Mitochondrial Cytochrome C Oxidase Subunit I Gene Research Articles

Exploring the Potential in Combining the Two Molecular Approaches, COI Barcoding and PCR-RFLP (COIBar-RFLP) in Identification of Selected Species of the Family Carangidae

The family Carangidae is considered a markedly diverse, widespread taxon. Due to the characteristic “cryptic diversity” and “hybrid speciation” within the family, there is an exigency for taxonomic approaches that go beyond traditional phenotypic modus in identifying species. Mitochondrial cytochrome c oxidase subunit - I (COI) barcoding gene region plays a significant role over phenotypic characters in identifying species. This study evaluates the combination of the two molecular approaches: the COI DNA barcoding and PCR-RFLP for judicious species discrimination. The partial mitochondrial COI gene region of the selected Carangid fish species was amplified, sequenced and confirmed sequences with a mean length of 655 bp were submitted to the main databases; NCBI and BOLD. Intraspecific and interspecific nucleotide divergences were computed by the Kimura-2-Parameter (K2P) and they ranged between (0.00–2.96 %) and (6.46–21.83 %), respectively. The possibility of acquiring the same RFLP profiles given by the restriction enzymes HaeIII and MbOII was observed by the theoretical cleavage of 250 reference sequences of the corresponding gene. Hence, major and minority composite haplotypes of each species were obtained based on the fragment types derived by both HaeIII and MbOII. The resulting divergence values were compatible with the previously reported values for marine fish species. All the species were clearly differentiated by both RFLP banding patterns and the highest probability assumption of getting the same RFLP profile was compatible with the most abundant composite haplotype of each species. This reveals the practicability of the combination of two consolidated molecular approaches, COI barcoding and PCR-RFLP (COIBar-RFLP).

Genetic diversity, variation, and structure of two populations of bigfin reef squid (Sepioteuthis lessoniana d’Orbigny) in Con Dao and Phu Quoc islands, Vietnam

BackgroundBigfin squid is one of the economically important seafood resources in Vietnam’s fisheries and the waters around Con Dao and Phu Quoc islands are two major fishing grounds where this species has been actively exploited. The start codon targeted polymorphism (SCoT) and CAAT box–derived polymorphism (CBDP) techniques were used to generate DNA fingerprinting data to analyze the genetic diversity, variation, and structure of the two populations in the waters surrounding Phu Quoc and Con Dao islands together with mitochondrial cytochrome C oxidase subunit I (COI) gene sequence data. ResultsCon Dao population possessed a higher diversity [expected heterozygosity (He) = 0.2254, Shannon index (I) = 0.3459, percentage of polymorphic bands (PPB) = 80.14%, nucleotide diversity (π) = 0.0336, haplotype diversity (h) = 0.910 with 16 haplotypes] than Phu Quoc population (He = 0.1854, I = 0.2873, PPB = 70.38%, π = 0.0246, h = 0.838 with 14 haplotypes). The genetic diversity at species level in the investigated region was at level of He = 0.2169, I = 0.3399, PPB = 86.41, π = 0.0289, and h = 0.892 with 24 haplotypes. Based on DNA fingerprinting data, the pairwise genetic similarity coefficients among individuals of the Con Dao population were lower (average of 0.7977) than the Phu Quoc population (average of 0.8316). Based on mitochondrial COI data, the pairwise genetic distances among individuals of the Con Dao population were higher (average of 0.0361) than the Phu Quoc population (average of 0.0263). Gene differentiation (GST) between two investigated populations was 0.0316 and 0.0310 leading to the genetic distance was 0.0573 and 0.0213 and the gene flow between them was Nm = 8.2209 and 11.4700 migrants per generation among populations based on DNA fingerprinting and based on COI gene sequence data, respectively. Genetic variation within individuals of both populations (WP) played the key role in total genetic variation at species level in surveyed region. ConclusionsFor the bigfin reef squid species in the surveyed region, the Con Dao population had the higher genetic diversity than the Phu Quoc population, between them existed a low to moderate genetic differentiation and a genetic exchange via gene flow. The DNA fingerprinting data better revealed the genetic differentiation between the two surveyed populations while the mitochondrial COI gene sequence data could show the phylogenetic relationship among the surveyed individuals and the other from the sea regions in Southeast Asia. Based on the results obtained, fisheries management strategies are suggested toward the conservation and sustainable exploitation of this species.

Haplotype Diversity in the Mitochondrial COI Gene of Barred Rainbowfish (Chilaterina fasciata) from Mamberamo River of Western New Guinea, Indonesia

A Barred rainbowfish (Chilatherina fasciata) is one of the native fish species found in Western New Guinea of Indonesia. This study aimed to observe the levels of haplotype diversity in the partial Cytochrome-c oxidase subunit I (COI) gene of Barred rainbowfish. For the DNA analysis, thirty (30) Barred rainbowfishes were caught from the Mamberamo River. Three (3) molecular packages of BioEdit, MEGA, and DNAsp were used to analyze twenty (30) forward sequences of the COI gene (502 bp). The research showed four (4) haplotypes for the examined population, a total of seven (7) mutations, and low genetic diversity detected in the partial COI gene with the haplotype diversity (Hd) = 0.405 and nucleotide diversity (pi) = 0.003. Meanwhile, the Fu's and Tajima's tests were 1.21 and -0.69, respectively. The UPGMA tree with 1,000 × bootstrap replications revealed that Barred rainbowfishes are grouped into similar clusters with Melanotaenia vanheurni, Chilatherina alleni, and Chilatherina bleheri. In conclusion, haplotype 3 (77%) was detected as the common haplotype for Barred rainbowfishes at the Mamberamo River of Western New Guinea.

Genetic Diversity and Phylogeography of Taenioides cirratus in Five Geographical Populations Based on Mitochondrial COI and Cytb Gene Sequences

The genetic diversity of Taenioides cirratus was investigated on the basis of mitochondrial cytochrome c oxidase subunit I (COI) and cytochrome b (Cytb) gene sequences. A total of 159 specimens collected from the Chaohu Lake (CL), Nansihu Lake (NL), Taihu Lake (TL), Pearl River (PR), and Nandu River (NR) were sequenced. The total length of the sequence was 2485 bp with 412 polymorphic sites. A total of 73 haplotypes were identified, with Hap1 being the most widely distributed. The PR and NR populations showed high genetic diversity, while the CL population showed low genetic diversity. TL and NL showed high haplotype diversity but low nucleotide diversity. The analysis of molecular variance demonstrated that the sequence variations were mainly occurred among populations. T. cirratus populations are declining, and rare alleles are present at low frequencies, as analysed using a neutral test and a mismatched distribution analysis. There was a relatively high level of genetic differentiation among the populations of the Yangtze River basin (including NL), PR, and NR (Fst > 0.15). The two similar phylogenetic trees constructed by the maximum likelihood (ML) and Bayesian inference (BI) methods presented three major lineages, of which lineage II contains haplotypes from PR and NR, lineage III contains haplotypes from CL, NL, TL, and PR, whereas lineage I contains only a portion of haplotypes from NR. Based on the neutral test, mismatch analysis, and Bayesian Skyline Plot (BSP), geological and climatic events were inferred to have played an important role in the historical dynamics of T. cirratus population. Hap1, Hap25, and Hap58 were inferred as possible ancestral haplotypes by network analysis. Our study offers an essential foundation for resource preservation and additional taxonomic clarification of T. cirratus.

The morphometric, meristic and genetic characteristics of European sprat (Sprattus sprattus) in the Black Sea

The European sprat (Sprattus sprattus) represents the unit stock shared among the Black Sea countries. It has a key role in the Black Sea ecosystem and is determined by its importance from both a commercial and an ecological point of view. Up to now, there are few studies on the meristic, morphometric and genetic characteristics of this species. In this study, the species were specified and studied for meristic, morphometric and genetic characteristics. Mitochondrial gene regions which 16S rRNA and cytochrome c oxidase subunit I (COI), were studied and compared with some of the family Clupeidae species in the National Center for Biotechnology Information (NCBI) and the phylogenetic relationship was examined. A total of 14 haplotypes were determined for the mitochondrial COI gene region and 3 haplotypes were determined for the 16S rRNA gene region. This study will contribute to the sustainable management of this species as well as be a basis for future studies.

Mitochondrial COI and Cytb gene as valid molecular identification marker of sandfly species (Diptera: Psychodidae) in China

The accurate identification of sandfly species is crucial because some species transmit medically significant diseases, including leishmaniasis, bartonellosis and sandfly fever. However, due to the high similarity of the external morphology in sandfly species, identification can only be performed using internal morphological characteristics after dissection, which is time consuming and requires highly experienced staff. Thus, the introduction of suitable molecular markers may solve these identification problems. This study screened suitable DNA barcodes to identify common sandfly species in China. The phlebotomine sandflies were collected from Sichuan, Henan and Hainan Provinces from 2014 to 2016. The species were identified by the morphological characteristics of the pharyngeal armature and spermatheca. The genomic DNA of sandfly was extracted individually, and mitochondrial DNA (mtDNA) cytochrome C oxidase subunit I (COI) and cytochrome B (Cytb) as well as the 18S subunit of ribosomal DNA (rDNA) were amplified using polymerase chain reaction (PCR). Additionally, intraspecific and interspecific differences (p-distance) were calculated to evaluate the feasibility of the three gene fragments as a DNA barcode. The phylogeny trees of all sandfly species in this study were constructed using neighbor joining (NJ) method. Six species were identified by the morphological features, belonging to Phlebotomus and Sergentomyia, as Ph. chinensis s. l., Ph. stantoni, Se. bailyi, Se. iyengari, Se. squamirostris, and Se. squamipleuris. Analysis based on three gene fragments revealed some degree of intraspecific polymorphism among these sandfly species in China. The largest intraspecific variation occurred in Ph. chinensis s. l. (mtDNA COI, p-distance = 0.042; mtDNA Cytb, p-distance = 0.071), but the 18S rDNA fragment showed a small variation (p-distance = 0.005). The ranges of interspecific p-distances for mtDNA COI and mtDNA Cytb were 0.138 - 0.231 and 0.128 - 0.274, respectively. However, the interspecific p-distances of 18S rDNA are relatively low ranging from 0.003 to 0.055. Both mitochondrial COI and Cytb gene fragments are valid molecular identification markers in theses sandfly species. The topological structure of phylogeny trees based on mtDNA COI, mtDNA Cytb and 18S rDNA genes were all consistent with morphological classification. And we also found there were significant intraspecies differences within Ph. chinensis s. l. (0.006-0.071) and Se. bailyi (0.002-0.032) based on mtDNA Cytb gene fragment. Sequence alignment data suggested that Ph. chinensis s. l. from Sichuan should be Ph. sichuanensis, and the sandfly specimen collected from Henan was Ph. chinensis s. s.. There could be cryptic species in Se. bailyi from China.

Molecular identification of ornamental loaches (Cypriniformes, Cobitoidei) of North East India using mitochondrial genes

North East (NE) India, referred as Biodiversity Hot Spot, is the natural habitat of a large variety of ornamental fishes. Among all the ornamental fishes available in NE India, Loaches are of great importance in the ornamental fish trade. In this study, 38 specimens from ten loaches species of North-eastern India are characterized using three mitochondrial genes i.e. cytochrome c oxidase subunit I (COI), 16S rRNA and cytochrome b (Cyt b). The average genetic distance values for all the three mitochondrial genes have increased gradually when moving up from species to genus to family levels. Among the genes, Cyt b gene showed relatively higher genetic distance values than mitochondrial 16S rRNA and COI genes. Some of the specimens of Botia and Lepidocephalichthys showed higher intraspecific genetic distance values compared to other specimens under analysis.

DNA Barcoding: Molecular Identification and Phylogenetic Analysis of Pheretimoid Earthworm (Metaphire sp. and Amynthas sp.) Based on Mitochondrial Partial COI Gene from Sialkot, Pakistan.

The extremely difficult and challenging process is identifying pheretimoid species, genus Metaphire and Amynthas involving increased homoplasy in various morphological characteristics. The molecular identification, phylogenetic relationships, and evolutionary divergence time of earthworms belonging to the pheretimoid complex were investigated in this study using partial mitochondrial COI (cytochrome C oxidase subunit I) gene sequences ranging from 550-680 bp. Results revealed that 86 pheretimoid earthworms were morphologically different from a total of 342 mature worms. Moreover, 11 pheretimoid species were molecularly identified, including Metaphire posthuma (02), M. anomala (01), M. houlleti (02), M. californica (01), M. birmanica (02), Amynthas minimus (01), A. morrisi (01), and M. bununa (01). A phylogenetic tree was constructed with bootstrap values of 95%, which supported a monophyletic lineage of two well-supported clades formed by 12 partial COI sequences and 48 GenBank sequences using Hirudo medicinalis as an outgroup. The monophyly of these obtained genera indicated overall similarity at species level. Today, species like Amynthas, Metaphire and Pheretima have worm diversity in the form of pheretimoid earthworms, which dates to the Late Miocene (11.2-5.3 Mya) and the Pliocene (5.3-2.4 Mya). Compared to all relevant pheretimoid species, genetic p-distance values ranged from 0.0% to 0.57% (less than 1%). These low range values demonstrated that both genera Metaphire and Amynthas, supported the theory, which states that there are shared similarities among the species, despite different morphology. The current study is the first attempt in Pakistan to identify earthworms through DNA barcoding thus providing a genomic stamp. The work explored the significance of COI gene sequences to construct molecular tools that will be useful to overcome the different obstacles in morphologically similar earthworm identification and their phylogenetic study.

Genetic Diversity and Variation in Mitochondrial COI Gene in Wild and Hatchery Populations of Saxidomus purpuratus.

To investigate the genetic diversity and genetic variations of four wild (Geoje, Jinhae, Yeosu, and Boryeong) and two hatchery (Goheung and Geoje) populations of purplish Washington clam (Saxidomus purpuratus), 421bp sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene were analyzed. A total of 149 haplotypes were identified from 358 individuals from the four wild and two hatchery populations with 109 substitutions. The genetic diversity of the wild populations and Geoje hatchery population were high, whereas the total number of haplotypes, population-specific haplotypes, and haplotype diversity were comparatively low in the Goheung hatchery population. The fixation index (FST) indicated that there was no significant genetic difference between the four wild populations. However, the Goheung hatchery population was significantly different from that of the Geoje hatchery, exhibiting the most pronounced difference, and two wild populations (Jinhae and Yeosu). The low genetic diversity indices exhibited by the Goheung hatchery population might have resulted from farm propagation using a limited parental stock. Therefore, to maintain genetic diversity, a proper breeding management program using more progenitors is required in hatcheries, in addition to regular monitoring of both hatchery and wild populations.

DNA Barcoding for Selected Mangrove-Based Estuary Fishes from Way Kambas National Park, Lampung Province, Indonesia

Over the past decade, DNA barcoding has provided new insight into fish ecology and biosystematics and led to new species' discovery. DNA barcoding is a method for the recognition and identification of species using short, standardised DNA fragments. The correct taxonomic identification of species is critical for the assessment and monitoring of biodiversity. This study applied DNA barcoding techniques to identify selected fish species from a mangrove-based estuary in Way Kambas National Park, Lampung Province, Indonesia. The gene encoding cytochrome c oxidase subunit I (COI) was amplified and bi-directionally sequenced from 22 specimens. The resulting 680 base pairs (bp) sequence was used to identify species, obtain phylogenetic information, and analyse genetic distances. A neighbour-joining tree was constructed based on the mitochondrial COI gene using the Kimura two-parameter model. This study also exhibits conservation status for those identified species. Our findings will facilitate future studies of fish species diversity in mangrove estuary-based ecosystems and provide preliminary data in policymaking in conservation areas such as National Park.

Phylogeography and shell morphology of the pelagic snail Limacina helicina in the Okhotsk Sea and western North Pacific

The pelagic snail Limacina helicina Phipps, 1774 is widely distributed in high-latitude seas and is a sensitive bioindicator of ocean acidification. It is known that the response patterns to ocean acidification differ among populations within or among species. Thus, it is important to understand their genetic population structure and identify the cryptic species. L. helicina displays different shell morphotypes, called “formae,” in different regions (North Atlantic, L. helicina forma helicina Phipps, 1774; Northwest Pacific, L. helicina f. acuta Spoel, 1967; Northeast Pacific, L. helicina f. pacifica Dall, 1871; Okhotsk Sea, L. helicina f. ochotensis Shkoldina, 1999: Spoel, 1967, pp. 257, 349). A recent study by Shimizu et al. (Journal of Molluscan Studies 84:30-37, 2018) showed clear genetic differentiation between two formae, L. helicina forma helicina (Svalbard in the Arctic Ocean) and L. helicina f. acuta (station K2 in the western North Pacific) (ΦCT = 0.59282), using partial mitochondrial cytochrome c oxidase subunit I (COI) gene sequences. However, whether other formae of this species are genetically distinct remain unknown. Here we focused on L. helicina f. ochotensis, which inhabits the Sea of Okhotsk, and compared its shell morphology and partial mitochondrial COI gene sequences with another forma, L. helicina f. acuta, which is found in the western North Pacific. We found differences in the shell morphology of L. helicina f. ochotensis collected from the Sea of Okhotsk (off the coast of Monbetsu, Hokkaido, Japan) and L. helicina f. acuta collected from the western North Pacific (station K2). However, molecular analysis of an mtDNA COI region (503 bp) revealed that most individuals collected from Monbetsu (Sea of Okhotsk) were haplotype 1 (75.5%), which is also the major haplotype found in L. helicina f. acuta (western North Pacific). Our results suggest that individuals of L. helicina are frequently dispersed between the Sea of Okhotsk and the western North Pacific by ocean currents. Thus, the two formae, L. helicina f. acuta and L. helicina f. ochotensis, are more likely to be attributable to phenotypic plasticity in response to different environmental parameters, such as temperature and salinity, than to differences in their genetic backgrounds.

Haplotype diversity and distribution pattern of Oecophylla smaragdina (Fabricius) (Hymenoptera, Formicidae) in Bangladesh based on mitochondrial COI genes

Abstract Climatic oscillation often have influenced the present distribution and intraspecific genetic diversity Oecophylla smaragdina through its wide range of geographical distribution. Previous phylogeographic study of Asian weaver ant population denotes the evidence of distribution of Indian types in Indian, Sri Lanka and SE Asian types in South Asian countries including Bangladesh. However, recent phylogenetic analysis reveals the overlapping distribution of the Indian and South East Asian clades of O. smaragdina in Bangladesh. The present study aims to identify the haplotypes and it’s networking in Bangladesh based on extensive materials. Sampling was executed according to zonation of 5 areas, demarcated by 3 main rivers during the years 2013 to 2018. Adult O. smaragadina workers were collected from 71 colonies of 67 localities belonging to 47 districts of Bangladesh. A total of 25 haplotypes were identified in Bangladesh comprises 13 and 12 of Indian and SE Asian types, respectively from 93 sequences of Cytochrome c oxidase subunit I (COI) gene of 639 bp. The geographical distribution of this haplotype reveals that the Indian haplotypes are mostly located at the western part of Bangladesh while SE Asian haplotypes were dominated in the Eastern part of the country. Central part of Bangladesh has overlapped with the mixture of both Indian and SE Asian haplotypes. The results of the haplotype network give the evidence of recent expansion of O. smaragdina population in Bangladesh and clarify the evidence of presence of many missing haplotypes in refugee.

Low genetic variation of cinereous vultures (Aegypius monachus) revealed by the mitochondrial COI gene in central Mongolia

The cinereous vulture Aegypius monachus is considered as the largest species among old world’s vultures, and it is also recognized as the important part of any ecosystem, as cleaner of dead animals with natural and non-natural mortality. We investigated genetic characteristics of the cinereous vulture (n = 39) using 738 base-pair (bp) long cytochrome c oxidase subunit I (COI) gene in mitochondrial DNA. The observed overall haplotype (Hd) and nucleotide (Pi) diversities were 0.279 ±0.0079 and 3.9 x 10-3, respectively. Relatively small genetic pairwise FST distance (FST = 0.027) resulted for weak geographical structure among studied populations (>95% of total variation due to within population). Conducting more investigation on species genetic diversity using more appropriate/polymorphic markers is crucial for better conservation of the cinereous vulture, especially for little known Asian populations.

Study of methylation of mitochondrial MT-COI of benzene poisoning

Objective: To research the mitochondrial cytochrome c oxidase subunit I (MT-COI) gene methylation levels in patients with occupational chronic benzene poisoning, and to explore effective molec μlar biomarkers in patients with occupational chronic benzene poisoning. Methods: 38 confirmed cases of occupational chronic benzene poisoning were selected in the case group. 46 healthy people who underwent physical in our hospital were selected in the control group. Pyrosequencing was used to detect the methylation sites of methylation sites, flow cytometry was used to detect peripheral blood cell count levels, and non-parametric statistical methods were used to analyze the differences in detection results between the two groups. Results: The methylation level of mitochondrial MT-COI site 1 (2.21±0.81) % in the case group was less than that in the control group, and the difference was statistically significant (P<0.05) . The methylation level of mitochondrial MT-COI site 2 (2.31±0.96%) in the case group was less than that in the control group, and the difference was statistically significant (P<0.05) . The methylation average level of mitochondrial MT-COI (2.26±0.75) % in the case group was less than that in the control group, and the difference was statistically significant (P<0.05) . Analysis of the average level of methylation found that the methylation level of mitochondrial MT-COI was correlated with WBC (P<0.05) . Analysis of the average level of methylation found that the methylation level of mitochondrial MT-COI was correlated with platelets (r=0.254、0.280, P<0.05) . Conclusion: The level of mitochondrial MT-COI gene methylation in patients with occupational chronic benzene poisoning may be related to the sensitivity to benzene exposure. Mitochondrial MT-COI gene methylation may serve as a potential predictive biomarker for benzene poisoning.

Molecular and morphological evidence for the identity of the blackspot shark, Carcharhinus sealei, and the Indonesian whaler shark, C. tjutjot, with notes on their population structures

The requiem sharks of the genus Carcharhinus are captured as bycatch in the Indo-Pacific region. The lack of morphometric data due to the common practice of head and fin removal of sharks, hinders the implementation of shark management measures. Carcharhinus specimens found in the waters of Brunei Darussalam were identified using morphological analysis, and their identification was further validated by mitochondrial cytochrome c oxidase subunit I (COI) gene sequence analysis. This study successfully identified twenty-seven specimens as either the blackspot shark, Carcharhinus sealei, or the Indonesian whaler shark, Carcharhinus tjutjot, by molecular genetic analysis, although the difficulty of accurately identifying these sharks solely on morphology was encountered. Mitochondrial COI gene sequence analysis also suggested that C. tjutjot has two genetically distinct populations/groups, while C. sealei had a single panmictic population in the Indio-Pacific region. The findings suggest that C. sealei could be a more highly migratory species than C. tjutjot in the region.

A review of taxonomy and flower-breeding ecology of the Colocasiomyia toshiokai species group (Diptera: Drosophilidae), with description of a new species from Indonesia

Flies of the Colocasiomyia toshiokai species group depend exclusively on inflorescences/infructescences of the aroid tribe Homalomeneae. The taxonomy and reproductive biology of this group is reviewed on the basis of data and samples collected from Southeast Asia. The species boundaries are determined by combining morphological analyses and molecular species delimitation based on sequences of the mitochondrial COI (cytochrome c oxidase subunit I) gene. For the phylogenetic classification within this species group, a cladistic analysis of all the member species is conducted based on 29 parsimony-informative, morphological characters. As a result, six species are recognised within the toshiokai group, including one new species, viz. C. toshiokai, C. xanthogaster, C. nigricauda, C. erythrocephala, C. heterodonta and C. rostrata sp. n. Various host plants are utilised by these species in different combinations at different localities: Some host plants are monopolized by a single species, while others are shared by two or three species. C. xanthogaster and C. heterodonta cohabit on the same host plant in West Java, breeding on spatially different parts of the spadix. There is a close synchrony between flower-visiting behaviour of flies and flowering events of host plants, which indicate an intimate pollination mutualism.

Molecular identification of the Danzhou chicken breed in China using DNA barcoding

Mitochondrial cytochrome C oxidase subunit I (COI) has been used as a DNA barcode to identify population genetic diversity and distinguish animal species as it is variable enough to distinguish between species, yet suitably conserved. A new native chicken breed, named Danzhou chicken was discovered in Hainan, China in 2014, although identification is difficult by morphological examination alone. The mitochondrial COI genes of six chicken breeds, including four local and two imported breeds (Danzhou, Wenchang, Bawang, Beijing-You, Hy-Line Brown, and Ross) were compared and assessed in terms of their efficacy for DNA barcoding. The results showed that the number of COI gene variants in Danzhou chickens was less than those of other breeds, except Bawang and the genetic structure was relatively stable. The Kimura 2-parameter genetic distance between Danzhou chickens and the five other breeds was from ∼0.001 to 0.734. The genetic distance of the six breeds was ∼0.001–0.339, with that of Danzhou being the highest (0.339). Danzhou chickens clustered with Bawang and Wenchang chickens in the phylogenetic tree due to geographic closeness. Danzhou chickens could be identified more accurately using COI barcoding. Multiple molecular markers combined with morphological differences were more persuasive for identifying species.

Molecular characterization and identification of three stored grain pests based on mitochondrial cytochrome C oxidase subunit I (COI) gene sequences

Stored grain pests are discovered in food as immature stages, which further complicates the identification process. A DNA barcode dataset of some important pests that can be used for easy and confirm identification in stages of life is constructed. COI genes of three stored grain insect pests i.e,, Sitophilus oryzae, Callosobruchus chinensis and Oryzaephilus surinamensis were sequenced. The sequenced genes were submitted to NCBI GenBank and obtained accession numbers MG967331.1, MG967332.1, MG967333.1 and MK041216.1. BLAST analysis showed 99 to 100% homology with existing GenBank sequences. The nucleotide composition analysis revealed that the value of A+T (64.8%) is greater than G+C (35.2%). Genetic distance among four sequences of three store pests were ranged from 0.00293-0.32807. Phylogenetic analysis showed that these three species are originated from different clades. Haplotype analysis of mitochondrial COI gene of the stored grain insect pests showed high genetic diversity among them. C. chinensis, O. surinamensis and S. oryzae were separated from their common ancestor by 80, 73 and 64 mutational steps. These information may be helpful for attempting any successful control measures against the pest species. In conclusion, present author established the first DNA barcode dataset of three store grain pests and confirmed its efficiency for identifying these pests.&#x0D; Bangladesh J. Zool. 47(1): 1-11, 2019

DNA barcoding of fishes from Lake Lanao, Philippines

Lake Lanao, the second largest lake in the Philippines and one of the 15 ancient lakes in the world, used to contain 20 endemic cyprinid species, which had attracted the attention of evolutionary biologists in the past. Over the years, there has been a steady decline in the abundance and diversity of endemic fishes in the lake because of overfishing and introduction of non-native species. This study represents the first molecular survey of the ichthyofauna of Lake Lanao. A total of 75 specimens of 12 different species belonging to nine genera, eight families, and five orders were DNA barcoded using the mitochondrial cytochrome c oxidase subunit I (COI) gene. Average Kimura 2-parameter genetic distances were 0.24% (within species), 8.31% (between species), 9.69% (within family), and 24.86% (between families). Possible hybrids between Oreochromis species were detected. Glossogobius spp. was highlighted for further taxonomic investigation because barcoding indicated unidentified species of this genus. The partial sequence of mitochondrial COI gene was found to be a good DNA barcode for fast and accurate species identification of fishes in Lake Lanao and for tagging species that warrant further taxonomic investigation.

Population genetic structure and molecular diversity of Leucinodes orbonalis based on mitochondrial COI gene sequences

Leucinodes orbonalis is a destructive pest found throughout eggplant cultivating fields of Tamil Nadu, India. The genetic diversity and its population structure were investigated in this pest using mitochondrial cytochrome c oxidase subunit I (COI) gene sequences from 20 populations of L. orbonalis collected from various agro-climatic conditions. The study indicated almost no genetic diversity among various populations. The COI nucleotide sequence based haplotype analysis also revealed no significant genetic variation among various populations. However, haplotype network analysis with three clades was nearly matching with the structure of phylogenetic analysis that showed geographical separations induced distribution of some genetic variation. The PCA and nMDS Shephard’s plot analyses were also illustrated that the populations sampled were nearly matched with phylogenetic tree and haplotype network. This study on phylogeographical structure using the mitochondrial COI sequence diversity of L. orbonalis therefore suggested presence of few genetically distinct populations due to some specific habitat requirements.