Cytochrome Oxidase I Research Articles

Development and characterization of brain cell line from Trachinotus blochii and its application in virological and gene expression studies.

A permanent cell line, SPB (Snubnose pompano brain) was established from Trachinotus blochii by the explant culture method. It has been sub-cultured more than 75 passages and showed optimal growth at 28°C using L-15 medium supplemented with 15% to 20% FBS. The SPB cells were cryopreserved at different passage levels for various applications. SPB cells were composed of fibroblastic and epithelial-like cells. The SPB cells were tested for mycoplasma contamination which was found to be negative. The origin of the SPB cell line from T. blochii was confirmed by amplification of the mitochondrial cytochrome oxidase I (COI) gene. The transfection efficiency of SPB cell line is 15% assessed by expression of green fluorescent protein using pEGFP-N1 plasmid. In addition, two CMV promotor plasmids pFNCPE42-DNA and pcDNAVP28 were transfected to SPB cells and it shows high expression levels of FNCP of fish nodavirus and VP28 protein of white spot syndrome virus by immunostaining. The SPB cells showed susceptibility to SJNNV and the infection was confirmed by RT-PCR, Western blot, ELISA, TCID50 and RT-qPCR. Experimental infection was carried out in T. blochii using SJNNV propagated in SPB cell line and found 100% mortality with clinical signs. The infection was confirmed by RT-PCR. The SPB cell line can be used for propagation of fish viral pathogens and production of the recombinant proteins.

GENETIC APPROACH OF THE COIBA ISLAND HOWLER MONKEY Alouatta coibensis coibensis FROM PANAMA, AND ITS CONSERVATION IMPLICATIONS

Studies on genetic diversity are key to conservation management because they may determine the resilience of primate populations under environmental and anthropogenic changes. Herein, we studied genetic diversity and connectivity in a population sample of the Coiba island howler monkey Alouatta coibensis coibensis from Coiba island in Panama. We collected 14 faecal samples from individuals at two sites on the northern and north-eastern sides of the island at the Gambute and Los Pozos trails, respectively. DNA was extracted from these samples, and partial sequences of cytochrome oxidase I (COI) were obtained and used as molecular markers to determine genetic diversity. Haplotypic diversity estimates ranged from 0.68 to 0.80 and from 0.0026 to 0.0041 for nucleotide diversity. Genetic connectivity based on reduced genetic distances and nonsignificant Hudson Snn test values suggests elevated connectivity between sites and the existence of a single population with good variability. Demographic history data identified positive Tajimas D as an indication of population contraction and reduced population size in this species. These results will be the baseline for establishing a better understanding of population structure, genetic health, connectivity patterns and reproductive behaviour along the largest island of the Central American Pacific. This information will allow scientists to understand and better evaluate the conservation status of this primate, confirming good availability of genetic flow even for this population living in isolation.

Non-lethal detection of Eubothrium crassum (Cestoda) in farmed Atlantic salmon, Salmo salar, using anal swabs and real-time PCR.

Detection of intestinal parasites in fish typically requires autopsy, resulting in the sacrifice of the fish. Here, we describe a non-lethal method for detecting the tapeworm Eubothrium crassum in fish using anal swabs and real-time PCR detection. Two assays were developed to detect cytochrome oxidase I (COI) mitochondrial DNA and 18S ribosomal DNA sequences of E. crassum, respectively. The assays were tested on swab samples from confirmed pathogen free Atlantic salmon (Salmo salar L.) and on samples from farmed Atlantic salmon, where the presence and intensity of parasites had been established through autopsy. The COI assay was shown to be specific to E. crassum, while the 18S assay also amplified the closely related E. salvelini, a species infecting Arctic charr (Salvelinus alpinus L.) in freshwater. The COI assay detected E. crassum in all field samples regardless of parasite load while the 18S assay failed to detect the parasite in two samples. The results thus demonstrates that this non-lethal approach can effectively detect E. crassum and can be a valuable tool in assessing the prevalence of infection in farmed salmon, aiding in treatment decisions and evaluating treatment effectiveness.

Cytochrome oxidase I DNA barcodes of crocodilians meat selling in Hong Kong

The crocodilians include true crocodiles, alligators, caimans, and gharial, and the trade of crocodilian products is regulated in accordance with the Convention of Wild Fauna and Flora (CITES). Hong Kong does not have her own wild crocodilians; thus, all crocodilians meat available is presumably imported with proper license. Here, we obtained a dataset of cytochrome oxidase I (COI) gene markers of 114 crocodilian meat samples (including frozen and dried crocodilian meat products) available in the contemporary market. We have also validated these barcodes in a phylogenetic approach with other data deposited on the GenBank, and detected 112 samples belonging to four crocodile species Crocodylus siamensis, C. porosus, C. niloticus and Alligator mississippiensis, and 2 samples belonging to snake Malayopython reticulatus. The dataset generated in this study will be useful for further studies including meat inspection, illegal trading, and enhancement of international and local legislations on illegal reptile importation.

Sparid species discrimination by COIBar-RFLP in commercial products

Processed seafood products are subject to fraudulent species substitution practices that pose problems not only economically but also for human health due to the risk of allergies. DNA-based molecular techniques offer an undoubted contribution to unraveling commercial fraud in processed seafood products, and several investigations have been conducted to develop specific and rapid assays for the identification of fish species. In this context, we hypothesize that the Cytochrome Oxidase I (COI) Barcode-Restriction Fragment Length Polymorphisms (COIBar- RFLP) strategy may be a useful molecular tool to quickly assess the authenticity of seafood products because (i) it takes advantage of the specific discriminatory power of the COI gene as a barcode and of the robust Restriction Fragment Length Polymorphism methodology and (ii) the interspecific variation in the digestion pattern obtained using the restriction enzymes allows bypassing the gene sequencing step. The Sparidae family includes species of high commercial value and many sparid species are difficult to recognize considering only their morphological features; thus, misidentifications are frequent. The aim of this work was to identify sparid species in processed products using the COIBar-RFLP strategy with the MspI restriction enzyme which yielded differential digestion patterns and unveiled two cases of species substitution. The proposed methodology could be used in food control laboratories to combat the widespread habit of fraudulent species substitution in the fishing industry.

MetaZooGene Atlas and Database: Reference Sequences for Marine Ecosystems.

The MetaZooGene Atlas and Database (MZGdb; https://metazoogene.org/mzgdb/ ) is an open-access data and metadata portal synchronized with the NCBI GenBank and BOLD data repositories. The MZGdb includes sequences for genes used for the classification and identification of marine organisms based on DNA barcoding and metabarcoding. The focus of the MZGdb is biodiversity of marine ecosystems, including phytoplankton and microbes, zooplankton and invertebrates, fish, and other marine vertebrates (pinnipeds, cetaceans, and sea turtles). DNA sequences currently included are mitochondrial cytochrome oxidase I (COI), 12S, and 16S rRNA, and nuclear 18S and 28S rRNA. The MZGdb provides data and mapping tools for assembling and downloading compilations of reference sequence data that are specific to selected genes, taxonomic groups, and/or ocean regions. An additional feature of the MZGdb is the Atlas which summarizes data coverage and proportional completeness based on statistics of species with available sequences versus species commonly found in each ocean region.This chapter is a collaborative effort of the Scientific Committee for Ocean Research (SCOR) Working Group WG157: MetaZooGene: Toward a new global view of marine zooplankton biodiversity based on DNA metabarcoding and reference DNA sequence databases ( https://metazoogene.org ).

The marine fishes from southern Mindanao, Philippines, including a DNA barcode reference library of commercially important species

The Philippines has been long known for its multispecies fisheries, and while there is a growing effort to document fish diversity, collections-based species inventories remain insufficient in southern Mindanao. Market survey efforts conducted in Pujada Bay, Davao Gulf, and Sarangani Bay in the last ten years resulted in documenting 556 species of marine fishes from 82 families, while underwater fish visual census (FVC) surveys conducted in Davao Gulf from 2019 to 2022 revealed 365 species in 42 families. Combining the data from market surveys, FVC, and published literature, we present 771 species of marine fishes (770 teleosts, 1 elasmobranch) belonging to 94 families. Of the 771 species documented, 130 are deep reef and deepwater species, while 20 species await further taxonomic investigations for species-level identifications.Moreover, 498 cytochrome oxidase I (COI) genetic barcodes were produced representing 357 species from 59 families, which covers 46% of the total number of species reported and 63% of the market survey data. Genetic distances based on taxonomic ranks were concordant with other barcoding studies on marine fishes. Samples (20 species) with pairwise genetic distances that did not conform with the expected intra- and interspecific threshold suggest cases that also need to be investigated further (e.g., incomplete lineage sorting, introgressive hybridization, crypticspeciation). All market survey data used in genetic barcoding correspond to tissue samples, live-color photographs, and preserved specimens. This work complements the DNA barcode libraries reported recently in the country, and this serves as an additional reference for future biodiversity management and conservation efforts.

Morphological and molecular evidences confirm a new species in Ophichthus (Anguilliformes: Ophichthidae) from the east coast of India

A new species of snake eel, Ophichthus suryai sp. nov., is discovered based on six specimens collected from three different estuarine ecosystems in Odisha, India. The new species can be distinguished from its closely allied congeners Ophichthus alleni, Ophichthus zophistius, and Ophichthus altipennis, and other members in this genus by having the dorsal fin origin (DFO) just above or slightly anterior to the gill opening, its unique vertebral count (7-8/45-47/142-142), and teeth patterns consisting of multiple rows on both maxilla and mandible. The distinctiveness of this new species is also supported at the molecular level by a strongly supported (bootstrap value >99%) monophyletic grouping of the mitochondrial DNA (mtDNA) Cytochrome Oxidase I (COI) gene sequences of the holotype and one paratype. The current study describes the morphometric and meristic characters and molecular phylogeny of Ophichthus suryai sp. nov.

Biodiversity of Drosophila species at a new university campus in Kunshan, China

The project aimed to explore the biodiversity of Drosophila species in Kunshan using genomic approaches. DNA sequences, specifically the Cytochrome Oxidase I (COI) gene, were utilized as genetic "barcodes" to identify the organisms. Three wild-caught fruit flies and a D. melanogaster control were selected, and their DNA was isolated through PCR amplification of the COI gene. The PCR products were sequenced, and the results were used to create phylogenetic trees and uploaded to the Barcode of Life Database Student Data Portal (BOLD-SDP) alongside species photos. The results identified 10 Drosophila species, with 6 species remaining unchanged over two years and 3 new species discovered this year. One sample was identified as D. neohypocausta, a Chinese endemic species, which had appeared only in the last two years in Kunshan. However, its sample size was small, suggesting it may not be native to the area. Further research revealed significant genetic differentiation between different clades of D. immigrans, which likely explained the limited number of D. neohypocausta samples, as most D. immigrans species are confined to specific regions. To gain a comprehensive understanding of biogeographic, ecological, and evolutionary patterns across the Drosophila genus, expanded sampling and taxonomic revision are necessary, particularly for the large immigrans species groups that have been inferred as polyphyletic in some studies. This study underscores the importance of genomic approaches in taxon diagnosis and highlights the need for further exploration to uncover the intricate relationships within the Drosophila genus.

A New Record of Panulirus homarus homarus (Panulirus spp.) from Malaysia Waters with its Molecular Phylogeny

Spiny lobsters Panulirus spp. of the family Palinuridae Latreille, 1802 occupies the shallow tropical and subtropical waters (<100 m depth). These species are ubiquitous and abundant, yet knowledge of its range, biodiversity, and population abundance in Malaysia is limited. Panulirus homarus is listed as “Least Concern” along with other 11 species out of 21 spiny lobster species in the International Union for Conservation of Nature and Natural Resources (IUCN) red list in 2022. A total of five species were reported from Malaysia waters. Whilst, this study reports the sixth spiny lobster species, Panulirus homarus homarus, with morphology and molecular genetic information (Cytochrome oxidase I (COI) gene) provided. The p-distance within P. h. homarus was 0.2 – 0.6%, n = 12; between P. h. homarus with P. h. rubellus and P. homarus “Brown” was 6.4 – 6.8%, n = 12 and 0.8 – 3.3%, n = 12, respectively. Intra-species p-distance within Panulirus spp. was below 3%, while inter-species was above 10%. This validates the collected specimen as P. h. homarus and P. h. rubellus is the subspecies, but leaving P. h. “Brown” taxonomic status unclear. Thus, genetic information is important in solving many of these systematic and taxonomic problems, because often these species are difficult to distinguished based on morphological criteria. A key to all Panulirus spp. identified in Malaysia waters was constructed. This study updates the marine biodiversity list in Malaysia, where the acquisition of biological knowledge is vital to the protection of the world’s natural resources as well as to the sustainable management of spiny lobster fisheries.

DNA barcoding of Tribolium castaneum (Coleoptera: Tenebrionidae) from selected states in Nigeria based on mitochondrial DNA sequences

Tribolium castaneum also known as red flour beetle is one of the most important pests of stored grain product with a cosmopolitan distribution in Nigeria and all over the world contributing to food spoilage. The aim of this study was to characterize the T. castaneum by morphometric and molecular analyses. Samples of yam flour with evidence of the red flour beetles present inside were obtained from four locations in Kwara, Kogi, Oyo and Ekiti states in Nigeria. Morphological and molecular identifications of T. castaneum were carried out using standard methods. A dissecting microscope was used to identify the beetles and measurements were taken using ImageJ. Genomic DNA was extracted and checked on 1.5% agarose gel to confirm the presence of DNA. Species-specific primers were used to amplify mitochondrial cytochrome oxidase I (COI) gene of T. castaneum and the PCR amplicon size was also checked on 1.5% agarose. Morphometric measurements showed that the highest mean number (33.00±4.24 mm) of T. castaneum larvae observed was recorded on day 61 in Ilorin and the lowest was in Iwo, Osun state (4.00±0.00 mm) on the same day. The mean of the total body length of larvae from sampling sites was (1.31±0.37 mm) with minimum and (1.63±1.14 mm) maximum lengths respectively. There was no significant difference (p>0.05) between the mean length of the larvae collected from the study locations. Aligned cytochrome oxidase subunit 1 (COI) sequences of 313bp were analyzed. Phylogenetic analysis inferred by maximum likelihood method showed that the T. castaneum sequences analyzed for this study and sequences obtained from GenBank formed a monophyletic group. The molecular and phylogenetic analyses confirmed the presence of a single species of T. castaneum. The results from this study showed low levels of genetic diversity and variability in the studied T. castaneum populations. The observed genetic similarity in T. castaneum could be due to the fact that they were probably from similar origin when compared with those in the GenBank database. However, further studies are needed with more samples to characterize T. castaneum species from stored food grains across Nigeria.

Morphological, molecular identification and evaluation of antioxidant activity of seahorses from the Moroccan coasts

Seahorses, part of the small marine teleost fish family Syngnathidae, are increasingly under threat due to habitat degradation and overfishing. Notably used in traditional Chinese medicine, these fish have demonstrated significant pharmacological and cosmetic properties. In Morocco, however, seahorses are minimally exploited. This study aims to explore the biodiversity of Moroccan seahorses, focusing on identifying species from the Atlantic and Mediterranean coasts both morphologically and molecularly, and evaluating their antioxidant activity.The research involved collecting 62 dried seahorses from local fishermen. These specimens were subjected to detailed morphological and molecular identification through the DNA barcoding method, concentrating on the mitochondrial marker Cytochrome Oxidase I (COI) gene. Following DNA extraction and amplification, the sequences were analyzed for species identification and phylogenetic relationships. Additionally, the antioxidant activities of the seahorses were quantified using assays such as ABTS, reducing power, phosphomolybdenum, and β-carotene-linoleic acid.The combined morphological and molecular analyses consistently identified all specimens as Hippocampus hippocampus, and phylogenetic trees suggested a close relation with European and Turkish counterparts. Furthermore, the antioxidant assays revealed significant activity, with the ABTS assay showing an IC50 of 14.571 mg/mL ± 0.334, and the β-carotene-linoleic acid assay showing an IC50 of 1.273 mg/mL ± 0.166. The reducing power and phosphomolybdenum assays recorded EC50 values of 1.868 mg/mL ± 0.033 and 1.156 mg/mL ± 0.112, respectively. These results confirm the high antioxidant potential of Moroccan seahorses, suggesting their therapeutic value and necessitating measures for their biodiversity preservation at a national level.

Barcoding a glass eel migration: a snapshot of taxa migrating upstream in the Palu River, Central Sulawesi, Indonesia

Eels of the genus Anguilla are high value food fish with a catadromous life cycle. As tropical anguillid glass eels migrate to freshwater in multi-species schools, effective management of these and other diadromous resources requires reliable data. Previous research using two morphological methods concluded that between three and five anguillid eels recruit to the Palu River in Central Sulawesi, Indonesia with interannual and seasonal variations in species composition, size structure, and co-migrating taxa. Some glass eels and other taxa could not be identified based on external morphology. To clarify the taxonomic uncertainty regarding species recruiting to the Palu River this study applied DNA barcoding using the Cytochrome Oxidase I (COI) mitochondrial DNA (mtDNA) molecular marker. Taxa identified from the first sampling of glass eels and other taxa recruiting in these mixed schools included three anguillid eels, five other fishes, two crustacea and one mollusc, presenting a snapshot of taxa migrating upstream in the Palu River. Current GenBank accessions did not enable species level identification of two fish larvae (families Eleotridae and Tetraroginae). The sequences will add to Indonesian accessions in the GenBank repository and inform resource management, including the use of environmental DNA (eDNA) methods for monitoring Indonesian anguillid eels.

Phylogenetic characterization of two common sand flies Phlebotomus major and P. kandelakii in the West Black Sea Region of Turkey based on mitochondrial genes sequence analysis

Research on the taxonomy and phylogenetic characterization of sand flies (Diptera, Psychodidae, Phlebotominae) has received increasing attention due to their potential role in the transmission of medically significant diseases, including leishmaniasis, bartonellosis, and sand fly fever. Phlebotomus major and Phlebotomus kandelakii are the members of Larroussius subgenus that includes important vector sand fly species. P. major, P. neglectus and P. syriacus from a well-known sand fly “Major” species group are present widely while P. kandelakii has constricted distribution in Turkey. All have the capability to transmit Leishmania infantum, the causative agent of visceral leishmaniasis. Here, we investigated the genetic diversity within each species collected from the West Black Sea Region of Turkey using mitochondrial DNA markers, specifically cytochrome oxidase I (COI) and cytochrome b gene sequences (Cytb). A total of 1889 sand flies specimens were collected from the study area in June 2021 and August 2022, 1596 (84.49%) were identified as P. major s.l., and 253 (13.40%) were identified as P. kandelakii. Nine and four haplotypes of P. major were determined in the study area based on COI and Cytb sequences, respectively. Analysis of the phylogenetic data sets generated from our isolates and published isolates in Genbank revealed high haplotype diversities within P. major (COI = 0.933, Cytb = 0.714). For P. kandelakii, we detected four and three haplotypes within the COI and Cytb sequences, and the haplotype diversities were also high in the datasets including our isolates and published isolates in Genbank (COI = 0.978, Cytb = 1.000). Pairwise mean genetic distance calculated from the COI and Cytb datasets were 0.4% and 1.4% for P. major, and 1.0% and 0.2% for P. kandelakii, respectively, suggesting the absence of cryptic species. Phylogenetic analyses revealed three and two major clusters of Larroussius subgenus in the COI and Cytb datasets, respectively.

Not one but two: examining the genetic origin and characterization of the non-native spectacled caiman (Caiman crocodilus) in Florida

The US state of Florida is home to an alarmingly large number of invasive species, many of which have proven detrimental to native ecosystems. Biological invasions of reptiles in particular have been a major concern in recent years. The spectacled caiman (Caiman crocodilus) was first introduced from Latin America to Florida in the 1950’s. Given there are now established breeding populations across southern Florida, there are ongoing efforts to control them. Therefore, there is a need to understand this species’ natural history and introduction pathways. Previous studies have cited the Caribbean Coastal region of Colombia as a primary, and possibly exclusive, origin of C. crocodilus in Florida, and the species was identified as belonging to the C. c. fuscus molecular lineage. However, previous genetic sampling has been limited and may have been biased by small sample sizes and limited geographic scale. We collected 27 genetic samples from caimans captured in Florida, and sequenced the mitochondrial genes, Cytochrome oxidase I (COI) and Cytochrome B (CytB) for comparison with homologous gene fragments available for the species at GenBank. We found genetic evidence for multiple introduction events and the taxonomic classification of the Florida caimans as two distinct molecular lineages (C. c. fuscus and C. c. crocodilus) originating from at least two different regions: the Magdalena River Basin in Colombia and the Upper Branco River Basin in northern Brazil. This study helps to elucidate the genetic history of Florida caimans and provides valuable insight for population management of the species in Florida.

The status of COI and 12S rRNA DNA barcode reference libraries for freshwater fish in South Africa: Implications for future eDNA projects

Environmental DNA metabarcoding (eDNA) is a rapidly emerging field in which high-throughput sequencing is used to catalogue the biodiversity of ecosystems through the amplification of DNA extracted from environmental samples (water, air, faeces and soil). Although eDNA has strong links to DNA barcoding, the molecular marker most often used to detect vertebrates in eDNA studies is a portion of the mitochondrial 12S ribosomal RNA (12S rRNA) and not the standard cytochrome oxidase I (COI) marker used in traditional DNA barcoding. eDNA methods rely on a comprehensive reference library to link sequence data to species, which are often lacking in hyper-diverse countries such as South Africa. In this study, we review the present state of DNA barcode reference databases for both 12S rRNA and COI for freshwater fish (native and introduced) found in South African aquatic systems. Analysis of DNA records available on GenBank and the Barcode of Life Database (BOLD) revealed incomplete records of the examined taxa for both markers. Our findings showed that 34 species, 6 genera and 0 families of native South African freshwater fish lack COI barcode records, while 86 species, 22 genera and 8 families lack 12S rRNA records. Unlike the native freshwater fish, the non-native fish all had barcode records available for both COI and 12S rRNA. Producing comprehensive reference libraries for both markers is an important first step in developing an eDNA protocol for the non-invasive monitoring of native and non-native freshwater fish in South Africa.

DNA metabarcoding reveals the dietary profiles of a benthic marine crustacean, Nephrops norvegicus.

Norwegian lobster, Nephrops norvegicus, are a generalist scavenger and predator capable of short foraging excursions but can also suspension feed. Existing knowledge about their diet relies on a combination of methods including morphology-based stomach content analysis and stable isotopes, which often lack the resolution to distinguish prey items to species level particularly in species that thoroughly masticate their prey. DNA metabarcoding overcomes many of the challenges associated with traditional methods and it is an attractive approach to study the dietary profiles of animals. Here, we present the diet of the commercially valuable Nephrops norvegicus using DNA metabarcoding of gut contents. Despite difficulties associated with host amplification, our cytochrome oxidase I (COI) molecular assay successfully achieves higher resolution information than traditional approaches. We detected taxa that were likely consumed during different feeding strategies. Dinoflagellata, Chlorophyta and Bacillariophyta accounted for almost 50% of the prey items consumed, and are associated with suspension feeding, while fish with high fisheries discard rates were detected which are linked to active foraging. In addition, we were able to characterise biodiversity patterns by considering Nephrops as natural samplers, as well as detecting parasitic dinoflagellates (e.g., Hematodinium sp.), which are known to influence burrow related behaviour in infected individuals in over 50% of the samples. The metabarcoding data presented here greatly enhances a better understanding of a species' ecological role and could be applied as a routine procedure in future studies for proper consideration in the management and decision-making of fisheries.

Molecular evidence for occurrence of endangered long-tailed goral in Seoul metropolitan city, South Korea

The study examined the habitation and the number of long-tailed gorals by molecular identification, sexing discrimination, and identity tests on feces and hair samples estimated to be endangered long-tailed goral in Mt. Yongmasan, Mt. Achasan and Mt. Inwangsan near Seoul metropolitan city. Mitochondrial cytochrome oxidase I (COI) gene sequences showed that the DNA samples from the three mountains were those of long-tailed goral (Naemorhedus caudatus). The molecular sexing results showed that there were a female and a male in Mt. Yongmasan, a male in Mt. Achasan, but no informative results for Mt. Inwangsan. The identity test results indicated that the males of Mt. Yongmasan and Mt. Achasan were the same male, estimating the shift of this male from Mt. Yongmasan to Mt. Achasan. In addition, the goral of Mt. Inwangsan had a different COI sequence from those of Mt. Yongmasan and Mt. Achasan estimated to be this male with a different maternal lineage. Our present findings provide molecular evidence that at least three gorals have been inhabiting or continuously visiting the mountainous areas of Seoul metropolitan city, suggesting that a management system may be necessary for protecting this natural habitat of endangered long-tailed goral.

Genetic evidence of the unique identity of the West African Mangrove Oyster (Crassostrea tulipa) from the Gulf of Guinea

This research enabled the genetic identification of the West African mangrove oysters, Crassostrea tulipa, as well as establishing the evolutionary relationship between it and other Crassostrea species. Essentially, the study assisted in clearing up a long-standing confusion over this species’ synonymy with C. gasar. Also, the population structure of 60 C. tulipa individuals, from three different ecotypes, was analyzed using the mitochondrial cytochrome oxidase I (COI) genes as a marker. Results provided the first genetic sequences for C. tulipa and deposited in the GeneBank. Optimal and consensus bootstrap Neighbor-Joining trees distinctively differentiated C. tulipa from other Crassostrea species and consistently formed a different clade with C. gasar, with no bootstrap value from either NJ, MPT, or UPG trees supporting their similarity. C. tulipa sequences occurred as different haplotypes from other Crassostrea sp, with a mutation value as high as 288 and a haplotype diversity of 0.893 between C. tulipa and C. gasar sequences. High estimates of genetic distance (1.40–1.55) and patristic divergence were recorded between C. tulipa and C. gasar, in the same range as with seven other species. The study thus reveals the unique identity of C. tulipa as genetically distinct from C. gasar and other Crassostrea species. Based on the population structure analyses from the neutrality test, a low to high haplotype diversity h (0.000–0.963) and low nucleotide diversity π (0.00–0.378) were obtained. A negative mean Tajima’s D (−0.65247), and a positive Fu’s Fs (3.194), suggest rare variations or low-frequency polymorphisms. In addition to serving as the basis for phylogeny, the identification of C. tulipa and the recent data on its population structure also serve as the basis for conservation efforts and hatchery-based aquaculture.

Mitochondrial genetic homogeneity of South American leafminer, Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae) in Tamil Nadu, India

The South American leafminer, Tuta absoluta is an exotic devastative pest on solanaceous vegetables, including tomatoes, which leads to a cent per cent economic loss in India. The molecular markers assist in assessing gene flow, migratory frequencies, and genetic variety, as well as helping to evaluate the genetic makeup and diversification of an exotic species population to indigenous ones. With this, the present study aimed to investigate the genetic divergence of T. absoluta in different districts of Tamil Nadu, India. The study depicted the examination of genetic divergence of T. absoluta by aiding amplified region of mitochondrial DNA encoding cytochrome oxidase I (COI) from the T. absoluta samples gathered from Coimbatore, Dharmapuri and Dindigul districts of Tamil Nadu. The findings showed that the phylogenetic tree constructed from all sequences of T. absoluta acquired from the NCBI (National Center for Biotechnology Information) and BOLD (The Barcode of Life Data System) databases exhibited 99 percent identity and aggregated together into a single clade. . 5Hence, the present study revealed the great genetic uniformity in T. absoluta populations in India and corroborates that most of the globe rely on the partial COI gene, evidenced by minimal nucleotide diversity.