Cytochrome Oxidase I Gene Sequences Research Articles

Comparative Study of Two Himalayan Snow Trouts, Schizothorax esocinus and Schizothorax curvifrons Within the Schizothoracinae and Other Nearest Relatives of Cyprinidae, Inferred from Mitochondrial Sequences of Cytochrome b (Cyt-b) and Cytochrome Oxidase I (Co-I) Gene.

The Himalayan region encompasses varied aquatic ecosystems, characterized by the presence of diverse ichthyofauna, particularly represented by members of the Schizothorax genus, commonly referred to as snow trout. The primary objective of this work was to examine the molecular phylogeny of Schizothoracinae, specifically focusing on the two species, Schizothorax esocinus and Schizothorax curvifrons, which are known to inhabit the northern and north-eastern regions of the Himalayas. This investigation was conducted by analyzing the entire mitochondrial Cyt-b and Co-I gene sequences. The aligned Cyt-b and Co-I sequences for S. esocinus, S. curvifrons, and related members within the subfamily Schizothoracinae, spanned 1130 to 1141 and 1536 to 1551 base pairs, respectively. Using these gene, phylogenetic trees were created to compare Schizothoracinae species to other subfamilies of the family Cyprinidae (Barbinae, Alburninae, Leuciscinae, Xenocyprinae, Cyprininae, and Cultrinae). Genetic distances for Cyt-b and Co-I sequence at three hierarchical levels shows significant disparities in their average score. For Cyt-b, average p-distances for intraspecies, intragenus, and intrafamily were 2.13%, 4.1%, and 15.23%, respectively. Similarly, for Co-I, average p-distances were 1.19%, 3.6%, and 13.8% for intraspecies, intragenus, and intrafamily, respectively. Total number of haplotypes (h) based on Cyt-b and Co-I gene were 6 and 12 within the target Schizothorax spp. In the present study, the observed range of haplotype diversity (hd) for the Cyt-b gene varied from 0.00 to 0.847, with an average haplotype diversity of 0.847 ± 0.034. Similarly, for the Co-I gene, the observed haplotype diversity ranged from 0.00 to 0.931, with an average value of haplotype diversity estimated to be 0.931 ± 0.024. The results of the present study clearly shows that the representative species exhibited close affinities with members of Barbinae and Cyprininae, while other subfamilies formed distinct groups. The findings of the study also indicated that the Cyt-b and Co-I gene exhibits polymorphism and has the potential to serve as a marker for identifying genetic differentiation among populations based on ecological habitats. Mitochondrial Cyt-b and Co-I have been established as a universally accepted and validated genetic marker within a comprehensive bio-identification system at the species level.

Determination of genetic diversity between natural and cultured populations of Common Dentex (Dentex dentex) fish in the East Aegean Sea

Common dentex (Dentex dentex) is a commercial species of fish that is a highly valuable food source living naturally near Mediterranean and Atlantic Coasts. Therefore, monitoring and maintaining common dentex habitats are of high importance. A total of 53 specimens were collected from 6 natural habitats (from the Eastern Aegean and from the Antalya coast, which is the closest coast to the Western Mediterranean), and one aquaculture facility in the Eastern Aegean Sea. The mitochondrial Cytochrome Oxidase I (COI) gene was used to detect a total of 26 haplotypes. Along with the COI gene sequence, real-time PCR and highresolution melting analyses were performed as rapid and inexpensive alternatives. Sequence analysis showed that the highest haplotype diversity was obtained from the aquaculture facility in Karaburun and Antalya Locations, Turkey. Analysis of Molecular Variance (AMOVA) based on the haplotype frequencies resulted in 92.54% genetic variation within localities and 7.46% genetic variation between/among localities. The mean fixation index (Fst) was calculated as 0.0746 (p < 0.001). Genetic distances were primarily in collaboration with geographical distances and were efficiently confirmed by high resolution melting (HRM) analysis. The results will be valuable in monitoring and maintaining natural habitats as well as aquaculture facilities where common dentex are grown.

Genetic analyses and detection of point mutations in the acetylcholinesterase-1 gene associated with organophosphate insecticide resistance in fall armyworm (Spodoptera frugiperda) populations from Uganda

BackgroundThe fall armyworm (FAW), Spodoptera frugiperda; J.E. Smith (Lepidoptera: Noctuidae), is now an economically important pest that causes huge losses to maize productivity in sub-Saharan Africa. Variations in sub-population genetics and the processes of rapid adaptation underpinning the invasion remain unclear. For this, the genetic identity and diversity of FAW populations in Uganda were revealed by sequencing 87 samples (collected across the country). Based on the partial mitochondrial cytochrome oxidase I (COI) gene polymorphisms, we further examined the mitochondrial haplotype configuration and compared the FAW in Uganda with sequences from other parts of the world. The molecular target for organophosphate and carbamate resistance, acetylcholinesterase, was also investigated.ResultsAnalysis of the partial COI gene sequences showed the presence of both rice (predominant) and corn strain haplotypes, with a haplotype diversity of 0.382. Based on the COI marker, pairwise difference distribution analyses, and neutrality tests, showed that the FAW populations in Uganda and the rest of Africa are evolving neutrally, but those in America and Asia are undergoing expansion. Our findings support observations that invasive FAW populations throughout the rest of Africa and Asia share a common origin. Sequencing of the S. frugiperda ace-1 gene revealed four amino acid substitutions, two of which (A201S and F290V) were previously shown to confer organophosphate resistance in both S. frugiperda and several other insect species. The other two previously reported new variations in positions g-396 and g-768, are presumed to be related to the development of insecticide resistance.ConclusionsThis research has increased our knowledge of the genetics of FAW in Uganda, which is critical for pest surveillance and the detection of resistance. However, due to the low gene polymorphism of COI, more evolutionary studies incorporating the Spodoptera frugiperda whole-genome sequence are required to precisely understand the FAW population dynamics, introduction paths, origin, and subsequent spread.

Phylogenetic Position of Eurihaline Rotifer Brachionus sp. Originated From Tumpaan Waters, South Minahasa, North Sulawesi

This study aims to determine the phylogenetic position of rotifer Brachionus sp. sample originated from Tumpaan coastal water, North Sulawesi in the phylogenetic tree of Brachionus spp. from 27 samples of rotifer selected from 100 samples available in NCBI Genbank. The phylogeny tree was constructed on the basis of COI (Cytochrome Oxidase I) gene sequences using MEGA7 software and the neighbor-joining method. Results show that the phylogeny tree was divided into 2 clades, the group (closely related group) and out-group (distantly related group). It is confirmed that the position of the rotifer originating from Tumpaan Coastal Water is within in group, which has closely related to the B. plicatilis complex BUS06 indicated by a bootstrap value of 80%. The group belongs to SS-type rotifers with an average body size of 149±1.3 μm. This rotifer group has been known as live prey for fish larvae with a mouth-opening size of 150 μm.

Identification of selected earthworm species of Northeast India using DNA barcoding

Aim: This study aimed at the species identification of selected indigenous earthworms of Manipur and Assam, Northeast India along with an exotic species using morpho-anatomical study and DNA barcoding. Methodology: Indigenous species of earthworms were collected from Imphal and Jorhat, North-eastern part of India. The exotic species of earthworm were collected from Indian Council of Agricultural Research Complex, Manipur. The samples were collected by digging and hand sorting method. Identification of samples was done by both conventional and molecular methods. Molecular characterization was accomplished through PCR amplification of the mitochondrial cytochrome oxidase I (COI) genes. Automatic sequencing reactions were performed for the amplified PCR products on ABI3100 Genetic Analyser (Applied Biosystems). Results: Out of five specimens (EM1, EM2, EM4, EG5 and EM6) examined through morpho-anatomical studies, three were identified to species level while the other two were identified to their genus level only. Out of EM1 and EM2 specimens in the genus Perionyx as per the morpho-anatomical studies, DNA barcoding could deduce the EM2 specimen up to the species level as P. excavatus. The exotic EM6 specimen morphologically identified as Eisenia fetida showed 99% COI gene sequence similarity with both E. fetida and E. andrei but its sequence divergence with E. andrei was less than 1%, so, it belonged to E. andrei. Interpretation: This study shows the reliability of clubbing DNA barcoding experiments with classical taxonomy in supplementing and strengthening the traditional taxonomy for accurate identification of earthworms. Key words: Earthworms, Mitochondrial cytochrome oxidase I gene, Morpho-anatomical studies, Species identification

Filogenetik Ikan Ekstremofil Edible Populasi Magelang Menggunakan Gen Cytochrome Oxydase I

The Cethol fish was used as a dietary raw material of chips fish by local people in Magelang. The population of the fish was decreased and impacted to fish chips production. The Cethol fish farming could be the one of solution to maintain the stock of this fish as dietary raw material. Nevertheless, the taxonomic status of Cethol fish as the primary information of in Magelang still unclear. Taxonomic status is of organisms is useful to inform biology, reproduction and traits of candidate species will be farmed. The aim of research is revealing the taxonomic status of Cethol fish in Magelang using common barcoding marker Cytochrome Oxidase I (COI) from mitochondrial DNA. The COI gene sequences of Cethol fish from Magelang and other sequence samples from NCBI were used to construct the phylogenetic tree and haplotype network approach to reveal the similarity and clustered of the fish sequence samples. The maximum likelihood and minimum evolution were considered as construction tree method by Kimura 2 parameter statistic model and 1000 bootstrap value. The Median joining statistic model was generated to reveal grouping form and substitution rate of each samples. The phylogenetic tree was constructed from COI gene of Cethol fishes from Magelang are grouped in the same clade and monophyletic with the Poecilia reticulata COI gene from South America as the origin of the fish species. Meanwhile, the P.reticulata from Bengkulu, Sumatera and Java were clearly separated with the samples from Magelang but still in haplogroup with the South America sequence samples. Those result are strengthen the previously notion that the Cethol fish in Magelang is a group species of P.reticulata from South America.

Application of COI gene for identification of some economically and forensically important muscid flies of India (Diptera: Muscidae)

Muscid flies are of great medical and veterinary importance because of their ability to transmit diseases to humans and animals. Their larvae are found on dead bodies and are used as a forensic indicator for estimating Post-Mortem Interval (PMI). A drawback of morphological identification of these larvae is lack of an identification key which covers all the life stages of the taxa. To overcome the problem, entomologists now focus on the alternative methods, which can speed up the identification process. Barcoding region of Cytochrome oxidase I (COI)l is believed to be the best among other markers for precise identification and to mark out phylogeny. During the present study, total 63 specimens of 24 species belonging to 7 genera representing the various muscid subfamilies were used to check the efficacy of COI gene in identification. 11 species were collected from various regions (Punjab, Haryana, Himachal Pradesh, Uttarakhand) of North India during the years 2015–2019, and sequences of rest of the species were downloaded from the database of Genbank. The percentage of intraspecific divergences ranged from 0%-0.5% for species of India and 0%-3.0% for the sequences from other countries. The interspecific divergence ranged from 3.1% to 17.3% and 3.3% to 16.7% respectively for Indian species and species from the other part of the world. 1000 bootstrapped Neighbor-joining with Kimura-2 parameter phylogenetic tree constructed based on COI gene sequences, clearly separated 24 species of these Muscid flies. This is the first ever study on COI gene based identification of medico-legal, veterinary and forensically important Muscid flies from India.

Molecular identification and genetic variation studies in fifteen polychaete species of the Vellar estuary by COI gene sequence

Identification of polychaetes from the Vellar estuary mangroves is very essential to assess their diversity status. In this study, we have used sequences of the Cytochrome Oxidase I (COI) from 15 species belongs to eight families to barcode and investigate the molecular variation among the Vellar estuary polychaetes. Based on the sequence data, it was observed that the maximum A+T content (62.00%) was recorded in Diopatra neapolitana and minimum (55.00%) in Laonice cirrata. Similarly, the maximum C+G value of 45.00% was observed in Laonice cirrata and least content of 38.00% was estimated in Capitella capitata and Diopatra neapolitana. The maximum K2P distance (1.459) was found between Lubrineridae and Capitellidae family. Whereas, the minimum K2P distance of 0.270 was observed between Nereididae and Spionidae. However, the maximum K2P distance within family was observed in Lubrineridae (0.197) and the minimum value of 0.005 was recorded in Spionidae.The maximum K2P distance (1.459) was found between the genus Capitella and Lumbrineris whereas the minimum distance (0.230) was observed between Platynereis and Perinereis. However, the maximum K2P distance within genus was observed in Perinereis (0.211) whereas the minimum distance of 0.005 was perceived in Laonice. The intra genus K2P genetic distance in Marphysa, Naineris, Platynereis, Capitella, Diopatra was zero. The maximum likelihood tree clearly demonstrates the efficacy of COI gene in discriminating polychaete individuals both at conspecific and congeneric levels. Further molecular tools such as microsattelite, RAPD is needed to assess the population structure of the above identified species.

Phylogenetic observation in Ariidae, Bagridae and Plotosidae catfishes by COI gene sequence analysis

To understand the phylogenetic status of Ariidae, Bagridae and Plotosidae catfishes, this study was planned using the barcode gene, cytochrome oxidase I (COI). Totally 71 species were used in phylogenetic reconstructions under maximum parsimony, maximum likelihood and Bayesian inference criteria. The one-way ANOVA showed that the three catfish families are significantly different (F= 19.79, d.f. = 3; 116, P< 0.0001 (Plotosidae); F= 44.21, d.f.= 3; 986, P< 0.0001 (Ariidae); F= 24.83, d.f.= 3; 1322, P< 0.0001 (Bagridae). In MP, ML and BI based phylogenetic tree of Ariidae, Plicofollis genus displayed as a monophyletic group with higher bootstrap and posterior probability values for all the species except two species of Neoarius, which intervened separating P. polystaphylodon. In the phylogenetic tree of Plotoside, Plotosus genus displayed as monophyletic group with higher bootstrap and posterior probability values for all the eight species. In the case of Bagridae phylogeentic tree, Mystus genus displayed as a monophyletic group with higher bootstrap and posterior probability values for all the species except Mystus montanus forming a distant and distinct clade whereas Mystus tengara collides into monophyletic clade when Neotropius genuswas removed. By this study we could establish a phylogenetic hypothesis for all the 36 catfish families and examine the monophyly status of the subfamilies and genera.

Molecular Characterisation using 16S rRNA and COI Gene Sequences in Hard Ticks of Gwalior, India

Tick infestation in humans and animals represents a global threat for different tick-borne diseases. In the present study, the ticks from the Gwalior region of India have been mapped to create a database of tick diversity. We explored 773 ticks collected from domestic animals and vegetation in Gwalior. Animals were screened visually, and ticks were collected manually, whereas the flag-drag method was used to collect ticks from the vegetation. The 16S rRNA and cytochrome oxidase I (COI) genes of tick samples were amplified and purified for sequencing and respective phylogenetic trees were constructed. The ticks were morphologically identified using taxonomical keys, revealing the presence of five genera in the region: Hyalomma, Haemaphysalis, Rhipicephalus, Boophilus, and Nosomma. Hyalomma spp. (Hy. annatolicum and Hy. marginatum) were the most abundant accounting for 69.598% of the total sample, followed by Rhipicephalus sanguineus (17.335%), Rhipicephalus microplus (7.115%), Haemaphysalis sp. (5.692%), and Nosomma monstrotum (0.258%). The tick sequences were submitted to the GenBank database. Phylogenetic analysis confirmed the morphological identification at the species level. The combination of molecular and morphological analyses of the ticks supported the result obtained with each method, thus providing more reliable estimates for continued surveillance studies.

Molecular identification and population genetic study of Elaeidobius kamerunicus Faust. (Coleoptera: Curculionidae) from Indonesia, Malaysia and Cameroon based on mitochondrial gene

Abstract. Tambunan VB, Apriyanto A, Ajambang W, Etta CE, Sahari B, Buchori D, Hidayat P. 2020. Molecular identification and population genetic study of Elaeidobius kamerunicus Faust. (Coleoptera: Curculionidae) from Indonesia, Malaysia and Cameroon based on mitochondrial gene. Biodiversitas 21: 3263-3270. Oil palm pollinating weevil Elaeidobius kamerunicus is a very important insect pollinator in oil palm plantation. However, there is still lack of information about molecular identification and population genetic study in this species. The purpose of this study was to explore the effectiveness of oil palm pollinating weevil identification using mitochondrial DNA of COI gene and to assess its genetic variation between different locations and countries. We sequenced the DNA barcode of 36 individuals of this species using the mtDNA Cytochrome Oxidase I (COI) gene to explore their genetic variation, identity and phylogenetic relationship. The COI gene sequences generated from this study were successful in identifying E. kamerunicus. Phylogenetic analysis also revealed 3 well-supported monophyletic haplogroups of E. kamerunicus population. In addition, genetic differentiation analysis revealed that most populations from Indonesia were different from Malaysian and Cameroonian populations indicating that there was a genetic variation between the population samples from these countries. The overall E. kamerunicus used in this study were geographically structured in two regions; outside Indonesia region (Cameroon and Malaysia) and Indonesia region. These results demonstrate the feasibility of using COI gene sequence for molecular identification and population genetic study of E. kamerunicus species.

Molecular characterization of black flies (Diptera: Simuliidae) in areas with pest outbreaks and simuliotoxicosis in Northeast Anatolia Region, Turkey

Accurate species identification provides the foundation for successful pest management and vector control of black flies. Accordingly, we examined the mitochondrial DNA cytochrome oxidase I (COI) gene sequences of four morphologically and chromosomally identified species of black flies (Simulium vernumgroup sp., S. bergi Rubtsov, S. bezzii (Corti), and S. kiritshenkoi Rubtsov) in Northeast Anatolia Region of Turkey where simuliid pest problems and simuliotoxicosis cases have been reported among cattle. COI gene sequences of these species and closely related species available in GenBank were used to provide species-level diagnoses and infer relationships. Both subgenera (Nevermannia and Simulium) were monophyletic, and subclades generally corresponded with species groups. Intraspecific genetic divergence was 0.2–1.6%, whereas the mean interspecific genetic divergence among the four species was 11.2–14.5%. The COI analysis produced results congruent with morphological concepts of the nominal species S. bergi and S. bezzii. Probable misidentifications in GenBank were revealed, especially for species in the S. ornatum and S. vernum groups, complicating identification capability. Sequence variation in the COI barcode region also might not be adequate for species delineation and identification among some species in these two species groups.

Population genetic analysis of trematode Parasaccocoelium mugili Zhukov, 1971 (Haploporidae Nicoll, 1914) from the Russian Far East and Vietnam based on ribosomal ITS and mitochondrial COI gene partial sequence data.

Intraspecific variation of Parasaccocoelium mugili collected from mullet fish of the south of Russian Far East and Vietnam has previously been estimated on the basis of two molecular markers: ribosomal internal transcribed spacer 1 (ITS1) rDNA and mitochondrial cytochrome oxidase I (COI) gene sequences. In the present study, molecular identification of this species from the Kievka River, Primorye and from Vietnam was performed by analysis of 28S rDNA sequences. Analysis of ITS1 rDNA sequences variation revealed two highly differentiated main groups, representing trematode specimens from the two regions. Genetic variation within each region was relatively low. Mitochondrial COI gene sequence data analysis revealed fixed nucleotide and amino acid substitutions, and supported the existence of two genetically different groups associated with geographical origin. Analysis of the COI gene fragments showed extremely high variation within Russian and Vietnamese P. mugili samples. Our results for P. mugili most probably represent a case of initial step of allopotric speciation for this trematode, caused by living strategy of its definitive host at evolutionary scale. Mitochondrial DNA sequence data show that existence of gene flow between local populations of P. mugili in the Primorye Region caused by definitive hosts can be proposed.

A case of imported furuncular cutaneous myiasis and cytochrome oxidaseI gene sequence analysis of the pathogenic Cordylobia anthropophaga

To report a case of imported furuncular cutaneous myiasis, and to analyze the sequence of the mitochondrial cytochrome C oxidase subunit Ⅰ (COⅠ) gene of the pathogenic Cordylobia anthropophaga. A 33-year-old female patient had a travel history to Ghana and Cameroon in Africa 1 month prior to the presentation. No anti-mosquito measures were taken during her stay, and she hung up the laundries outside to dry for several times. Skin examination showed furuncular protuberances with diameters of 1 - 2 cm on the inner side of the left upper arm as well as on the outer side of the left chest, which were bright red and hard on palpation with irregular borders and a small hole on their central surface. Morphological identification revealed that the larva squeezed from the lesion was suspected as myiasis. After PCR amplification of the COⅠ gene of the larva, an about 650-bp PCR product was acquired. Sequencing and BLAST analysis showed that this product was most closely related to the COⅠ gene (GenBank accession number: FR719158.1) of Cordylobia anthropophaga isolated in Cameroon in 2010 with the sequence similarity being 99.84%, and they were grouped together on the phylogenetic tree. According to the clinical features and travel history of the patient and the sequencing results of the pathogenic Cordylobia anthropophaga, this case was confirmed as imported furuncular cutaneous myiasis caused by Cordylobia anthropophaga. Key words: Hypodermyiasis; Muscidae; Electron transport complex Ⅳ; Furuncular cutaneous myiasis; Cordylobia anthropophaga

Genetic diversity of Culicoides species within the Pulicaris complex (Diptera: Ceratopogonidae) in Turkey inferred from mitochondrial COI gene sequences

Identification of Culicoides (Diptera: Ceratopogonidae) biting midges to species has become important due to their potential role in the transmission of arboviruses such as bluetongue virus, bovine ephemeral fever virus, Akabane virus, African horse sickness virus, epizootic haemorrhagic disease virus and Schmallenberg virus. In several studies, molecular tools, used for the identification of biting midges, revealed the presence of cryptic and undescribed species especially within Pulicaris complex. The presence of cryptic species within species complexes raise questions about their role in viral disease transmission as there are apparent differences in the vectorial capacity between closely related species. In this study, we analyzed the mitochondrial DNA cytochrome oxidase I (COI) gene sequences of species within the Pulicaris complex present in Turkey and determined their phylogenetic relationships. Twenty-one haplotypes within the already described species C. pulicaris P1, C. lupicaris, C. lupicaris L2, C. newsteadi, C. newsteadi N1, C. punctatus, C. fagineus F2 and C. flavipulicaris were determined from the study areas. The molecular analysis revealed further two haplotypes belonging to new non-described cryptic species named as C. lupicaris L3 and Culicoides WBS corresponding to C. lupicaris and Fagineus complex which diverged by 17.9% to 25.7% and 18.7% to 31.8%, respectively from other species in the subgenus Culicoides. Genetic divergence within species was <2.0% and phylogenetic analyses of the COI dataset revealed 22 different monophyletic separate clades within two major cluster. The results of this study emphasize the applicability of COI sequences as a diagnostic marker for differentiating Culicoides species and revealing cryptic species.

Phylogenetic Analysis of Duck Species from Tegal Indonesia Using 18S Ribosomal RNA and Mitochondrial COI Gene

Background and Objective: Tegal duck is a domestic waterfowl species known as a major producer of eggs that is traditionally used for making the famous salted egg by the local people. This study aimed to analyze the phylogenetic relationship of the Tegal duck through the gene encoding 18S ribosomal RNA (rRNA) and mitochondrial cytochrome oxidase I (COI). Methodology: We amplified and sequenced part of the 18S rRNA and COI gene of Tegal duck. These data were used to determine their similarity with other Anas species retrieved from GenBank and analyzing phylogenetic relationship. Results: The size of the PCR product of partial 18S rRNA was approximately 485 bp, whereas the size of the partial mitochondrial DNA (mtDNA) of the COI gene sequence was 751 bp. The 18S rRNA data showed that the Tegal duck is closely related to A. platyrhynchos (84.4% similarity). The COI gene data of the Tegal duck confirmed this relationship, with 99% homology with A. platyrhynchos voucher NHMO-BC399. However, the COI gene fragment of the Tegal duck also showed 99% homology with A. poecilorhyncha. Conclusion: Tegal duck has a close phylogenetic relationship with not only A. platyrhynchos but also A. poecilorhyncha.

Phylogenetic analysis and genetic structure of the seahorse, Hippocampus fuscus from the Arabian and Red Sea based on mitochondrial DNA sequences

The unique body morphology and specialized life history traits make seahorses excellent flagship species for many issues in marine conservation and biological evolution. In this study, the complete mitochondrial genome of Hippocampus fuscus was determined. Phylogenetic analyses showed that H. fuscus had a close genetic relationship to Hippocampus reidi, which give us a new insight into the speciation and dispersal among seahorse genus. A total of 843 base pairs of cytochrome b (Cytb) gene and a 646 base pairs of cytochrome oxidase I (COI) gene were obtained from 36 H. fuscus and 26 H. reidi from three populations. Population genetic analysis revealed a relatively high genetic diversity across the populations of H. fuscus compared with H. reidi. Neighbour-joining (NJ) tree of COI and Cytb gene sequences showed that H. fuscus haplotypes formed one cluster. The result of median-joining network of haplotypes based on COI and Cytb indicated a lack of structure in populations of H. fuscus. This study addressed the information about the evolution history and genetic structure of an Arabian seahorse H. fuscus, which provides insight into the genetic conservation and sustainable management for this species.

Monitoring conservation effects on a Chinese indigenous chicken breed using major histocompatibility complex B-G gene and DNA Barcodes.

ObjectiveWe report monitoring conservation effect for a Chinese indigenous chicken (Langshan) breed using major histocompatibility complex (MHC) and DNA barcords.MethodsThe full length of MHC B-G gene and mitochondrial cytochrome oxidase I (COI) gene in generations 0, 5, 10, 15, 16, and 17 was measured using re-sequencing and sequencing procedures, respectively.ResultsThere were 292 single nucleotide polymorphisms of MHC B-G gene identified in six generations. Heterozygosity (He) and polymorphic information content (PIC) of MHC B-G gene in generations 10, 15, 16, and 17 remained stable. He and PIC of MHC B-G gene were different in six generations, with G10, G15, G16, G17 >G5>G0 (p<0.05). For the COI gene, there were five haplotypes in generations 0, 5, 10, 15, 16, and 17. Where Hap2 and Hap4 were the shared haplotypes, 164 individuals shared Hap2 haplotypes, while Hap1 and Hap3 were the shared haplotypes in generations 0 and 5 and Hap5 was a shared haplotype in generations 10, 15, 16, and 17. The sequence of COI gene in 6 generations was tested by Tajima’s and D value, and the results were not significant, which were consistent with neutral mutation. There were no differences in generations 10, 15, 16, and 17for measured phenotypic traits. In other generations, for annual egg production, with G5, G10, G15, G16, G17>G0 (p<0.05). For age at the first egg and age at sexual maturity, with G10, G15, G16, G17>G5>G0 (p<0.05).ConclusionCombined with the results of COI gene DNA barcodes, MHC B-G gene, and phenotypic traits we can see that genetic diversity remained stable from generations 10 to 17 and the equimultiple random matching pedigrees conservation population conservation effect of Langshan chicken was effective as measured by these criteria.

Genetic relationship between neuropteran families (Insecta, Neuropterida, Neuroptera) based on Cytochrome oxidase-i sequences

The studied specimens belonged to five species of three families of Chrysopidae, Myrmeleontidae and Ascalaphidae (order Neuroptera). They were collected from Shush and Dezful, south of Iran. These insects are useful insects in biological control as the important predators of aphids, psyllids, caterpillars, ants and other insects. The Sequence alignment of parts of Cytochrome Oxidase-I (COI) gene of those species was studied. The insect bodies were entirely ground in a microtube. The PCR products of COI were sequenced. Pairwise alignment of nucleotides sequences belonging to five species of Neuroptera was carried out using MegAlign and EditSeq softwares. The sequencing results in Palpares solidus and Creoleon remanei showed the mutation potentials in locations of 699, 702, 726, 735 and 750 of COI gene of mtDNA. According to COI gene sequences, Chrysopa pallens and Palpares solidus species showed the maximum genetic similarity (98.2%). There was the minimum genetic similarity (75.9%) between Chrysopa viridana and Creoleon remanei species.

A history of invasion: COI phylogeny of Manila clam Ruditapes philippinarum in Europe

The Manila clam Ruditapes philippinarum – synonym Venerupis philippinarum (Adams and Reeve, 1850) is now one of the top 5 most commercially valuable bivalve species worldwide. Originally from the Indo-Pacific region, it has been introduced in many countries for fisheries and aquaculture, including estuarine environments along Atlantic and Mediterranean European coasts. Yet despite its commercial value and widespread distribution, the precise origins of stocks remain speculative and the genetic diversity of introduced populations is poorly known. Thus, the aim of this work was to collect mtDNA COI (Cytochrome oxidase I) gene sequences from 5 European countries with Manila clam stocks and compare them with native Asian populations to evaluate their genetic diversity and identify possible routes of invasion. The COI gene sequencing supported a strong founder effect in the European populations with 3 main haplotypes occurring at high frequencies, derived from Japan. However, high haplotype diversity was also observed due to the occurrence of 10 rare haplotypes. This supports hypotheses (i) there have been additional, previous unrecorded, introductions as previously hypothesized by analysis of 16S rDNA, and (ii) there has been a limited loss of genetic diversity in introduced populations, as previously suggested by microsatellite data. This is the first genetic comparison of Manila clam populations introduced in to Europe with native clams. Genetic data herein presented are fundamentally important for the traceability of clam products and stock management programmes and will also inform discussion on the potential resilience of exploited Manila clam populations.