mtCOI Gene Sequences Research Articles

Prevalence Rate and Molecular Characteristics of Oestrus ovis L. (Diptera, Oestridae) in Sheep and Goats from Riyadh, Saudi Arabia.

Heads of sheep (n = 600) and goats (n = 800) slaughtered at Al-Aziziah Abattoir in Riyadh, Saudi Arabia, were inspected for the presence of O. ovis larvae (L). Heads were split along the longitudinal axes, and larvae (L1, L2, and L3) were gathered. The infestation rate was significantly higher in goats (44.5%; 356/800) than that in sheep (22.3%; 134/600). Out of the 151 collected larvae from sheep, 0% were L1, 1.3% were L2, and 98.7% were L3. Out of the total of 468 larvae from goats, 0% were L1, 1.2% were L2, and 98.8% were L3. The infestation rate was significantly higher in males than that in females. Myiasis-causing larvae collected from Riyadh, Saudi Arabia, were authenticated as O. ovis, according to morphological characteristics. Polymerase chain reaction (PCR) amplification of a partial fragment (600 bp) of the mitochondrial cytochrome c oxidase subunit I (mtCOI) gene further confirmed the species. Phylogenetic analysis based on the partial mtCOI gene sequence demonstrated that 23 unique sequences showed high similarity based on nucleotide pairs of O. ovis accessions retrieved from GenBank.

Genetic Analysis of White Leafhopper Cofana spectra (Distant) from Samosir Island, Indonesia Based on DNA Barcode

White leafhopper Cofana spectra is a pest of paddy and could act as a vector of pathogenic viruses on rice. This research aims to find out its genetic data, namely its identification, nucleotide composition and its phylogenetic based on DNA barcode-mtCOI gene. The researchmethods included leafhopper sampling in rice field, DNA isolation, PCR, electrophoresis, sequencing and blasting. The software Mega X was used to analyze the genetic data. The mtCOI DNA gene sequence obtained was 333 bp in size and blasting result showed that leafhopper belongto white leafhopper Cofana spectra (Distant) species. The dendrogram from the sequence showed that white leafhopper species from Samosir island had the closest relationship with species from Kerala, India. The frequency of nucleotide of T (U), C, A and G of leafhopper were 41.96, 15.47, 28.57 and 13.98%, respectively. Therefore, this mtCOI gene sequence was rich in A/T (70.53%), while G/C was 29.45%. The information obtained from this study stated that the identification of the white leafhopper C.spectra based on molecular character using mtCOI DNA gene sequence confirmed the identification result based on the morphological traits and can be used to control and in monitoring the spread of the white leafhopper.

Parasitoid Distribution and Parasitism of the Fall Armyworm Spodoptera frugiperda (Lepidoptera: Noctuidae) in Different Maize Producing Regions of Uganda.

Simple SummaryThe fall armyworm (FAW), a native of the Americas that was confirmed in Africa in 2016, has been reported to cause substantial damage to maize and sorghum in all sub-Saharan African countries. In Uganda, farmers rely mainly on synthetic insecticides, which can be harmful to humans, the environment, and significantly increase the cost of production. To lessen the disadvantages associated with synthetic insecticides, the use of parasitoids could be exploited. Fall armyworm parasitoids have been reported from the Americas, Asia, and some African countries, but not from Uganda. In this study, we aimed to determine the identity and distribution of FAW parasitoids in Uganda. We found 13 species of parasitoids attacking FAW in the surveyed locations. These included 11 species of insects in the wasp order and two in the fly order. Four of these are wasps that attack the eggs of FAW, while the remaining seven wasps and two fly species attack the larvae of FAW. Two wasp genera (Chelonus and Coccygidium spp.) were more abundant and widely distributed when compared with the other parasitoid species. All parasitoids contributed to an average of 9.2% FAW larval mortality rate across the study locations.The fall armyworm (FAW) Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae) has successfully invaded Africa, where it has significantly impacted maize and sorghum production. Management of FAW in Africa predominantly relies on synthetic insecticides, which are expensive, and negatively impact the environment and beneficial insects. We, therefore, conducted field surveys in Uganda in 2017 and 2019 to identify egg and larval parasitoids of FAW for possible use in integrated pest management (IPM) programs. Parasitoids were identified by their mitochondrial DNA cytochrome c oxidase subunit 1 (mtCOI) gene sequences. We identified 13 parasitoid species belonging to three families of Hymenoptera: Platygastridae, Braconidae and Ichneumonidae, as well as one Dipteran family (Tachinidae). Coccygidium spp. and Chelonus bifoveolatus were the most abundant and widely distributed parasitoids. Overall, parasitism averaged 9.2% and ranged from 3.1% to 50% in 2017, and 0.8% to 33% in 2019. Parasitism by Sturmiopsis parasitica, Diolcogaster sp., and Cotesia flavipes on FAW in maize crops are reported for the first time. Our results suggest high biological diversity of FAW parasitoids, which should be exploited in the IPM of the FAW in Uganda.

Two new species of planthoppers from India (Hemiptera: Auchenorrhyncha: Delphacidae) in the genera Parasogata and Eoeurysa

The genus Parasogata Zhou, Yang & Chen, 2018 is here reported from India represented by the new species Parasogata sexpartita sp. nov. collected in a recent exploration and survey of delphacids from Nagaland in northeastern India. A second species of Eoeurysa Muir, 1913 from India, the new species Eoeurysa sagittaria sp. nov., was found in Rampur, Una, Himachal Pradesh. Both new species are described with illustrations, and a molecular identification is given with the mtCOI gene sequence. A modified key to species of the genera is also provided.

Morphological and molecular analysis of the freshwater copepod Heliodiaptomus viduus (Calanoida: Diaptomidae)

Morphological identification of the commonest Indian freshwater calanoid copepod Heliodiaptomus viduus has been facing a lot of controversies. To solve this problem, additional molecular support is needed. Hence, molecular analysis, along with morphological identification of the species using scanning electron microscopy (SEM) and optical microscopy, was carried out. The genetic distance between the intraspecific sequences in the 18SrRNA observed to be 0.000, while the interspecific distance within genus sequences varied from 0.000 to 0.002. Besides, it was noted that both the sequences (intraspecific) were present within a single clade of the phylogenetic trees with 100% bootstrap value. The genetic distance between the intraspecific sequences in the mtCOI observed to be 0.000, while the interspecific distance within genus sequences varied from 0.000 to 0.267 and lay in a separate clade in the phylogenetic tree from the within genus clade. Besides, it was noted that both the sequences (intraspecific) were present within a single clade of the phylogenetic tree with above 75% bootstrap value. Hence, the 18S rRNA (MH145356, MK457456) and mtCOI (MK621900) gene sequences of the present study are well supported the identification of H. viduus and it serves as the first molecular database besides providing morphological authentication (SEM images) of H.viduus. This combined analysis is envisioned to be helpful in selecting the ecologically and nutritionally important species for practical aquaculture

Exploring the genetic variability of citrus butterfly (Papilio demoleus) using DNA barcode

The present study is first and initial report from India on developing barcodes and molecular identification of citrus swallow tail butterfly (Papilio demoleus L.) based on mtCOI region and species composition from Abohar, Jalandhar, Ludhiana, Sangrur areas of Punjab on citrus host plants. The corresponding genomic DNA isolation, PCR amplification, detectable genetic divergence, molecular identification and phylogenetic tree were assessed. Using the specific set of primers the samples yielded specific fragment of 658 bp. The amplified PCR product was sequenced and identified as Papilio demoleus and submitted to BOLD database. The 658 bp mtCOI gene sequences from Abohar, Ludhiana, Jalandhar were 100% similar however the sequence from Sangrur region show mutations at three different positions showing a variation of 0.45% from rest of the populations of Punjab. The phylogenetic tree was developed and it was revealed that all the populations of Punjab are in same cluster and when compared with populations from other countries, it form two main clusters which are different from each other by 3.70%. The cluster one includes all the populations of Australia, India, USA and Pakistan and the cluster two include totally different populations from Canada. In cluster one the populations from Australia and USA forms one subgroup while populations from India and Pakistan form second subgroup.

Dasybranchus geojedoensis sp. nov. (Annelida: Capitellidae), a New Capitellid Species from Southern Korea

Dasybranchusgeojedoensis sp. nov., obtained from the soft sublittoral bottom in southern Korea, is described as a new species. This new species of Dasybranchus is easily distinguishable from its congeners by the protruded parapodial lobes in the final few thoracic chaetigers. Dasybranchus geojedoensis sp. nov. closely resembles D. bipartitus (Schmarda, 1861) in number and position of abdominal branchiae but differs in position of genital pores and lateral organs, range of thoracic tessellated chaetigers, and denticulation of the abdominal hooks. The partial mtCOI gene sequences of the new Korean species were significantly distinct from those of undescribed species of Dasybranchus from Australia. In this study, a key for known species of Dasybranchus is also provided.

Genetic diversity of Asian rice gall midge based on mtCOI gene sequences and identification of a novel resistance locus gm12 in rice cultivar MN62M.

The rice gall midge (RGM), Orseolia oryzae (Wood-Mason), is one of the most destructive insect pests of rice, and it causes significant yield losses annually in Asian countries. The development of resistant rice varieties is considered as the most effective and economical approach for maintaining yield stability by controlling RGM. Identification of resistance genes will help in marker-assisted selection (MAS) to pyramid the resistance genes and develop a durable resistance variety against RGM in areas with frequent outbreaks. In this study, a mitochondrial cytochrome oxidase subunit I (mtCOI) was used to analyze the genetic diversity among Thai RGM populations. The phylogenetic tree indicated that the Thai RGM populations were homogeneously distributed throughout the country. The reactions of the resistant rice varieties carrying different resistance genes revealed different RGM biotypes in Thailand. The Thai rice landrace MN62M showed resistance to all RGM populations used in this study. We identified a novel genetic locus for resistance to RGM, designated as gm12, on the short arm of rice chromosome 2. The locus was identified using linkage analysis in 144 F2 plants derived from a cross between susceptible cultivar KDML105 and RGM-resistant cultivar MN62M with single nucleotide polymorphism (SNP) markers and F2:3 phenotype. The locus was mapped between two flanking markers, S2_76222 and S2_419160. In conclusion, we identified a new RGM resistance gene, gm12, on rice chromosome 2 in the Thai rice landrace MN62M. This finding yielded DNA markers that can be used in MAS to develop cultivars with broad-spectrum resistance to RGM. Moreover, the new resistance gene provides essential information for the identification of RGM biotypes in Thailand and Southeast Asia.

Genetic variability, community structure, and horizontal transfer of endosymbionts among three Asia II-Bemisia tabaci mitotypes in Pakistan.

Endosymbionts associated with the whitefly Bemisia tabaci cryptic species are known to contribute to host fitness and environmental adaptation. The genetic diversity and population complexity were investigated for endosymbiont communities of B. tabaci occupying different micro‐environments in Pakistan. Mitotypes of B. tabaci were identified by comparative sequence analysis of the mitochondria cytochrome oxidase I (mtCOI) gene sequence. Whitefly mitotypes belonged to the Asia II‐1, ‐5, and ‐7 mitotypes of the Asia II major clade. The whitefly–endosymbiont communities were characterized based on 16S ribosomal RNA operational taxonomic unit (OTU) assignments, resulting in 43 OTUs. Most of the OTUs occurred in the Asia II‐1 and II‐7 mitotypes (r 2 = .9, p < .005), while the Asia II‐5 microbiome was less complex. The microbiome OTU groups were mitotype‐specific, clustering with a basis in phylogeographical distribution and the corresponding ecological niche of their whitefly host, suggesting mitotype‐microbiome co‐adaptation. The primary endosymbiont Portiera was represented by a single, highly homologous OTU (0%–0.67% divergence). Two of six Arsenophonus OTUs were uniquely associated with Asia II‐5 and ‐7, and one occurred exclusively in Asia II‐1, two only in Asia II‐5, and one in both Asia II‐1 and ‐7. Four other secondary endosymbionts, Cardinium, Hemipteriphilus, Rickettsia, and Wolbachia OTUs, were found at ≤29% frequencies. The most prevalent Arsenophonus OTU was found in all three Asia II mitotypes (55% frequency), whereas the same strain of Cardinium and Wolbachia was found in both Asia II‐1 and ‐5, and a single Hemipteriphilus OTU occurred in Asia II‐1 and ‐7. This pattern is indicative of horizontal transfer, suggestive of a proximity between mitotypes sufficient for gene flow at overlapping mitotype ecological niches.

Descriptions of larvae of three Philopotamidae species from China (Insecta, Trichoptera)

Adults and larvae of the family Philopotamidae from Zhejiang Province, China, were examined and mtCOI gene sequences were extracted and analyzed, males and larvae of 3 species were successfully associated. The larvae of Chimarra sadayu Malicky 1993, Dolophilodes bellatula Sun Malicky 2002, Wormaldia unispina Sun 1998 are described in detail and their diagnostic photographs and illustrations are presented. Diagnostic characters for genera and species are discussed.

Molecular analysis of rice green leafhopper, Nephotettix virescens (Distant) from Samosir Island-Indonesia using mitochondrial COI gene

Present study is aimed to identify and analyse the genetic character of N. virescens and also its phylogeny to related species based on mt COI or DNA barcoding. The steps of this genetic analysis are leafhopper sample catching in rice field, DNA extraction, DNA amplification, product purification and DNA sequencing. Primer COI AB 976528 has been used in mtCOI-DNA amplification step. The research result showed that mtCOI-DNA fragment of N. virecens has length 677–681 bp. This mtCOI-DNA gene sequence was dominated by A and T bases with concentration 69.59%, whereas CG content was 30.39%. The concentration average of T (U), C, A and G nucleotides in the mtCOI gene sequence were 37.83, 15.96, 31.76 and 14.43%, respectively. Based on molecular phylogeny analysis, green leafhopper N. virescens Samosir populations was similar (98.60%) into green leafhopper N. virescens populations originated from Bangladesh. Identification of N. virescens based on this mtCOI-DNA gene sequence confirmed the identification result based on its morphological characters.

Molecular identification and characterization of medically and veterinary important flies of Bangladesh based on mitochondrial COI gene sequences

Flies are considered serious pests which cause health problems of human and animal, transmitting many pathogenic microbes. Pest management programs depend on proper identification of pests. The present research work is an initiative to identify the medically and veterinary important flies based on mitochondrial COI gene sequences. Eleven species of the fly pests were identified. Among them, four fly species were the first record from Bangladesh. The phylogenetic analysis of retrieved sequences confirmed that the evolution of these species occurred from a common ancestor. Highest AT percentage (69.9%) was found in Haematobia irritans exigua and lowest GC percentage (30.4%) was found in Haematobia irritans exigua. The substitution rate of codon was found 1.88 in 1st position, 0.73 in 2nd position and 1.22 in 3rd position, respectively. Interspecific genetic divergence range of flies sequences was 5-20%. Haplotype network showed that Atylotus agrestis was mostly diverged from its common ancestors by 37 mutational steps. This research is the first molecular approach to identify the medically and veterinary important flies based on MT-COI gene sequences along with the establishment of first DNA barcode dataset for accurate identification in Bangladesh.

Genetic Lineage of &lt;i&gt;Zeugodacus caudatus&lt;/i&gt; (Diptera:Tephritidae) Detected with &lt;i&gt;mtCOI&lt;/i&gt; Gene Analysis from India

Zeugodacus caudatus (Fabricius) is a pest of cucurbit plants. The present study was conducted to draw the relationship among Indian Z. caudatus populations with the other defined genetic lineage of the species. A total of 18 individuals’ mtCOI gene sequences from 3 populations of India were analysed along with 34 individuals’ mtCOI gene sequences from Malaysia, Indonesia, Thailand and China and generated 14 haplotypes. Phylogenetic study revealed the presence of distinct genetic lineage in Z. caudatus populations collected from India. The genetic distance between three distinct lineages of Z. caudatus was 0.057, 0.055 and 0.018 between Indonesia and Malaysia, India and Indonesia, and India and Malaysia, respectively and also evident from phylogenetic analysis. Further, the mitochondrial cytochrome oxidase I (COI) gene sequences developed in this study will help detection and geographical distribution of new haplotypes and lineages of the species in future.

Molecular characteristics of Indian population of Deanolis sublimbalis Snellen (Crambidae: Lepidoptera) using mitochondrial and nuclear genes

ABSTRACT Red Banded Mango Caterpillar (RBMC), Deanolis sublimbalis Snellen (Lepidoptera: Crambidae) is a serious pest of mango fruits in several regions of South and South East Asia. Molecular characterisation of twenty nine different populations was done using the mitochondrial gene, Mitochondrial Cytochrome Oxidase-I (mtCOI) and nuclear gene, Elongation Factor 1 Alpha (EF-1α) to estimate the genetic variability among the RBMC populations. Nucleotide analysis of genetic diversity and phylogenetic analysis of the mtCOI, EF-1α and concatenated sequences (both COI and EF-1α) indicated that the RBMC populations from different geographical regions used in this study are homogenous. The nucleotide diversity (π) and overall mean distance for mtCOI and EF-1α were 0.003635, 0.004 ± 0.001, and 0.00, 0.00, respectively. Moreover, nucleotide diversity and overall mean distance of concatenated sequences were π = 0.009809 and 0.010 ± 0.002. Four mtCOI gene sequences of RBMC (Two from India, Two from Canada) from GenBank were juxtaposed with Indian test populations while building phylogenetic tree indicated that the RBMC from India and Canada are less divergent. With respect to mtCOI, no significant molecular diversity within the RBMC populations of different geographical locations of India as well as Canada was found. However, the phylogenetic tree implied the probability of emerging genetic differences in RBMC populations.

First mtCO-I based molecular identification of two cryptic species of Bemisia tabaci from Afghanistan

B. tabaci exists as a complex of morphologically very similar but genetically different variants previously termed as biotypes and more recently as cryptic species. Using a region of mitochondrial cytochrome oxidase, I (mtCO-I) gene sequences this study for the first time identified at molecular level the presence of two cryptic species of B. tabaci; Asia-I and Asia-II-5 from cotton grown in the fields of Bland Ghar, Bihsud district, Nangarhar province of Afghanistan. It is the first report of its type as this insect was not reported earlier from any crop or area of this country at species level.

Description of larva of Euphaea superba Kimmins, 1936 (Odonata: Zygoptera: Euphaeidae) from China.

The final stadium larva of Euphaea superba Kimmins, 1936 is described and illustrated based on a male and a female specimens collected in Zhejiang province, China. The larvae were associated with the adults by mtCOI gene sequence. The larva of E. superba is diagnosed from other described members of the genus by the gena having 2-4 spines on outer side, the movable hook about 1.6 time as long as median cleft and female with primary genitalia extending to the posterior margin of abdominal segment 10.

DNA barcoding identified two endangered dolphins: threats on living aquatic mammals in India

DNA barcode data of both endangered dolphin species, Platanista gangetica, and Orcaella brevirostris are lacking in the global database. The study generated partial mitochondrial cytochrome c oxidase subunit I (mtCOI) gene sequences of the two highly threatened dolphin species from India. The family Platanistidae with one species and family Delphinidae with 12 species were showed 1.2%–19.7% between species genetic divergence in the studied dataset. Both P. gangetica and O. brevirostris were revealed distinct clade in neighbor-joining (NJ) phylogeny. Further, D. delphis, S. coeruleoalba, and T. truncatus have shown more than one clade and comparatively high genetic divergence within the species suggested prominent genetic variation between different populations. The study recommends generating more DNA barcode data from diverse habitats of P. gangetica and O. brevirostris to evaluate the exact population structure and adopting better conservation strategies thereafter.

Genetic diversity of mango leafhopper, Amritodus atkinsoni (Hemiptera: Cicadellidae) based on mtCOI gene sequences from India

The mango leafhopper, Amritodus atkinsoni is a serious and an endemic insect pest of mango in India. We analyzed mtCOI gene sequences from six Indian populations of A. atkinsoni for genetic diversity and population structure. The analysis of mtCOI sequence revealed 14 unique haplotypes and a low level of nucleotide diversity. mtCOI gene sequence analysis also revealed that A. atkinsoni specimens were clearly differentiated from other closely related species with a high level of accuracy.

A new species of Chimarra from China (Trichoptera, Philopotamidae) with description of its larva.

The adult male and larva of a new species in the genus Chimarra Stephens, Chimarra paramonorum n. sp., are described, diagnosed, and illustrated based on the specimens collected in Zhejiang Province, China. The larva and adult male were associated by mtCOI gene sequences. The male can be separated from C. monorum and C. thienemanni mainly by small preanal appendages and by wrinkled, hairless endotheca. The larva of the new species can be separated from other congeners by a combination of characters including the notch on the anterior margin of the frontoclypeus, the teeth of the mandibles, and the length of the seta-bearing process of each forecoxa. The larval description is the first for Chimarra in China.

An integrative approach to discovering cryptic species within the Bemisia tabaci whitefly species complex

Bemisia tabaci is a cryptic whitefly-species complex that includes some of the most damaging pests and plant-virus vectors of a diverse range of food and fibre crops worldwide. We combine experimental evidence of: (i) differences in reproductive compatibility, (ii) hybrid verification using a specific nuclear DNA marker and hybrid fertility confirmation and (iii) high-throughput sequencing-derived mitogenomes, to show that the “Mediterranean” (MED) B. tabaci comprises at least two distinct biological species; the globally invasive MED from the Mediterranean Basin and the “African silver-leafing” (ASL) from sub-Saharan Africa, which has no associated invasion records. We demonstrate that, contrary to its common name, the “ASL” does not induce squash silver-leafing symptoms and show that species delimitation based on the widely applied 3.5% partial mtCOI gene sequence divergence threshold produces discordant results, depending on the mtCOI region selected. Of the 292 published mtCOI sequences from MED/ASL groups, 158 (54%) are low quality and/or potential pseudogenes. We demonstrate fundamental deficiencies in delimiting cryptic B. tabaci species, based solely on partial sequences of a mitochondrial barcoding gene. We advocate an integrative approach to reveal the true species richness within cryptic species complexes, which is integral to the deployment of effective pest and disease management strategies.