding studies at a small geographical scale and support the use of the COI marker as a suitable source of information for species identification and evaluating the diversity of communities from a historical perspective.